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Fabrication of Robust Biomimetic Nanopore for Biomolecular and Biomedical Analysis

Permanent Link: http://ufdc.ufl.edu/UFE0021979/00001

Material Information

Title: Fabrication of Robust Biomimetic Nanopore for Biomolecular and Biomedical Analysis
Physical Description: 1 online resource (108 p.)
Language: english
Publisher: University of Florida
Place of Publication: Gainesville, Fla.
Publication Date: 2008

Subjects

Subjects / Keywords: conical, dna, drug, gold, multilayer, nanopore, nanotube, polymer, protein, template
Chemistry -- Dissertations, Academic -- UF
Genre: Chemistry thesis, Ph.D.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract: The goal of this research is to develop new methods based on robust nanopores for sensing biomolecules and drug molecules. The first part of this work is to sense a cationic hydrophobic drug based on ion-current rectification phenomenon observed for conically-shaped nanopores. The second part focuses on improving the selectivity and sensitivity of the above-mentioned sensor described in the first part. Interesting result is that the detection limit for the drug with the highest binding constant shifts to submicromole. The third part of this dissertation presents a new approach to sensing DNA through a conically-shaped nanopore embedded in PET polymer. The fourth part of this work presents a new approach to control the conical pore diameter by applying a layer-by-layer technique to fabricate multilayers of proteins within the inner surface of the conical nanopore. These controllable single nanopores enable us to investigate the sensing properties of biomolecules.
General Note: In the series University of Florida Digital Collections.
General Note: Includes vita.
Bibliography: Includes bibliographical references.
Source of Description: Description based on online resource; title from PDF title page.
Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Thesis: Thesis (Ph.D.)--University of Florida, 2008.
Local: Adviser: Martin, Charles R.

Record Information

Source Institution: UFRGP
Rights Management: Applicable rights reserved.
Classification: lcc - LD1780 2008
System ID: UFE0021979:00001

Permanent Link: http://ufdc.ufl.edu/UFE0021979/00001

Material Information

Title: Fabrication of Robust Biomimetic Nanopore for Biomolecular and Biomedical Analysis
Physical Description: 1 online resource (108 p.)
Language: english
Publisher: University of Florida
Place of Publication: Gainesville, Fla.
Publication Date: 2008

Subjects

Subjects / Keywords: conical, dna, drug, gold, multilayer, nanopore, nanotube, polymer, protein, template
Chemistry -- Dissertations, Academic -- UF
Genre: Chemistry thesis, Ph.D.
bibliography   ( marcgt )
theses   ( marcgt )
government publication (state, provincial, terriorial, dependent)   ( marcgt )
born-digital   ( sobekcm )
Electronic Thesis or Dissertation

Notes

Abstract: The goal of this research is to develop new methods based on robust nanopores for sensing biomolecules and drug molecules. The first part of this work is to sense a cationic hydrophobic drug based on ion-current rectification phenomenon observed for conically-shaped nanopores. The second part focuses on improving the selectivity and sensitivity of the above-mentioned sensor described in the first part. Interesting result is that the detection limit for the drug with the highest binding constant shifts to submicromole. The third part of this dissertation presents a new approach to sensing DNA through a conically-shaped nanopore embedded in PET polymer. The fourth part of this work presents a new approach to control the conical pore diameter by applying a layer-by-layer technique to fabricate multilayers of proteins within the inner surface of the conical nanopore. These controllable single nanopores enable us to investigate the sensing properties of biomolecules.
General Note: In the series University of Florida Digital Collections.
General Note: Includes vita.
Bibliography: Includes bibliographical references.
Source of Description: Description based on online resource; title from PDF title page.
Source of Description: This bibliographic record is available under the Creative Commons CC0 public domain dedication. The University of Florida Libraries, as creator of this bibliographic record, has waived all rights to it worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law.
Thesis: Thesis (Ph.D.)--University of Florida, 2008.
Local: Adviser: Martin, Charles R.

Record Information

Source Institution: UFRGP
Rights Management: Applicable rights reserved.
Classification: lcc - LD1780 2008
System ID: UFE0021979:00001


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9eb679159696e471250e93a1ec3e5d42
4f11b6ba5ae1e28cd815a86b52c596e97a4d5684







FABRICATION OF ROBUST BIOMIMETIC NANOPORE FOR BIOMOLECULAR AND
BIOMEDICAL ANALYSIS




















By

JIAHAI WANG


A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY

UNIVERSITY OF FLORIDA

2008



































2008 JIAHAI WANG

































To my family









ACKNOWLEDGMENTS

I would like to thank Dr. Charles Martin and the entire Martin group for the opportunity to

work with them over the course of my tenure. Dr. Martin was continuously supportive in

guidance throughout my scientific development at the University of Florida. Also, I would like to

thank Dr. Martin for educating me to become a professional scientist. The Martin group

members have been very supportive and terrific examples of ingenuity and perseverance. Dr

ShiFeng Hou, Lane Baker, Youngseon Choi, Punit Kohli, Q Trofim and Fatih Buyukserin

showed great patience in offering many hours of guidance and helpful ideas. Mario Caicedo,

Dooho Park, John Wharton, Fan Xu, Pu Jin, Lindsay Sexton, Lloyd Home, Kann Kececi and

Peng Guo have helped me by giving insightful advice on experiments.

I would like to thank my family for their love and encouragement, which gave me great

spiritual force.









TABLE OF CONTENTS

page

A C K N O W L E D G M E N T S .............. ...........................................................................................4

L IS T O F T A B L E S .............................................................................. ............... 7

L IST O F FIG U R E S ............................................................................... 8

ABSTRACT ................... ............... ......... ... ...... ... .............

CHAPTER

1 INTRODUCTION AND BACKGROUND ........................................ ....................... 13

Introdu action ................... .......................................................... ................. 13
Ion T rack -E tch ............... ............................................................................ ....... ..... 15
Form action of Latent Ion Tracks....................................................... .................. ......... 15
Preferentially Etching of Ion Tracks ................................. ........................................... 15
T em p late S y n th e sis ....................... .. ... .......................................................................... 17
Synthetic Strategies in Tem plate Synthesis................................... ...................... 18
Electroless D position ................................................. ....... .. ........ .... 18
B biological Ion C channels ........................ .. .......................... .... ............. .. ...... 20
V oltage-G ated Ion C channel .......................................................................... ....................2 1
Resistive-Pulse Sensing .................. ................................... .......... ............... 22
Ion-C current R ectification ............................................................................... ... ............26
Dissertation Overview .................. ............. ...................... ............ 29

2 A NEW DRUG-SENSING PARADIGM BASED ON ION-CURRENT
RECTIFICATION IN A CONICALLY SHAPED NANOPORE.......................................38

In tro d u ctio n ................... ................... ...................8..........
E x p erim en tal ................... ................... ...................9..........
M materials and M methods .......................................................................... ....................39
Etching the Conical Nanopore in the Tracked Membrane ...........................................39
Sensing the A nalyte M olecules ............................................... ............................ 41
R results and D discussion .................... .... .................................. ...... ............ .... ...... .... 4 1
Ion-Current Rectification by the Conical Nanopore ................................................. 41
Effect of Hoechst 33258 on Rectification .................................................................... 42
Effect of Benzyl and Methyl on Rectification........................................43
Langmuir Analysis of the Hoechst 33258 Adsorption Data .........................................44
C onclu sions.......... ............................... ................................................46

3 SELECTIVE DETECTION OF DRUGS BASED ON ION-CURRENT
RECTIFICATION IN A CONICALLY-SHAPED NANOPORE ...................................51

In tro d u ctio n ................... ......................................................... ................ 5 1









E x p erim mental ................... ...................5...................2..........
M materials and M methods .......................................................................... ....................52
Etching the Conical Nanopore in the Tracked Membrane ...........................................52
Sensing the A nalyte M olecules ............................................... ............................ 54
R results and D discussion .................... .. .......................... .. ...................... .. .... ........ 55
Ion-Current Rectification by the Conical Nanopores................... ................................55
Effect of Hoechst 33342 on Rectification .............. .. ...........................55
Langmuir Analysis of the Hoechst 33342 Adsorption Data ..................................57
Effect of Amitriptyline and Bupivacaine on Rectification................... ....... ............58
Sum m ary and F future w ork .......................................................................... .....................58

4 INVESTIGATION OF SELF-ASSEMBLED PROTEIN DIMERS THROUGH AN
ARTIFICAL ION CHANNEL FOR DNA SENSING.........................................................67

In tro d u ctio n ................... ...................6...................7..........
E x p erim mental ................... ...................6...................9..........
M materials and M methods .......................................................................... ....................69
Preparation of the Conical Nanopores................................ ........................ ......... 69
A ssem bly of DN A -Protein Com plex.................................. ..........................................70
Current-Pulse M easurem ents........... ................. ............................. ............... 71
Results and D discussion ................ ........................... .. ..... ... ........ ... 71
Calculation of the tip Diameter of the Single Conical Nanopore............................. 71
Current-Pulses of the Self-Assembled Complex......................................................73
C on clu sion ........... ..... ........... ................ ........... .................................. 7 5

5 FUNCTIONALIZATION AND DIAMETER CONTROL OF SINGLE CONICAL
NANOPORE IN ION-TRACK PET MEMBRANE VIA LAYER-BY-LAYER
M E T H O D ......................................................................................................................... 8 1

In tro d u ctio n ........................................................................................................... 8 1
E xperim mental ..................... ........................................ ...........................83
M materials ............... ....... .. ........ .................... ...................... 83
Preparation of the Conical Nanopores............................. ........................83
Determination of the Diameter of Nanopore..... .................. ...............84
Layer-by-Layer Protein Assembly ............................................................................ 84
Results and Discussion ................................. .... ... ........ ............ 85
Calculation of the Tip Diameter of the Single Conical Nanopore ............................. 85
Controlling tip Diameter of Single Conical Nanopore................ ...............86
Stability of Protein N anopore .......................................................... ............... 88
C o n clu sio n ................... ...................8...................8..........

6 CONCLUSIONS ..................... ........ ............... ............... .. 97

L IST O F R E F E R E N C E S ..................................................................................... ..................100

B IO G R A PH IC A L SK E T C H ......................................................................... .. ...................... 108




6









LIST OF TABLES


Table page

2-1 Rectification ratio in various concentration of Hoechst 33258 at transmembrane
potential difference of 6V ........................................................................ ...................49

2-2 Current values in various concentration of Hoechst 33258 at transmembrane
p potential -6V ........................................................... ................. 50

3-1 Rectification ratio in various concentration of Hoechst 33342 at transmembrane
potential difference of 2 V ....................................................................... ..................64

3-2 Rectification ratio in various concentration of Amitriptyline at transmembrane
potential difference of 2 V ....................................................................... ..................65

3-3 Rectification ratio in various concentration of Bupivacaine at transmembrane
potential difference of 2 V ............................ ............... .................................... .....66

5-1 Diameter of tip opening and base opening after each protein layer assembly within
nanopore A. DO represents initial pore size, D1,,D2, D3 and D4 represent the pore
size after deposition of Biotin labelled BSA, deposition of Streptavidin, deposition of
Biotin labelled BSA and deposition of Streptavidin respectively. ...................................94

5-2 Diameter of tip opening and base opening after each protein layer assembly within
nanopore B. DO represents initial pore size, D1,,D2, D3, D4, D5 represent the pore
size after deposition of multi-Biotin labelled polylysine, deposition of Streptavidin,
deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of
mulit-Biotin labelled BSA respectively. ................... .................. ...... ...95

5-3 Diameter of tip opening and base opening after each protein layer assembly within
nanopore C. DO represents initial pore size, Dl, D2, D3 represent the pore size after
deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of
B iotin labelled IgA ..................................................... ....................... ...... ....... 96









LIST OF FIGURES


Figure page

1-1 (A) The heavy ion beam forms a latent ion track in the dielectic membrane. (B)
Chemically etching will selectively remove the latent track and form a cylindrical
sh ap e .......................................................... ................................... 32

1-2 Definition of cone half-angle a, bulk etch rate VB and track etch-rate VT .......................32

1-3 Scanning electron microscopic images of different nanoporous materials developed
by ion-track-etching process. ...................................................................... ..................33

1-4 Scanning electron microscopic images of different template........................................33

1-5 Schematic diagram ofAu electroless plating procedure........................................34

1-6 Schematic illustration of Au nanotubes obtained from electroless gold deposition..........34

1-7 Schematic illustration of open and close state of K+ channel................. ............... 35

1-8 Schematic illustration of resistive-pulse sensing. ...................................... .............35

1-9 Protein channel embedded in lipid bilayer .......................... ..................................... 36

1-10 (A) I-V curve and current rectification for nanopore without charge. (B) I-V curve
and current rectification for nanopore with negative charge. (C) I-V curve and
current rectification for nanopore with positive charge.................................................36

1-11 (A) Scheme of an axial cut of a conical pore; (B) profile of electrical potential,V(z),
inside a tapered-cone pore, calculated from Eq. 1............................ .... .... ........... 37

1-12 Ratchet model for ion current recification in a conical nanopore with excess negative
surface charge on pore w all.. .............................. ... .......................................... 37

2-1 Molecular structure of different drug molecules and polymer. .......................................47

2-2 I-V curves for a conical nanopore sensor (tip diameter =67 nm, base diameter 1.43
[tm) in the presence of the following concentrations of Hoechst 33258: 0 nM (black
square), 1.25 iM (red circle), 2.5 iM (green triangle), 5 iM (blue triangle), 10 iM
cyann square), 15 [iM (magenta), 25 [iM (yellow). ................................ ..................47

2-3 I-V curve for conical nanopore in Kapton membrane (tip diameter 48 nm, base
diameter 2.0 tm) with different molecules: 2.3 mM benzyl viologen cyann square),
ImM benzyl viologen (blue triangle), control buffer (black square), 1 mM methyl
viologen (red circle), 2.3 mM methyl viologen (green triangle). ......................................48

2-4 Plot of surface coverage (theta) versus concentration of Hoechst 33258.......................48









3-1 M olecular structure of different drug molecules .................................... ............... 60

3-2 I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21
[pm) in the presence of the following concentrations of Hoechst 33342: 0 nM (black
square), 5.3 |tM (red circle), 15 |tM (green triangle), 2.3 mM (blue triangle). .................60

3-3 Plot of surface coverage (theta) versus concentration of Hoechst 33342......................61

3-4 I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21
[pm) in the presence of the following concentrations of Amitriptyline: 0 nM (black
square), 90 |iM (red circle), 390 |iM (green triangle), 11.2 mM (blue triangle). ..............61

3-5 Plot of surface coverage (theta) versus concentration of Amitriptyline. .........................62

3-6 I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21
ptm) in the presence of the following concentrations of Bupivacaine: 0 nM (black
square), 0.67 mM (red circle), 2 mM(green triangle), 11.6 mM (blue triangle)................62

3-7 Plot of surface coverage (theta) versus concentration of Bupivacaine............................63

4-1 Scheme of the experimental setup with the conductivity cell. The left compartment is
filled with a stopping solution (1.0 M KC1 and 1.0 M Formic acid), and the right
compartment is filled with a etching solution (9.0 M NaOH). ...........................76

4-2 The current-voltage curve of conical pore in 1 M KC1 with applied -1.0 V voltage.
The tip opening of the nanopore is 9nm and the base opening is 530 nm.......................76

4-3 Analytical sensor based on conical nanopore embedded in PET membrane. In the
absence of target DNA or in the existence of unspecific DNA, the translocation of
Streptavidin conjugated DNA probes was not detectable from base to tip. The size of
target DNA induced self-assembled DNA-protein complex is double that of
Streptavidin conjugated DNA probes; the translocation of the complex will cause
current-pulses ...............................................................................77

4-4 Current-time transients for a bare conical nanotube sensor with tip diameter =9 nm.......77

4-5 Histograms of DNA-protein complex current-pulse-peak amplitude data for
nanotube with tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 pM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential was -1000 mV .................................. ........ ........ ...... ......... 78

4-6 Histograms of DNA-protein complex current-pulse-duration data for nanotube with
tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 pM Streptavidin and 100
nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV. ......78

4-7 Scatter plot of current-pulse magnitude (Ai) vs. current-pulse duration(t) for DNA-
protein complex. Tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 pM









Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential w as -1000 m V ........................................................................ ...................... 79

4-8 Scatter plot of current-pulse magnitude (Ai) vs. current-pulse duration(t) for DNA-
protein complex. Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 tM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential w as -1000 m V .................. ............................... ... .. ....... .. ...... ...... 79

4-9 Scatter plot of current-pulse magnitude (Ai) vs. current-pulse duration(t) for DNA-
protein complex. Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 tM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential was -2000 mV. ......................... .......... .. ....... ... ....... ..... 80

5-1 Scheme of the experimental setup with the conductivity cell. During etching the left
compartment is filled with stopping solution ( 1.0 M KC1 and 1.0 M formic acid), the
right compartment is filled with etching solution ( 9.0 M NaOH). ................................ 90

5-2 Schematic diagram for Layer-by-layer assembly of proteins on single conical PET
m em b ran e ...................................... ..................................................... 9 0

5-3 I-V curves after each assembly step with nanopore A: Black line (square) represents
data for nanopore after second step etch, red line (circle) for nanopore after multi-
Biotin labelled BSA nonspecific adsorption, green line (triangle) for nanopore after
Streptavidin adsorption, blue line (triangle) for nanopore after Biotin BSA
adsorption, turquoise (square) for nanopore after Streptavidin adsorption .....................91

5-4 Diameter of tip opening as a function of the number of protein layers within
nanopore B. The first layer is multi-Biotin labelled polylysine, second layer is
Streptavidin, third layer is multi-Biotin labelled BSA, fourth layer is Streptavidin,
and fifth layer is multi-Biotin labelled BSA. ............................... ............................... 92

5-5 Diameter of tip opening as a function of different protein layer within nanopore C.
The first layer is multi-Biotin labelled BSA, second layer is Streptavidin, and third
layer is B iotin labelled IgA ....................................................................... ...................92

5-6 Diameters of tip opening versus 7 days for three single nanopores. Black circle
represents the tip diameter of nanopore A, green triangle represents that of nanopore
B, blue square represents that of nanopore C. ........ ........... ......... .. ............ 93









Abstract of Dissertation Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Degree of Doctor of Philosophy

FABRICATION OF ROBUST BIOMIMETIC NANOPORE FOR BIOMOLECULAR AND
BIOMEDICAL ANALYSIS

By

JiaHai Wang

May 2008

Chair: Charles R. Martin
Major: Chemistry

The goal of this research is to develop new methods based on robust nanopores for sensing

biomolecules and drug molecules. The first part of this work is to sense a cationic hydrophobic

drug based on ion-current rectification phenomenon observed for conically-shaped nanopores.

The nanopore walls in the Kapton membrane are hydrophobic and have fixed carboxylate groups

that give the walls a net negative charge. The analyte drug molecule, Hoechst 33258, is cationic

yet also hydrophobic. When the membrane is exposed to this molecule, the molecule adsorbs to

the pore walls and neutralizes the anionic surface charge, thus lowering the extent of ion-current

rectification. The change in rectification is proportional to the concentration of the drug. This

nanopore sensor is selective for hydrophobic cations relative to anions, neutral molecules, and

less hydrophobic cations.

The second part focuses on improving the selectivity and sensitivity of the above-

mentioned sensor described in the first part. We have selected three positive drugs with different

hydrophobicity. We can successfully discriminate these drugs. The highest binding constant was

obtained for the drug with highest hydrophobicity. Another interesting result is that the detection

limit for the drug with the highest binding constant shifts to submicromole.









The third part of this dissertation presents a new approach to sensing DNA through a

conically-shaped nanopore embedded in PET polymer. The translocation of each protein

conjugated probe is undetectable because the size is much smaller than the tip opening of a bare

conical nanopore. The translocation of the protein dimer linked by target DNA is detectable

because the size of the target DNA linked protein dimer is double the size of each component

and also comparable to the diameter of the tip opening of the nanopore. The control DNA will

not induce the assembly of two protein conjugated probes; no events will be observed. By this

way, we can detect the target analyte without interference of probes.

The fourth part of this work presents a new approach to control the conical pore diameter

by applying a layer-by-layer technique to fabricate multilayers of proteins within the inner

surface of the conical nanopore. Multilayer constructions were based on the strong interaction

between Streptavidin and Biotin modified protein. In addition, we can modify the nanopore with

any biomolecular-recognition agents labelled with Biotin. These controllable single nanopores

enable us to investigate the sensing properties of biomolecules, such as various sizes and

biofunctional proteins.









CHAPTER 1
INTRODUCTION AND BACKGROUND

Introduction

In the past decades, nanomaterials have been the subject of tremendous interest. These

materials which have specific feature size have great potential for application in biomedicine,

chemistry, and electronics.1-10 Nanomaterials can be ceramics, metal, polymeric materials, or

composite materials. The defining feature for these materials is the size in the range of 1-100

nanometers (nm). Nanomaterials are not simply another step in miniaturization, but a totally

different field. At the nanomaterial level, some material properties behave by the laws of atomic

physics, rather than behave as traditional bulk.

Although nanomaterials were of widespread interest, the concept was raised over 40 years

ago by physicist Richard Feynman who delivered a talk in 1959 entitled "There's plenty of

Room at the Bottom." 11 Among the nanomaterials, nanopores play a very important role.

Molecular transporting through nanopores has attracted a very large scientific interest because of

its relevance to those issues in biology and biotechnology. Biological nanopores such as channels

and pores in biomembranes of cells are involved in almost all physiological processes of a living

organism. These channels and pores are the principal nanodevices mediating the communication

of a cell with other cells via exchange of ions and neutral molecules. Biological channels

perform various physiological functions.

Inspired by the studies of biological nanopores, there has been intense interest in artificial

nanopores. Given the fact that solid-state nanopores are highly stable over a wide range of pH

values, salt conditions, temperature, and bias voltages, and are highly portable, it will be

promising to continue to explore potential applications of nanopores. On the other hand, we can









do something beyond the biological nanopore: change the size of nanopores by well controlling

the experimental conditions; Sense different analytes unreachable by biological ion channel.

Nanoporous materials can be synthesized by using many different techniques using

different materials. The template-based synthesis pioneered by the Martin research group and

others is a general method for preparing nanomaterials.12' 13 This method entails the synthesis or

deposition of a desired material within the pores of a nanopore membrane that serves as a

template. These template membranes contain uniform pores that are typically cylindrical in

geometry, and the pore diameter can be varied at will from tens of nanometers to tens of

microns. Since typical pore geometries are cylindrical, correspondingly cylindrical

nanostructures are usually synthesized via the template method; these nanotube membranes have

been widely used for biomolecular analysis and batteries.

Recently, our research team and others have become interested in conically-shaped

nanopores.14-23 A number of applications can potentially benefit from conical pore geometry.

For instance, it has been shown that such conically-shaped nanopores can be used as the sensing

element for new types of small molecule,24 DNA,25 26,27,28 protein,29 and particle30 sensors.

Conically-shaped gold nanotubes deposited within such pores can also act as mimics of voltage

gated ion channels.31 Membranes used for separations might also benefit from a highly

asymmetric pore structure. Finally, in addition to sensing and separations platforms, conical

nanostructures prepared by more conventional methods have been proposed for use as cathodes

in field-emission displays.32

In this dissertation, several techniques and knowledge have been used: Ion track-etch

process, template synthesis, biological ion channel, resistive-pulse sensing, and ion rectification.









Ion Track-Etch

The ion track etch process3334 based on the availability of accelerated heavy ions enables

one to prepare nano- and micro-pores with a high aspect ratio and various shapes in many

dielectric solids. Polymers and mica due to their mechanical and chemical strength, and their

high susceptibility for selective ion track etching are suitable for practical application.

Formation of Latent Ion Tracks

Heavy ion accelerators create ion beams of defined isotopic mass and energy suited for a

well-defined generation of ion tracks. Every ion hitting and potentially penetrating the polymer

leads to a permanent modification of its chemical and physical properties along its path. The

result of this modification is latent ion track. The strength of the modification depends on the

radiation sensitivity of the material, on the deposited energy density, and on the storage

conditions of the polymer after the ion irradiation, such as temperature, environmental gases, and

illumination conditions.

Preferentially Etching of Ion Tracks

Chemical etching can preferentially remove latent ion tracks (Figure. 1-1). The resulting

shape of the etched track depends on the type of material, the concentration of the etchant, and

the temperature of the etch bath. As the density of the material in the track core is lower than the

density of pristine polymer,35 the selective etching of the track core can be attributed to its

increased free volume36 corresponding to nanovoids with increased freedom for rearrangements

of the chain segments. The increased free volume facilitates chain rupture under chemical attack.

Preferential etching can be impeded by a cross-linked zone around the track core. After removal

of the cross-linked zone, the track radius grows linear in time. The result is an etch trough, pore,

or channel that can be used as a selective gate for ions or fluid-suspended particles or may be

used as a template for deposition of other materials.









For large track etch velocities, the etch cone transforms into a cylinder. In general, heavier

ions induce a stronger modification, improving the local definition of the modified zone and the

selectivity of the etch process. After selective removal of the strongly modified ion track core,

etching can be retarded by a polymerized zone. Further etching proceeds at bulk etch velocity,

i.e., the track radius increases linear in time at the same rate as the polymer surfaces recede. The

etch process is finally interrupted by replacing the etchant with water or with a dilute acid. The

interruption can be induced at a chosen time or at a chosen electrolytical conductivity across the

membrane.3

The cone half-angle is defined by the relation sin a=VB /VT (Figure 1-2). For the high track

etch ratio, sin a can be replaced by a. The track-etch-ratio is usually treated as constant as long

as the ion range exceeds the thickness of the material. It depends on the energy density along the

ion path, the radiation sensitivity, and the selectivity of the etch process, i.e., its ability to

differentiate between irradiated and pristine material.

The central figure of merit for ion track etching is the selectivity of the track-etch process.

It is given by the ratio of the etch velocity along the ion track,VT, and the etch velocity of the

removing the bulk material,VB, the so-called track etch ratio,VT/VB The track etch ratio is also

responsible for the shape of the porous structure. The shape is defined as a self-organized process

given by the energy deposition density, the direction of etch attach, the material used, the etch

medium, the etch time, and the etch temperature. The rate of etching can be increased by raising

the temperature, for example, in high throughput development which is used in industrial

applications. Also, the concentration of the etchant influences its bulk etch rate VB, and its track-

etch rate, and the selectivity s=VT /VB. There are many different materials which are ideal

candidates for preparing high aspect ratio ion track-etch pores in a free standing membrane.









These materials include PC (polycarbonate), PET (polyethylene terephthalate), PP

(polypropylene), PVDF (polyvinylidenefluoride), PI (polyimide), and CR 39

(polydiethyleneglycolbisallylcarbonate). The use of ion track-etching technology allows the

opportunity for the production of many different type of nanoporous material which is illustrated

in Figure 1-3.33 34 These different materials can then be used as templates for the development of

a variety of other nanostructured materials. One technique which entails the use of a template to

produce the production of nanostructure materials is a process called template synthesis.

Template Synthesis

In recent years, the Martin group has pioneered a general method for the preparation of

nanostructured materials called template synthesis.1, 3,38 In the template synthesis method, the

material of interest is deposited within the nanoporous material of a host solid. The size and

shape of the nanomaterial depend on the dimensions of the nanocavities within the host template.

Membrane-based template synthesis entails deposition of desired materials within the pores of a

host solid. Depending on the membrane and synthetic method used, the obtained nanostructured

material can be solid nanofibers or hollow nanotubes.

There are a variety of interesting and useful characteristics associated with template

synthesis. One of the most useful features of the method is that it is very general with regards to

the type of materials that can be prepared. This method has been used to prepare nanofibers and

nanotubes composed of metals,39' 40-46 polymer,47-50 carbon,51-53 and semiconductors.54 55 Also, it

is possible to prepare composite nanostructured materials both concentric tubular composites56'

57 and segmental composite nanowires.58 This method has also been used to prepare materials

with a very small diameter, such as, conductive polymer nanofibers with diameters of 3nm have

been prepared.59









Finally, template synthesized nanostructured materials can be assembled into a variety of

different architectures. For example, the nanostructured material can remain inside the pores of

the template membrane; or they can be freed from the template membrane and collected by

filtration. Alternatively, if the nanostructure-containing membrane is attached to a surface and

the membrane is removed, an ensemble of nanostructures can protrude from the surface like the

bristle of a brush.

Synthetic Strategies in Template Synthesis

There are two commonly used templates; organic ion track-etched polycarbonate

membranes and inorganic A1203 membranes (Figure 1-4). There are a variety of different

synthetic strategies adapted from the preparation of bulk materials including chemical and

electrochemical polymerization, and sol-gel chemistry.

Electroless Deposition

The electroless deposition method involves the use of a chemical reducing agent to plate a

metal from a solution onto a surface. Unlike electrochemical deposition, a conductive surface is

not necessary. The key requirement of electroless deposition is arrangement of the chemistry

such that the kinetics of homogeneous electron transfer from the reducing agent to metal ions is

slow. This is extremely important because otherwise the metal ions would simply be reduced in

the bulk solution. One caveat of electroless deposition is that a catalyst is needed on the pore

walls so that the reduction of the metal ion will only occur at the pore surface. Figure 1-5 shows

the schematic representation of the electroless deposition chemisty that was used to prepare gold

nanowires and nanotubes within polycarbonate track-etched membranes. The polycarbonate

membrane is first exposed to a sensitizer (Sn2+). This is accomplished by simply immersing the

membrane for 45 minutes in a solution that is 0.026 M in SnC12 and 0.07 M in trifluoroacetic

acid in 50/50 methanol/water. The sensitizer binds to the pore walls and the membrane surfaces









via complexation with amine, carboxyl and hydroxyl groups.60 After sensitization of ammoniac

silver nitrate (0.029 M Ag(NH3)2+) for 5 minutes, a redox reaction occurs in which the surface

bound tin(II) is oxidized to tin(IV) and the Ag+ is reduced to elemental Ag. As a result, the pore

walls and the membrane surface becomes coated with nanoscopic Ag particles. The membrane is

again thoroughly rinsed with methanol. The silver coated membrane is then immersed into a gold

plating bath that is 7.9x 10-3 M in Na3Au(S03)2, 0.127 M Na2SO3, and 0.625 M in formaldehyde

at 40C. The Au galvanically displaces the Ag particles because the reduction potential Au is more

positive than that of Ag. As a result, the pore walls and surface become coated with Au particle.

These particles are excellent catalytic sites for the oxidation of formaldehyde and the concurrent

reduction of Au(I) to Au(0).60 Without a catalyst, the kinetics of the electron transfer from the

reducing agent(formaldehyde) to Au(I) is slow; therefore, the gold plating continues on the gold

particle instead of in bulk solution. The reaction can be represented as follows:

2Au(I) + HCHO + 30H =HCOO-+2H20 +2Au(0) (1-1)

This method yields Au nanowires or nanotubes within pores plus a Au surface layer on

both faces of the membrane. These structures run through the entire thickness of the template

membrane (Figure 1-6). By controlling the plating time, the inside diameter of the nanotubes can

be varied because the thickness of both the Au surface films and the nanotube walls increase

with plating time.

By controlling the plating time, the inside diameter (ID) of the nanotubes can be varied,

even as low as 1 nm in diameter.48 As a result, these membranes can be used in a simple

membrane permeation experiment to cleanly separate thiols to an Au nanotube walls based on

the well known gold thiol chemistry, the Au nanotube membrane can be made to preferentially

transport cation vs. anions and hydrophobic vs. hydropholic molecules.40'44 45'61 In addition, the









Au nanotube membrane is electronically conductive and can be charged electrostatically in an

electrolyte solution.40 This introduced ion-transport selectivity, allows the Au nanotube

membranes to be electromodulated between ideal-cation and ideal-anion transport states.40 Thus

these Au nanotube membranes are ideal model systems for studying how pore size, chemistry,

and charge affect the transport selectivity at the nanometer scale.

The electroless gold deposition method has also been used in the study of ion current

rectification within single nanopore track-etched membranes.62 These systems can be used as

robust synthetic systems for the study of voltage-gating and ion current rectification which is

present in the biological voltage-gated ion channel.2023 These systems have the potential of

offering a greater understanding of the different functional mechanisms which are present within

biological ion channels.

Biological Ion Channels

Biological ion channels enable the functioning of a living organism and mediate the

communication of a cell with other cells via ion transport, 63 Three types of ion channels were

studied before: The ligand gated channel, the mechanically gated channel, and the voltage-gated

channel.63 The ligand gated channel is unique in that it will open and close in response to the

binding or unbinding of a particular "ligand" or molecule. The mechanical gated ion channel

open and closes by the mechanical deformation of the cells of stretch receptors. The voltage-

gated channel is very unique in that it will open and close in response to the change in the

transmembrane potential. The voltage-gated ion channels also control the excitability of nerve,

muscle, and endocrine and other cell types, thereby regulating a broad spectrum of cellular

processes.









Voltage-Gated Ion Channel

The ion channel conducting potassium across the cell membrane down the electrochemical

gradient for K+ underlies many different cellular processes including cell volume regulation,

hormone secretion, and electrical impulse formation in electrically excitable cells.63 All known

K channels are related members of a single protein family. They are found in bacterial, archeal,

and eukaryotic cells both plant and animal and their amino acid sequences are very easy to

recognize because the potassium channels contain a highly conserved segment called the K

channel signature sequence.64 The sequence forms a structural element65' 66 known as the

selectivity filter (Figure 1-7), which prevents the passage ofNa+ ions but allows K+ ions to

conduct across the membrane at rates approaching the diffusion limit. This is the hallmalk of K

channels: nearly perfect selectivity for K+ ions over Na+ ions in the setting of very high K+

conduction rates.

Determination of the molecular sequence and primary structure of many of their protein

components has put new insights into the physiological functions and biophysical properties of

these channels. Yet the mechanism by which these proteins sense changes in membrane potential

has remained elusive. Now, YouXing Jiang and Roderick MacKinnon and colleagues have

published the crystal structure of a full-length voltage dependent K+ channel.67 Their findings

reveal an unexpected and surprisingly simple design in the voltage sensor. The functional unit of

a voltage-gated ion channel is tetramer. Each of the four subunits of the tetramer is a protein with

six transmembrane domains. Reasoning dictates that the voltage sensor would be a charged

sequence located within the cell membrane that would move from one side to the other in

response to changes in potential across the membrane. The fourth transmembrane domain,

known as S4, is a likely candidate for the voltage sensor because of two properties. First, it is

hydrophobic, which indicates that it should be located within the lipid layer of the membrane or









embedded within the interior of a protein. Second, S4 contains four to seven positive charges,

depending on the channel type, which would confer voltage sensitivity to this segment of the

protein. For these seasons S4 has been the focus of numerous studies on voltage sensing in ion

channels.68

One of the main characteristics of the potassium voltage-gated ion channel is that it is an

ion current rectifier. Rectifier is a term that comes from electronics, referring to devices that

conduct electrons only in one direction. These potassium voltage-gated ion channels show a

nonlinear current-voltage characteristic which says that they are ion current rectifiers. Ion current

rectification suggests that there is a preferential flow of ions through these ion channels.

Although the structure of these channels are known,68-71 there are still many aspects of ion

transport that are not yet well understood. The phenomenon of ion current fluctuations is one of

the unsolved puzzles.72 Also, there are open questions regarding ion current rectification and

pumping within these channels. These questions have motivated researchers to design biosensors

and learn more about ion transport with nanochannels. To design biosensors and learn about ion

transport in nanochannels, it would be very helpful to have a synthetic, robust system that is

much easier to understand and describe. This would also allow researchers to perform

experimental studies not applicable to biological channels due to their fragile nature. First

however, we have to determine whether it would be possible with synthetic pores in a synthetic

film of dimensions similar to those biological channels, to observe similar transport properties,

such as, ion current fluctuations, rectification, and pumping.

Resistive-Pulse Sensing

It has been shown that a protein nanopore (for example, the a-hemolysin channel) can

function as a biosensor for the detection ofbiomolecules, for example, DNA.73 The sensing

procedure used is based on a technique called resistive-pulse sensing. In the simplest terms, this









method is based on an electrochemical cell in which a small aperture separates two ionically-

conductive salt solutions. Within each side of the cell an electrode is placed and an ionic current

is passed through the aperture. A charged analyte species with a diameter that is comparable to

that of the inside diameter of the single aperture is electrophoretically driven through the

aperture. When the analyte species enter the aperture the channel pathway is partially obstructed.

This change in ionic current can be used to determine the size, identity, surface charge and even

the concentration of the analyte species present within the system. Figure 1-8 shows a schematic

representation of how this process works. Because many biomolecules are charged, this detection

method can potentially be very widely applied and does not require any chemical pretreatment of

the molecules, which is a big advantage over other detection techniques.

The classic example of a resistive-pulse sensor is the coulter counter (Beckman Coulter,

Fullerton, CA), a commercially available device used to count and size biological cells and

colloidal particles.74-76 The Coulter counter uses a small diameter aperture (from 20tm to as

large as 2mm) separated by two electrolyte solutions and a constant ionic current is passed

through this aperture. The aperture is typically fabricated through a man-made sapphire, the

thickness of which is comparable to the diameter of the aperture. An electrolyte solution is

placed on each side of the aperture. The suspended biological cells (or other particles) to be

counted are introduced on one side of the aperture. This solution is then forced to flow through

the aperture. Flow of the solution is driven by a pressure gradient across the aperture, and with

modern instruments, the volume of liquid sampled can be precisely controlled.76

When a particle enters the aperture it effectively displaces a volume element of electrolyte

solution equivalent to the particle volume. As a result, the resistance through the aperture

increases during the obstructed time of the particle within the aperture. This transient increase in









the aperture resistance is monitored via the corresponding increase in voltage drop across the

aperture. The number of such voltage pulses provides a count of the particles suspended in the

electrolyte. The height of the pulse is proportional to the volume of the particle within the

aperture. Therefore, from this information, particle size information can be obtained. Also, the

distribution of pulse amplitudes reflects the relative distribution of the volumes of the particles

counted.7 This process can be used to size several thousand particles per second. Commercially

available instruments can measure particles with diameters ranging from as small as 400nm to as

large as ImM.74-76 The diameter of the particle to be counted determines the diameter of the

aperture used in the instrument.

As would be expected, the smaller the particles to be counted, the smaller the aperture

used. Therefore, to detect smaller analyte species smaller aperture systems are needed. The

model system to date which is used in the stochastic sensing of individual analytes is the use of a

bioengineered a-hemolysin protein channel (Figure 1-9).77,78,79 These channels have been used

in the detection of divalent metal ions,8' 81 organic analytes,82 proteins,83' 84 polymers, 85 DNA,
86-90 and peptides.91 Even though these channel proteins have proven to be an instrumental tool in

the development of a molecular stochastic sensor they still possess limitations which need to be

overcome for future applications. The biggest limitation of this protein channel system is the

stability of the biological support system (lipid bilayer membrane). This limitation has sparked

an increased interest for researchers to develop a synthetic nanopore system which has similar

sensing capabilities but overcomes the stability limitations encountered by biological systems.

There has been a significant amount of effort focused toward the development of a

synthetic single aperture system which would be able to analyze individual analytes at the

molecular level. The first system was demonstrated by DeBlois and Bean.91-94 They used a









system which incorporated a 500 nm diameter single pore within a track-etched polycarbonate

membrane. Because of the smaller aperture, this device could detect particles with diameters as

small as 60 nm. For example,Virus particles were detected with this device.92 Also, Li and

Crooks developed a single nanopore device which was made up of a single carbon nanotube

embedded within a support material.95'96 These single nanotube systems had an aperture

diameter of-60nm and a path length of 1.0 [tm. These systems have been used for analysis of

nanoparticles.

There have been several single nanopore systems developed from inorganic solid-state

materials. One such system employs the use of a feedback-controlled sputtering system, based on

irradiating the materials with ion beams.14,97 This technique allowed the preparation of a single

nanopore in a Si3N4 support with diameter down to 1.8nm. Another method used to produce

pores in silicon oxide with an aperture diameter of several nanometers was developed in the

group of Dees Dekker. The pores are manufactured by electron beam lithography and anisotropic

etching in combination with high-energy beam in transmission electron microscope.98 There is

also a technique which uses classical lithographic methods combined with micromolding of

poly(dimethylsiloxane). This approach produces larger channels of approximately 200 nm in

diameter,15' 16 Finally, the track-etching process has been used to produce single nanopore

membranes in polyamide ( kapton 50 HN, DuPont).19 All of these systems have been used in the

detection or discrimination of biomolecules.

Within this dissertation we will discuss application of the single conical nanopore within a

PET (polyethylene terephthalate) film which is not currently available within the present

synthetic single nanopore systems. The first advantage is that we are able to control the diameter

of the nanopore over a very large diameter range. We have demonstrated that we can make









single nanopores with diameters > 200nm and diameters as small as 1.9nm. Also, the length of

the nanopore can be systematically altered for each desired experimental setup. By using the

track-etch process to fabricate single nanopore systems, the effective length of the nanopore can

be changed from a large effective length of 12 [tm to a value of <100 nm. This flexibility offers

one the control over a very important parameter within single nanopore systems which is the

effective detection zone within the channel. This detection zone is the area within the channel in

which the particular analyte is detected. By reducing the length of this zone you are able to then

in turn detect smaller analytes.

The practical side of this system is that it allows the researcher the ease of preparation.

With the track-etch process there is no need for expensive equipment in which a highly

experienced technician is needed to perform the task. This allows for a more stream line process

which is very important in future directions of mass production of these single nanopore

membranes. This system also has an advantage in characterizing the nanopore. There has been a

large amount of research directed at studying the nanopore track-etched membrane within Martin

group.

Ion Current Rectification

Conical nanopores in polymer films and glass have attracted increasing attention due to

their application as biomimetic systems for models of biological channels and as biosensors.99

One particular transport phenomenon has been observed in this kind of conically-shaped

nanopore, which is due to the nanometer-sized opening. It has been found that these asymmetric

nanopores and nanocapillaries rectify ion current, although the concentration and pH of the

electrolyte in contact with pore openings are the same. The rectification is observed as an

asymmetric current-voltage (I-V) curve, with the current recorded for one voltage polarity higher

than the current recorded for the same absolute value of voltage but different polarity.









The ion current rectification is dependent on the electrolyte concentration, pH value, and

voltage, nanopore diameter and surface charge density of the nanopore. Conical nanopores

rectify ion current only when the pore walls possess an excess surface charge. Chemically

etching polymeric materials (PET and Kapton) result in the formation of carboxylate groups on

the pore wall. The density of carboxylate groups has been estimated to be 1.5 groups nm-2. 100 A

direct consequence of the presence of carboxylate groups is the possibility that the surface charge

can be defined by immersing the membranes into the electrolytes with various pH values. For

example, at neutral and basic conditions, the carboxylate groups are deprotonated and the net

surface charge is negative. Lowering the pH to values close to the isoelectric point of the track-

etched surface neutralizes the surface charge.22

Several mechanisms have been suggested to explain the ion-current rectification effect

observed in synthetic nanoporous systems. Here is a explanation of one ratchet model introduced

by Swiy et al.101-103 The ratchet model has been formed on the basis of experimental observation

of conditions at which the nanoporous systems rectify ion current. The main experimental

observations were summarized: i) the opening diameter of the tip is comparable to the thickness

of the electrical double layer, ii) there is an excess surface on the pore walls, and iii) the

interactions of ions with the pore walls, induced either by the size of the openings or surface

charge, are asymmetric at the two entrances of the pores. It has been shown that the sign of the

surface charge determines the direction of ion-current rectification (Figure 1-10): Rendering the

surface charge positive or negative makes the nanotubes rectify in opposite directions. This

observation provides evidence that the rectification effect originated from electrostatic

interactions between the ions passing through the nanopore and the pore wall. Interaction of ions









with the pore wall is the basis of pore selectivity, because excess negative surface charge allows

mainly cations to enter the pore, while anions are rejected.40' 104

When the cation moves along the nanopore, the interaction between cation and the

negatively charged pore wall was assumed to be a Debye-type interaction. The interaction

between passing ions and the surface charges occur only if the pore is sufficiently narrow, with a

diameter comparable to the thickness of the electrical double layer. This is caused by the short-

range character of electrostatic interactions in an electrolyte solution, resulting from a strong

screening induced by the presence of other ions.104 To calculate the electrical potential of a

cation at a given position z at the pore axis, they used the following formulal01103

V(z) = -2;rp dz' h(z')e '(* / R(z, z') (1-2)

where p is the surface-charge density at the pore wall, R is the distance between the cation

on the pore axis and negative charges on the pore walls (Figure 1-11), L stands for length of the

pore, h(z') is the radius of the pore at point z' and X indicates the inverse screening length related

to the thickness of the electrical double layer. The integration indicates that the potential of a

cation at a given position z results from interactions with carboxylate groups on the entire

surface of the pore. The problem has been treated in two-dimensional and three-dimensional

space.107 For conical nanopores, without any voltage applied from outside, the shape of the

internal potential has been shown to be asymmetric and toothlike, reminiscent of the shape of a

ratchet potential. The potential minimum is situated at the tip of a conical nanopore.

Assuming a simple superposition of the externally applied voltage with the internal

electrical field, one can obtain the resultant potential profiles for the two polarities of the applied

voltage. Figure 1-12 shows that for positive voltages, a trap of electrostatic origin is created,









causing an off state of the pore, i.e., low conductivity. Applying voltage of the opposite polarity

does not lead to formation of the trap and the ion currents are higher.

Dissertation Overview

The main focus of my research is to develop a new method which can be used to improve

the quality of nanopore membranes and to create new approaches for sensing drug molecules,

DNA and proteins based on track-etched conical nanopore embedded in polymer membrane. The

previous part of chapter 1 has reviewed the background information for this dissertation

including the ion track-etch process, membrane based template synthesis, biological ion channel,

potassium-gated ion channels, stochastic chemical sensing, and ion current rectification.

In chapter 2, a new paradigm making use of the well-known ion-current rectification

phenomenon displayed by conically-shaped nanopores is demonstrated. The sensor element in

this case is a single conically-shaped nanopore in a polyimide (Kapton) membrane. The sensing

paradigm entails placing electrolyte solutions on either side of the membrane and using

electrodes in each solution to scan the applied transmembrane potential and measure the

resulting ion current flowing through the nanopore. As has been discussed in detail by us and

others, conically-shaped nanopores with excess surface charge on the pore walls, and sufficiently

small tip openings, show non-linear current voltage curves; i.e., such pores are ion-current

rectifiers. Because the polyimide nanopores used here have excess anionic surface charge,

rectification is observed at positive applied transmembrane potential. We have found that when

the nanopore is exposed to a very hydrophobic yet cationic, drug molecule (Hoechst 33258),

adsorption of this molecule on the pore walls neutralizes the excess negative surface charge. As a

result, the nanopore does not rectify as strongly, and the magnitude of the decrease in

rectification scales with the concentration of the drug molecule. Ultimately at high

concentrations of the drug, the sign of the excess surface charge switches from net negative to









net positive, and the nanopore rectified at negative applied transmembrane potential. We

describe this new nanopore-based sensing paradigm here.

In chapter 3, we demonstrate the ability of a conical nanopore embedded in a polymer

membrane to selectively sense drug molecules based on ion current rectification phenomenon.

As has been pointed out in chapter 2, hydrophobicity is the dominant force which contributes to

the absorption of positive drugs to the hydrophobic pore wall of the Kapton membrane. This

conclusion paves the foundation for exploration of selectivity based on hydrophobicity. We

choose three positive drugs which have different hydrophobicity. In this chapter, we demonstrate

that three hydrophobic drugs can be be totally discriminated due to different binding constant.

We believe that this powerful sensing ability based on ion current rectification can be extended

to sense other interesting biomolecules, for example, DNA and proteins.

In chapter 4, we demonstrate a promising tool for sensing DNA-linked protein dimmers

which are relevant to a biological process, for example, gene expression, DNA degradation, and

virus detection. The sensing device investigated is a bare conically-shaped nanopore embedded

in track-etched PET membrane. A Biotin-labelled DNA probe reacts with excess Streptavidin to

form a Streptavidin conjugated DNA probe. Two Streptavidin conjugated monovalent DNA

probes can bind two distinct segments of target DNA. The size of the target DNA linked

complex is double that of each Streptavidin conjugated monovalent DNA probe. By precisely

controlling the tip diameter of the conical nanopore embedded in PET polymer, the events due to

the translocation of the streptravidin conjugated monovalent DNA probes through the nanopore

can be filtered and undetected on purpose; the current-pulses due to translocation of the target

DNA linked complex can thus be detected. In order to confirm that the two Streptavidin

conjuaged DNA probes are linked by target DNA ,we test if the wo protein conjugated DNA









probes can be linked by multi-mismatched DNA. The multi-mismatched DNA will not induce

the complex formation. The current-pulse signatures for the self-assembled complex can be used

to confirm the existence of target DNA and DNA linked protein dimer. The concept of size

dependent detection of self-assembled complexes on the molecule level shows strong promise

for detection of biomolecules without interference of probes.

In chapter 5, we demonstrate a new way to tailor the single conical nanopores embedded in

PET (polyethylene terephthalate) membranes via a layer-by-layer assembly technique, which is

based on strong interaction between Biotin and Streptavidin. Single conical nanopores are

fabricated in ion-tracked PET membranes by using a two-step etch procedure. Multi-Biotin

labelled BSA (or multi-Biotin labelled polylysine) were driven into the tip of the single conical

nanopore from the base of the pore opening by applying a transmembrane potential difference

(1V), and nonspecifically adsorbed onto the inner wall of the nanopore as a first layer.

Streptavidin was then placed on both sides of the nanopore, and specifically interacted with the

multi-Biotin labelled protein and was thus deposited as a second layer by alternately applying a

transmembrane potential difference of 200mV and -200mV. Multilayers were formed by

repeating the same procedure for depositing the second layer. Most importantly, the diameter of

the tip opening can be adjusted by controlling the number of protein layers. The conical

nanopore can also be made selective with this method by depositing any Biotin labelled ligand

on the final layer, which can be used for specifically sensing target analytes. The layer-by-layer

assembled conical protein nanopores have shown great stability and may allow for fabricating

practical biosensors based on these conical nanopores.















a


Etched track










Latent track


(A)


(B)


Figure 1-1. (A) The heavy ion beam forms a latent ion track in the dielectic membrane. (B)
Chemically etching will selectively remove the latent track and form a cylindrical
shape.


Original' ,
---.~~.~..~,---------------- -------

Surface
after time t "


---------------Vet
./ VBt


Figure 1-2. Definition of cone half-angle a, bulk etch rate VB and track etch-rate VT.


Latent ion track































Figure 1-3. Scanning electron microscopic images of different nanoporous materials developed
by ion-track-etching process. (A) Kapton (B) PC (C) PET (D) Mica.


Figure 1-4. Scanning electron microscopic images of different template. (A) Polycarbonate
membrane and (B) Alumina membrane.













+ SnCI2


Ag
,Sn4+
Ag
Ag
n4+
/ Ag


Sr2+


Au+

Formaldehyde 40C


Ag+


Figure 1-5. Schematic diagram of Au electroless plating procedure.


Membrane Face


Top View
Pore (dia. = 30 nm)

PEleltiolees
D PlPitiiio


Gold surface film


(D


Side View


M Plating
Membrane Pores


Au nanotubes
lining the pores

M


Figure 1-6. Schematic illustration of Au nanotubes obtained from electroless gold deposition.


Ag


Ag

SnO
Ag


+ Ag+


>Sn














0 --


S4.S5,


l


Closed


Figure 1-7. Schematic illustration of open and close state of K channel. [Adapted from Long, S.
B.; Campbell, E. B.; MacKinnon, R. Science 2005, 309, 897-903.]


Steady State
Current No Analyte


0 +


S


Time


S


0 0 =ions


= analyte


Time


Figure 1-8. Schematic illustration of resistive-pulse sensing.
















100 A



'I


Stem


Figure 1-9. Protein channel embedded in lipid bilayer.


Membrane


I-V curve


V f = I(-6V) / I(+6V) = 1


+
v f = I(-6V)/ I(+6V) > 1




+ f = I(-6V) / I(+6V) < 1
+


Figure 1-10. Current-voltage curve for conical nanopore with different charge, the voltage scan
from positive potential in base side to negative potential in based side: (A) I-V curve
and current rectification for nanopore without charge. (B) I-V curve and current
rectification for nanopore with negative charge. (C) I-V curve and current
rectificationfor nanopore with positive charge.


Cap
---I1A ---


Current rectification











-,
0 .v(Z)






0 6 z (m) 12


Figure 1-11. (A) Scheme of an axial cut of a conical pore; (B) profile of electrical potential,V(z),
inside a tapered-cone pore, calculated from Eq. 1-2. [Adapted from Siwy, Z. Adv.
Funct. Mater. 2006, 16, 735-746.]









x


x

SCaton
...... ...Caton
Vr;_._TA.rap


X


K+

NO cation
trap


Figure 1-12. Ratchet model for ion current recification in a conical nanopore with excess
negative surface charge on pore wall: (A) schematic representation of the electric
potential for cation inside a nanopore without external voltage; (B) solution voltage
drop for cations, left: positive voltage, right; negative voltage; (C) profile of the
electric potential resulting from superposition of the profile shown in (A) with the
two profiles from (B). Appling positive voltages results in formation of an
electrostatic trap and consequently lower ion current. [Adapted from Siwy, Z. Adv.
Funct. Mater. 2006, 16, 735-746.]









CHAPTER 2
A NEW DRUG-SENSING PARADIGM BASED ON ION-CURRENT RECTIFICATION IN A
CONICALLY SHAPED NANOPORE

Introduction

There is increasing interest in using nanopores in synthetic14-17' 92-94, 105-118 or biological77'

79-80, 83-86, 119-129 membranes as biosensors. Perhaps the most popular nanopore-based sensing

paradigm is the well-known resistive-pulse, or stochastic-sensing, method which entails counting

individual analyte molecules as they are driven through the nanopore sensor element.105-129

Prototype sensors for analyte species as diverse as proteins114, DNA109 and small molecules110

have been described. While we too are exploring resistive-pulse sensors,109110, 130 we have also

been investigating other sensing paradigms based on artificial nanopores 1. One such paradigm

makes use of the well-known ion-current rectification phenomenon displayed by conically

shaped nanopores.21' 26 31, 37, 130-134

The sensor element in this case is a single conically shaped nanopore in a polyimide

(Kapton) membrane.37' 110 The sensing paradigm entails placing electrolyte solutions on either

side of the membrane and using electrodes in each solution to scan the applied transmembrane

potential and measure the resulting ion current flowing through the nanopore. As has been

discussed in detail by us26' 62 and others21' 31, 131-133, conically shaped nanopores with excess

surface charge on the pore walls, and sufficiently small tip openings, show non-linear current

voltage curves; i.e., such pores are ion-current rectifiers. Because the polyimide nanopores used

here have excess anionic surface charge, rectification is observed at positive applied

transmembrane potential.31

We have found, however, that when the nanopore is exposed to a very hydrophobic, yet

cationic, drug molecule (Hoechst 33258, Figure 2-1), adsorption of this molecule on the pore

walls neutralizes the excess negative surface charge. As a result the nanopore does not rectify as









strongly, and the magnitude of the decrease in rectification scales with the concentration of the

drug molecule. Ultimately at high concentrations of the drug, the sign of the excess surface

charge switches from net negative to net positive, and the nanopore rectifies at negative applied

transmembrane potential.62 We describe this new nanopore-based sensing paradigm here.

Experimental

Materials and Methods

Polyimide (Kapton, Scheme 1) membranes (diameter = 3 cm, thickness = 12 [im) that had

been irradiated with a heavy ion of 2.2 GeV kinetic energy to create a single damage track

through the membrane were obtained from GSI, Darmstadt, Germany.37 110 We refer to these as-

received membranes as the "tracked" membranes. Hoechst 33258, methyl viologen dichloride

hydrate, benzylviologen and sodium hypochlorite (13% active chloride) were purchased from

Sigma-Aldrich and used as received. Bis-Tris propane, used to prepare the buffer solutions, was

also obtained from Aldrich. All other chemicals were used as received. Purified water was

prepared by passing house-distilled water through a Millipore Milli-Q water purification system.

Etching the Conical Nanopore in the Tracked Membrane

We have recently described a two-step etching procedure for reproducibly preparing

conically shaped nanopores in tracked poly(ethylene terphthalate membranes).135 A variant of

that method was used to etch the conical nanopores in the tracked Kapton membranes used for

these studies. The tracked Kapton membrane was irradiated under UV light (320 nm) for 15

hours, and then mounted in a two-compartment cell135 such that electrolyte solution could be

placed on either side of the tracked membrane.

The first etch step, developed by Apel, et al.,37 entailed placing a solution that etched the

damage track (13% NaOC1, pH =12.6) on one side of the membrane and a solution that

neutralizes the etchant (2 M KI, the "stop" solution) on the other side.110 The temperature during









etch was 50 C. Each half cell contained a Pt wire (dia = 0.2 cm, length -7.6 cm), and a Keithley

6487 picoammeter/voltage-source (Keithley Instruments, Cleveland, OH) was used to apply a

transmembrane potential of IV, during etching and measure the resulting current ionic flowing

through the nascent nanopore. The current was initially zero but increased suddenly when the

etch solution broke through to the stop solution. This first etch step was terminated when the

current increase up to 0.1 nA. At this point, stop solution was placed in both half cells to quench

the etch.

As per our prior work,110 the diameter of the base opening after the first etch step was

determined by obtaining scanning electron micrographs of the base side of multi-track Kapton

membranes etched in the analogous way. Multi-track membranes (1* 106 tracks cm-2, also from

GSI) were used because it is difficult to find the base openings by electron microscopy in etched

single-track membranes. These studies yielded an etch rate of 8.3 nm min-, in close agreement

to the value of 7.0 nm min-1 obtained by Siwy et al.23 Our studies with PET membranes showed

that by varying the etch time (or final etch current) or the transmembrane voltage applied during

etching, the base diameter can be reproducibly controlled during this first etch step.135-136 We

found, however, that it is difficult to reproducibly control the tip diameter. This led us to subject

the membrane to a second etch step which allows us to control and fine-tune the tip diameter.135

The second etch step entailed placing the NaOCl etch solution on both sides of the

membrane. A transmembrane potential of 200 mV was applied, and again the transmembrane

current was monitored during the etch. The key innovation is that this etch is stopped at a

prescribed value of the transmembrane current rather than at a prescribed time.135 We have found

that this allows for excellent reproducibility in both tip and base diameter.135 The base and tip

diameters after the second etch were measured using the electrochemical method described in









detail previously.135 Membranes with two different base and tip diameters were used for these

studies. The first had base diameter of 1.43 [tm and tip diameter of 67 nm. The second had base

diameter of 2.0 [m and tip diameter of 48 nm.

Sensing the Analyte Molecules

The membrane containing the conically shaped nanopore was mounted in the two-

compartment cell,135 and a solution containing the desired analyte molecule (Figure 2-1) was

placed on the side on the membrane containing the tip opening. This solution was prepared in

10mM Bis-tris propane (pH = 7.0) that was also 3 mM in MgC12, and the same buffer solution,

devoid of the analyte, was placed on the opposite side on the membrane. A Ag/AgCl electrode

was placed into each solution, and the Keithley 6487 was used to obtain a current-voltage (I-V)

curve associated with ion transport through the nanopore. The working Ag/AgCl electrode was

in the half-cell facing the base opening, and the potential of this electrode was controlled relative

to the counter Ag/AgCl electrode in the opposite solution. The I-V curve was obtained by

stepping the potential in 300 mV steps through desired potential range. The sign convention

used here is the same as used in our prior studies,62 negative transmembrane potentials mean

that the cathode is in the solution facing the base opening and the anode is in the solution facing

the tip opening.

Results and Discussion

Ion-Current Rectification by the Conical Nanopore

Figure 2-2 shows I-V curves for a conical nanopore in a Kapton membrane with and

without the analyte drug molecule Hoechst 33258. In the absence of this drug, the I-V curve is

non-linear, indicating that the nanopore strongly rectifies the ion current flowing through it.21' 31,

62, 131-134 There seems to be some disagreement in the literature as to the precise mechanism by

which conical nanopores rectify the ion current. All extant theories agree on the following:









Rectification requires that excess charge density be present on the pore walls and that the

diameter of the tip opening be comparable to the thickness of the electrical double layer

extending from the pore wall.

The ion-current rectification phenomenon can be described by defining "on" and "off'

states for the nanopore rectifier.62 In agreement with previous results for conically shaped

Kapton nanopores, Figure 2-2 shows that in the absence of Hoechst 33258, the "on" state occurs

at negative potentials and the "off' state at positive potentials.62 This indicates that rectification

is caused by fixed anionic carboxylatee) groups on the pore wall.23' 31 The extent of rectification

can be quantified by the rectification ratio26 62 defined here as the current at -6.0 V divided by

the current at +6.0 V (Table 2-1).

Effect of Hoechst 33258 on Rectification

The key experimental observations of these studies are: 1. As Hoechst 33258 is added, the

extent of rectification decreases (Figure 2-2). 2. The extent of rectification scales inversely with

the concentration of Hoechst 33258 (Table 2-1). 3. Ultimately at high drug concentrations, the

rectification is reversed (Figure 2-2). This reversal in rectification is signaled by the fact that at

high drug concentrations the "on" state is at positive potentials and the "off' state is at negative

potentials. Rectification with this polarity causes the rectification ratio to be less than unity

(Table 2-1). We have shown that rectification with this polarity requires excess positive charge

on the pore walls.62

At pH = 7.0 Hoechst 33258 is cationic with a net charge of +1,137 due to protonation of the

methyl-substituted piperdine-like N. In addition, this drug is quite hydrophobic, as is Kapton

polyimide, dielectric constant = 3.4. We have shown that such hydrophobic cationic drug

molecules can adsorb to hydrophobic surfaces and impart positive charge to the surface.138 These

prior studies provide a simple explanation for the results in Figure 2-2. Exposure of the









hydrophobic Kapton membrane to the cationic and hydrophobic Hoechst 33258 causes this

molecule to adsorb to the pore wall, thus neutralizing the surface-carboxylate sites, and this

neutralization of the negative surface charge causes the observed decrease in ion current

rectification (Table 2-1). The reversal of polarity at high drug concentrations (Figure 2-2), and

concomitant less-than-unity rectification ratios (Table 2-1), indicate that ultimately the quantity

of adsorbed cationic charge due to the drug exceeds the quantity of fixed negative charge due to

the carboxylates.

This reversal in the sign of the surface charge illustrates an interesting chemical point. At

low drug concentrations where the net surface charge is negative, there is no question that part of

the interaction between the drug and the surface is electrostatic the surface needs a charge

balancing cation and it chooses the hydrophobic drug over the inorganic cations present in the

solution. However, this electrostatic component is augmented by the hydrophobic component, as

indicated by the fact that when the net surface charge becomes positive at high drug

concentrations, the drug continues to adsorb. For example the less-than-unity rectification ratio

for 25 [aM drug (Table 2-1) indicates that the surface has net positive charge when the membrane

is exposed to this drug concentration.

Effect of Benzyl and Methyl on Rectification

To explore the surface chemical interactions further, we obtained analogous data for two

other relatively hydrophobic cationic molecules methyl and benzyl viologen (Scheme 1).

Current voltage curves for a conical nanopore sensor before and after exposure to these

molecules are shown in Figure 2-3. The black curve was obtained in the absence of the

viologens, and as before, shows the strong surface-carboxylate-induced rectification

phenomenon. In analogy to Hoechst 33258 the more hydrophobic benzyl viologen engenders a

concentration dependent decrease in the extent of rectification. However, the concentrations









required to produce a measurable change are about three orders of magnitude higher than the

concentration needed for Hoechst 33258. This clearly shows that benzyl viologen adsorbs much

more weakly to the Kapton surface than Hoechst 33258.

This observation helps us understand the relative contributions of hydrophobicity vs.

molecular charge to the interaction of the adsorbing molecule with the Kapton surface. Recall

first that benzyl viologen is a divalent cation, whereas Hoechst 33258 is monovalent. If the

interaction between the adsorbing molecule and the Kapton surface was dominated by

electrostatics, then benzyl viologen would adsorb much more strongly, and this is not what is

observed experimentally. Hence it is clear that the hydrophobic effect is the dominant force that

causes adsorption to the Kapton surface. This is in agreement with our early observation that

cationic Hoechst 33258 continues to adsorb even after the Kapton surface has net positive

charge.

The dominance of the hydrophobic effect is also strongly reinforced by the methyl

viologen data in Figure 2-3. Methyl viologen retains the 2+ charge of benzyl viologen, but

because it lacks the two benzene rings, it is much less hydrophobic. As a result, no evidence for

methyl viologen adsorption is observed in Figure 2-3. A slight increase in current, relative to the

I-V curve obtained in the absence of adsorbing molecule, is observed because at the ImM and

higher concentrations used, the divalent methylviologen makes a measurable contribution to the

bulk conductivity of the electrolyte.

Langmuir Analysis of the Hoechst 33258 Adsorption Data

We can write the following general equation for Langmuir adsorption of a molecule to a

surface138

0 = KC/(1 + KC) (2-1)









where 0 is the fractional coverage of the molecule on the surface, K is the binding constant

with units of L molP1 and C is the concentration of the drug in the contacting solution phase. 0 is

also given by

0= moleD,i/ moleD,max (2-2)

where moleD,i is the moles of molecule on the surface when the surface is exposed to some

concentration of drug i and moleD,max is the maximum adsorption capacity of the surface

obtained at some very high concentration of the molecule.

Table 2-2 shows values of the ion current, at 6.0 V, for a conical nanopore sensor at high

concentrations of Hoechst 33258. We see that the current decreases to a minimum and then

increases again at concentrations above about 1 mM. This increase at high concentration results

because the drug concentration is comparable to the electrolyte concentration and the drug

begins to contribute to the bulk conductivity of the electrolyte. Based on these results, we

assume that moleD,max occurs for a solution drug concentration, and we call the current obtained

Imin. If we call the current obtained in the absence of drug Io, then moleD,max is proportional to

the difference Io Imin.

Likewise, if we call the current observed at some intermediate drug concentration, i, Ii then

moleD,i is proportional to the difference Io Ii. This allows us to calculate 0 for any concentration

of drug, I, via

0 = (Io I)/ (Io Imin) (2-3)

equating these 0 values to the corresponding concentration values (Equation 2-1) allows us

to plot out the Langmuir isotherm, and by fitting the experimental data to Equation 2-1, the value

of the binding constant K can be obtained. Figure 2-4 shows the experimental and calculated









plots and a value ofK = 2x105 L/Mol was obtained from the best fit. This K quantifies what the

experimental data already taught us Hoechst 33258 binds very strongly to the Kapton surface.

Conclusions

The sensor described here is reminiscent of much earlier work on ion-selecitive electrode.

Potentiometric sensors, for hydrophobic drug molecules.139-140 Both sensors use a hydrophobic

membrane with fixed negative charge to extract hydrophobic cations into the membrane. In both

cases, the sensor has greater selectivity for hydrophobic analytes relative to more hydrophilic

analytes. In the case of the ion-selective electrode, this was quantified by investigating the

response of the device to a homologous series of alkyl ammonium ions.140 We are currently

conducting studies of this type for the sensor described here.

The disadvantage of this hydrophobic-based selectivity paradigm is that the device can not

discriminate between analytes of similar mass and charge. In successful (commercially available)

ion-selective electrodes, this problem is solved by incorporating a highly selective ionophore in

to the membrane. This could be accomplished with the sensor described here by simply attaching

the ionophore to the pore wall. Finally, it is important to point out that with our current sensor

design; the drug molecule binds not only to the pore walls but also to the faces of the membrane.

This is because the pore walls and membrane faces are chemically identical. If adsorption to the

membrane faces could be blocked, then a much smaller number of sites, only those along the

pore walls, would be available for analyte adsorption. This would shift the isotherm to much

lower analyte concentrations, and lower detection limits would be achieved. This could be

accomplished by attaching a neutral and hydrophilic chemical species to the membrane faces.











HIC--K rn


NH


Hoechst 33258
OH









Kapton


Benzyl o[ogeen dichlonde




Mellylviologen dichloride





Melhylviologen dichloride


Figure 2-1. Molecular structure of different drug molecules and polymer.


101


ransmembrane potential (V)


.25
Figure 2-2. I-V curves for a conical nanopore sensor (tip diameter =67 nm, base diameter 1.43
ipm) in the presence of the following concentrations of Hoechst 33258: 0 nM (black
square), 1.25 pM (red circle), 2.5 pM (green triangle), 5 pM (blue triangle), 10 pM
cyann square), 15 pM (magenta), 25 pM (yellow).











10"
Transmembrane potential (V)


NI
-I
-v -10"


-20


P," -40- b

-50

-6C
Figure 2-3. I-V curve for conical nanopore in kapton membrane (tip diameter 48 nm, base
diameter 2.0 itm) with different molecules: 2.3 mM benzyl viologen cyann square), 1
mM benzyl viologen (blue triangle), control buffer (black square), 1 mM methyl
viologen (red circle), 2.3 mM methyl viologen (green triangle).






1.0-


0.8-


0.6-


S0.4-


0.2


0.0-

0 5 10 15 20 25
Concentration (lM)


Figure 2-4. Plot of surface coverage (theta) versus concentration of Hoechst 33258.









Table 2-1. Rectification ratio in various concentration of Hoechst 33258 at transmembrane
potential difference of 6V.
Concentration (pM) 0 2.5 5 10 15 25

Rectification ratio 19.58 10.84 4.91 1.86 1.24 0.672










Table 2-2. Current values in various concentration of Hoechst 33258 at transmembrane potential
-6V.
Concentration (pM) 0 2.5 5 10 15 25 500 1000 1500

Current value (nA) -21.90 -14.8 -9.75 -6.96 -5.43 -3.60 -4.60 -5.99 -6.06









CHAPTER 3
SELECTIVE DETECTION OF DRUGS BASED ON ION-CURRENT RECTIFICATION IN A
CONICALLY-SHAPED NANOPORE

Introduction

There is increasing interest in using nanopores in synthetic14-17' 92-94, 105-118 or biological77'

79-80, 83-86, 119-129 membranes as biosensors. Perhaps the most popular nanopore-based sensing

paradigm is the well-known resistive-pulse, or stochastic-sensing, method which entails counting

individual analyte molecules as they are driven through the nanopore sensor element.1105-129

Prototype sensors for analyte species as diverse as proteins,114 DNA,109 and small molecules110

have been described. While we too are exploring resistive-pulse sensors,109-110' 130 we have also

been investigating other sensing paradigms based on artificial nanopores.107 One of these

paradigms makes use of the well-known ion-current rectification phenomenon displayed by

conically-shaped nanopores.21'26 31 37,130-134

The sensor element in this case is a single conically-shaped nanopore in a polyimide

(Kapton) membrane.37' 110 The sensing paradigm entails placing electrolyte solutions on either

side of the membrane and using electrodes in each solution to scan the applied transmembrane

potential and measure the resulting ion current flowing through the nanopore. As has been

discussed in detail by us26' 62 and others,21 31, 131-133 conically-shaped nanopores with excess

surface charge on the pore walls, and sufficiently small tip openings, show non-linear current

voltage curves, i.e., such pores are ion-current rectifiers. Because the polyimide nanopores used

here have excess anionic surface charge, rectification is observed at positive applied

transmembrane potential.31

We have reported141 that when the nanopore is exposed to a very hydrophobic, yet cationic,

drug molecule (Hoechst 33258), adsorption of this molecule on the pore walls neutralizes the

excess negative surface charge. As a result the nanopore does not rectify as strongly, and the









magnitude of the decrease in rectification scales with the concentration of the drug molecule.

Ultimately at high concentrations of the drug, the sign of the excess surface charge switches from

net negative to net positive, and the nanopore rectifies at negative applied transmembrane

potential.62

In the previous report,141 selectivity has not been explored. Here we have clearly

demonstrated that the conical-shaped nanopore embedded in the Kapton membrane can be used

to selectively discriminate cationic hydrophobic drugs based on ion-current rectification and

three drugs including Hoechst 33342, Amitriptyline and Bupivacaine were chosen to explore this

powerful ability. Hoechst 33342 is a more hydrophobic analog of Hoechst 33258, and

Amitriptyline and Bupivacaine are less hydrophobic.

Experimental

Materials and Methods

Polyimide (Kapton, Scheme 1) membranes (diameter = 3 cm, thickness = 12 [tm) that had

been irradiated with a heavy ion of 2.2 GeV kinetic energy to create a single damage track

through the membrane were obtained from GSI, Darmstadt, Germany.37, 110 We refer to these as-

received membranes as the "tracked" membranes. Hoechst 33342, Amitriptyline, Bupivacaine

and sodium hypochlorite (13% active chloride) were purchased from Sigma-Aldrich and used as

received. Bis-Tris propane, used to prepare the buffer solutions, was also obtained from Aldrich.

All other chemicals were used as received. Purified water was prepared by passing house-

distilled water through a Millipore Milli-Q water purification system.

Etching the Conical Nanopore in the Tracked Membrane

We have recently described a two-step etching procedure for reproducibly preparing

conically-shaped nanopores in tracked poly(ethylene terphthalate membranes).135 A variant of

that method was used to etch the conical nanopores in the tracked Kapton membranes used for









these studies. The tracked Kapton membrane was irradiated under UV light (320 nm) for 15

hours, and then mounted in a two-compartment cell135 such that electrolyte solution could be

placed on either side of the tracked membrane.

The first etch step, developed by Apel, et al.,37 entailed placing a solution that etched the

damage track (13% NaOC1, pH =12.6) on one side of the membrane and a solution that

neutralizes the etchant (2 M KI, the "stop" solution) on the other side.110 The temperature during

etch was 50 C. Each half cell contained a Pt wire (dia = 0.2 cm, length -7.6 cm), and a Keithley

6487 picoammeter/voltage-source (Keithley Instruments, Cleveland, OH) was used to apply a

transmembrane potential of IV, during etching and to measure the resulting ionic current flowing

through the nascent nanopore. The current was initially zero but increased suddenly when the

etch solution broke through to the stop solution. This first etch step was terminated when the

current increased up to 0.1 nA. At this point, stop solution was placed in both half cells to

quench the etch.

As in our prior work,110 the diameter of the base opening after the first etch step was

determined by obtaining scanning electron micrographs of the base side of the multi-track

Kapton membranes etched in the analogous way. Multi-track membranes (1* 106 tracks cm2,

also from GSI) were used because it is difficult to find the base openings by electron microscopy

in etched single-track membranes. These studies yielded an etch rate of 8.3 nm min-, in close

agreement to the value of 7.0 nm min- obtained by Siwy et al.23 Our studies with PET

membranes showed that by varying the etch time (or final etch current) or the transmembrane

voltage applied during etching, the base diameter can be reproducibly controlled during this first

etch step.135-136 We found, however, that it is difficult to reproducibly control the tip diameter.









This led us to subject the membrane to a second etch step which allows us to control and fine-

tune the tip diameter.135

The second etch step entailed placing the NaOCl etch solution on both sides of the

membrane. A transmembrane potential of 200 mV was applied, and again the transmembrane

current was monitored during the etch. The key innovation is that this etch is stopped at a

prescribed value of the transmembrane current rather than at a prescribed time.135 We have found

that this allows for excellent reproducibility in both tip and base diameters.135 The base and tip

diameters after the second etch were measured using the electrochemical method described in

detail previously.135 Membranes with a base diameter of 1.21 tm and tip diameter of 57 nm were

used for these studies.

Sensing the Analyte Molecules

The membrane containing the conically-shaped nanopore was mounted in the two-

compartment cell,135 and a solution containing the desired analyte molecule (Figure 3-1) was

placed on the side of the membrane containing the tip opening. This solution was prepared in

10mM Bis-tris propane (pH = 7.0) that was also 3 mM in MgC12, and the same buffer solution,

devoid of the analyte, was placed on the opposite side on the membrane. A Ag/AgCl electrode

was placed into each solution, and the Keithley 6487 was used to obtain a current-voltage (I-V)

curve associated with ion transport through the nanopore. The working Ag/AgCl electrode was

in the half-cell facing the base opening, and the potential of this electrode was controlled relative

to the counter Ag/AgCl electrode in the opposite solution. The I-V curve was obtained by

stepping the potential in 300 mV steps through desired potential range. The sign convention

used here is the same as used in our prior studies,62 negative transmembrane potentials mean

that the cathode is in the solution facing the base opening and the anode is in the solution facing

the tip opening.









Results and Discussion

Ion-Current Rectification by the Conical Nanopores

Figure 3-2 shows I-V curves for a conical nanopore in a Kapton membrane with and

without the analyte drug molecule Hoechst 33342. In the absence of this drug, the I-V curve is

non-linear, indicating that the nanopore strongly rectifies the ion current flowing through it.21' 31,

62, 131-134 While there is currently some disagreement in the literature as to the precise mechanism

by which conical nanopores rectify the ion current. All extant theories agree on the following:

Rectification requires that excess charge density be present on the pore walls and that the

diameter of the tip opening be comparable to the thickness of the electrical double layer

extending from the pore wall.

The ion-current rectification phenomenon can be described by defining "on" and "off'

states for the nanopore rectifier.62 In agreement with previous results for conically-shaped

Kapton nanopores, Figure 3-2 shows that in the absence of Hoechst 33342, the "on" state occurs

at negative potentials and the "off' state at positive potentials.62 This indicates that rectification

is caused by fixed anionic carboxylatee) groups on the pore wall.23' 31 The extent of rectification

can be quantified by the rectification ratio26 62 defined here as the current at -2.0 V divided by

the current at +2.0 V (Table 3-1).

Effect of Hoechst 33342 on Rectification

The key experimental observations for studies41 with Hoechst 33258 can be reproduced by

Hoechst 33342 which is one more hydrophobic analog of Hoechst 33258, which are: 1. As

Hoechst 33342 is added, the extent of rectification decreases (Figure 3-2). 2. The extent of

rectification scales inversely with the concentration of Hoechst 33342 (Table 3-1). 3. Ultimately

at high drug concentrations, the rectification is reversed (Figure 3-2). This reversal in

rectification is signaled by the fact that at high drug concentrations the "on" state is at positive









potentials and the "off" state is at negative potentials. Rectification with this polarity causes the

rectification ratio to be less than unity (Table 3-1). We have shown that rectification with this

polarity requires excess positive charge on the pore walls.62

At pH = 7.0 Hoechst 33342 is cationic with a net charge of +1,137 due to protonation of the

methyl-substituted piperdine-like N. In addition, this drug is quite hydrophobic, as is Kapton

polyimide, dielectric constant = 3.4. We have shown that such hydrophobic cationic drug

molecules can adsorb to hydrophobic surfaces and impart positive charge to the surface.138 These

prior studies provide a consistent explanation for the results in Figure 3-2. Exposure of the

hydrophobic Kapton membrane to the cationic and hydrophobic Hoechst 33342 causes this

molecule to adsorb to the pore wall, thus neutralizing the surface-carboxylate sites, and this

neutralization of the negative surface charge causes the observed decrease in ion current

rectification (Table 3-1). The reversal of polarity at high drug concentrations (Figure 3-2), and

concomitant less-than-unity rectification ratios (Table 3-1), indicate that ultimately the quantity

of adsorbed cationic charge due to the drug exceeds the quantity of fixed negative charge due to

the carboxylates.

The similarity of molecular structures between Hoechst 33258 and Hoechst 33342 tell us

that the interaction of Hoechst 33342 and nanopore wall in Kapton can also be explained by

hydrophobicity which was used to explain the interaction mechanism between Hoechst 33258

and the nanopore wall in the kapton.41 Similar to analysis of Hoechst 33258, electrostatic force

was not the dominant force since Hoechst 33342 continues to adsorb to the nanopore wall after

excess positive charge exists on the surface. For example the less-than-unity rectification ratio

for 15 [tm drug (Table 3-1) indicates that the surface has net positive charge when the membrane









is exposed to this drug concentration; yet the smaller ratio observed at 2.3 mM drug indicates

that additional drug adsorbed after exposure to this higher drug concentration.

The Hoechst 33342 was expected to adsorb to the nanopore wall of the Kapton stronger

than Hoechst 33258. This can be confirmed by the binding constant 2.27x105 obtained by fitting

the experimental data with equation 3-1 (Figure 3-2).

Langmuir Analysis of the Hoechst 33342 Adsorption Data

We can write the following general equation for Langmuir adsorption of a molecule to a

surface55

0 = KC/(1 + KC) (3-1)

where 0 is the fractional coverage of the molecule on the surface, K is the binding constant with

units of L mol-1 and C is the concentration of the drug in the contacting solution phase. 0 is also

given by

0 = moless, / moless,max (3-2)

where moless,i is the moles of molecule on the surface when the surface is exposed to some

concentration of drug i and moleSs,max is the maximum adsorption capacity of the surface

obtained at some very high concentration of the molecule.

We assume that moless,max occurs for a solution drug concentration, and we call the current

obtained Imin. If we call the current obtained in the absence of drug Io, then moless,max is

proportional to the difference Io Imin.

Likewise, if we call the current observed at some intermediate drug concentration, i, Ii then

moless,i is proportional to the difference Io Ii. This allows us to calculate 0 for any

concentration of drug, I, via

0 = (Io I)/ (Io Imin) (3-3)









Equating these 0 values to the corresponding concentration values (Equation 3-1) allows us to

plot out the Langmuir isotherm, and by fitting the experimental data to Equation 3-1, the value of

the binding constant K can be obtained. Figure 3-3 shows the experimental and calculated plots

and a value ofK = 2.27x105 L/Mol was obtained from the best fit. This K quantifies what the

experimental data already taught us Hoechst 33342 binds very strongly to the Kapton surface.

Effect of Amitriptyline and Bupivacaine on Rectification

Hydrophobicity of Amitriptyline and Bupivacine are much weaker compared to Hoechst

33342. The first and second key experimental observations for Hoechst 33342 and 33258 can be

reproduced with Amitriptyline and Bupivacine (Figures 3-4 and 3-6). As either Amitriptyline or

Bupivacine was added, rectification was decreased; the rectification scales inversely with the

concentration of Amitriptyline or Bupivacine. The rectification was not reversed and remain

above unity even when the concentration of Amitriptyline or Bupivacine was beyond 10 mM

(Table 3-2 and Table 3-3). This means that the surface charge of the Kapton membrane has not

been reversed even when the maximum coverage of the drug was reached.

Amitriptyline was much more hydrophobic than Bupivacaine even there is only a 3%

difference in the molecular weights of Amitriptyline and Bupivacaine. Bupivacaine presents two

additional opportunities for hydrogen bonding with water: the lone pairs on the carbonyl group

and the lone pair of the nonprotonated nitrogen. It was expected that Bupivacaine will be the

most poorly detected of the three drugs. The bind constant (6.3x102 L/Mol, Figure 3-7) for

Bupivacaine to the nanopore wall in the Kapton membrane is lower than that for Amitriptyline (

3.97x103 L/Mol, Figure 3-5) and that for Hoechst 33342 ( 2.27x105 L/Mol, Figure 3-3)

Summary and Future Work

The sensor we developed here has great selectivity toward hydrophobic cationic drugs.

More hydrophobic cationic drug can be easily discriminated from those less hydrophobic









cationic drugs. The highest binding constant of Hoechst 33342 toward the nanopore wall in the

Kapton membrane offers the lowest detection limit. In future work, we will focus on extending

the application of an ion-current rectification based Sensor, for example, immobilze a

negative(or positive) charged molecular recognition agent onto the pore wall of a conical

nanotube for sensing positive (or negative) analyte.

















Amitriptyline Hydrochloride




HCH2CH2CH2C


H3C-N N



CH H
N

Hoechst 33342

OCH2CH3


N c


-N HCI
H _/


Buplvacaine hydrochloride

Figure 3-1. Molecular structure of drug molecules.


@0 -5.

U -10


U
*


5

IIIm JU'r!Y tm m fl


Iransmembrane Potential (1)





I
1*10
I-


-15


-20-


-25-


Figure 3-2. I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21
itm) in the presence of the following concentrations of Hoechst 33342: 0 nM (black
square), 5.3 giM (red circle), 15 giM (green triangle), 2.3 mM (blue triangle).


---- ---


m _

















0.8-


2 0.6-

o
0 0.4-


S0.2-
CV)

0.0

0 50 100 150 200 250
Concentration('M)

Figure 3-3. Plot of surface coverage (theta) versus concentration of Hoechst 33342.


-2 -1
. -- a.


A -5

i/
-10


-15
/


-20-


transmembrane Potential (Vn





.Iz


o


Figure 3-4. I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21
[tm) in the presence of the following concentrations of Amitriptyline: 0 nM (black
square), 90 pM (red circle), 390 pM (green triangle), 11.2 mM (blue triangle).












1.0.

0.8.
0
e 0.6
0
w 0.4

= 0.2-

0.0.

0 2000 4000 6000 8000 1000012000
Concentration(pLM)
Figure 3-5. Plot of surface coverage (theta) versus concentration of Amitriptyline.





-2 -1

y Transmembrane Potential (V)

'vv -5.





S.
,N -10o I





S-20


-25.

Figure 3-6. I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21
[tm) in the presence of the following concentrations of Bupivacaine: 0 nM (black
square), 0.67 mM (red circle), 2 mM (green triangle), 11.6 mM (blue triangle).















0.8


^ 0.6
o
S0.2
o 0.4.


0.2.


0.0

0 2000 4000 6000 8000 10000 12000
Concentration (I4M)
Figure 3-7. Plot of surface coverage (theta) versus concentration of Bupivacaine.









Table 3-1. Rectification ratio in various concentration of Hoechst 33342 at transmembrane
potential difference of 2 V.
Concentration (pM) 0 5.3 15 2.3 mM

Rectification ratio 33.2 10.9 0.94 0.07









Table 3-2. Rectification ratio in various concentration of Amitriptyline at transmembrane
potential difference of 2 V.
Concentration (pM) 0 90 390 11.2 mM

Rectification ratio 33.4 22.03 15.7 1.03









Table 3-3. Rectification ratio in various concentration ofBupivacaine at transmembrane
potential difference of 2 V.
Concentration (mM) 0 0.67 2 11.6

Rectification ratio 34 26.4 17.8 6.3









CHAPTER 4
INVESTIGATION OF SELF-ASSEMBLED PROTEIN DIMERS THROUGH AN ARTIFICIAL
ION CHANNEL FOR DNA SENSING

Introduction

Resistive-pulse105 sensors, which when applied to molecular and macromolecular

analytes 14, 17, 19, 24, 27, 29, 79, 81, 82, 94, 105, 114, 121, 122, 142-145 are sometimes referred to as stochastic

sensors,105, 145 use a nanopore in a synthetic or biological membrane as the sensor element. In

resistive pulse sensing, the membrane containing the nanopore is mounted between two

electrolyte solutions, and analytes are driven through the nanopore by applying a transmembrane

potential difference across the pore. The resulting ionic current flowing through the nanopore is

measured and as the analytes translocate through the nanopore downward current pulses are

produced by the transient blocking of ion current. The frequency of such current pulses is

proportional to the concentration of the analyte, and the magnitude and duration of the current

pulse encodes the identity of the analyte.

The majority of ideal resistive pulse sensing work has utilized the biological protein

nanopore, a-hemolysin(a-HL), embedded in a supported lipid-bilayer membrane as the sensing

element. The a-HL nanopore can be made selective by biological or chemical engineering, and

has been used to detect numerous different analytes including metal ions,121 DNA,122'143

proteins,81 and small molecules.144 However, there is a key impediment to developing practical

sensors based on this biological technology. This problem concerns the fragility of the supported

lipid-bilayer membrane that houses the nanopore, which leads to extremely short lifetimes.145

In order to replace the biological nanopore, artificial nanopores embedded in a

mechanically and chemically robust synthetic membrane30' 89 have been prepared. One of the

techniques used to create these artificial nanopores is a microlithographic method, which uses a

focused ion14 or electron17 beam to bear the nanopore into a silicon or Si3N3 membrane. In order









to achieve specific counting and detection of analytes, such as DNA, DNA probe functionalized

single nanopores have been used.147 We and others have been exploring an alternative

technology, named the track-etching method,34' 37, 148, 149, 150 for preparing nanopores for resistive-

pulse sensors.130

In the current study, we describe selectively resistive-pulse sensing of short stranded DNA

(40 bases) through a conically-shaped nanopores embedded in track-etched PET membrane.

Numerous studies have been done before to understand the behavior of translocation of ssDNA

and double stranded DNA through a nanopores.14, 117-118 In order to improve the selective

translocation of DNA through a nanopore, functionalized solid-state nanopore147 has been used

to selectively detect DNA. However the lifetimes of these selective nanopores will decrease after

the conformation of immobilized probe DNA change due to translocation of the target DNA.

Another issue concerning the functionalized nanopores is that one pore can be justly used to

detect one certain target DNA. Here we explore another strategy of using a bare conically-shaped

nanopore embedded in a PET polymer. The tip diameter of the nanopore is 9 nm with a 520 nm

base diameter. The two Streptavidin conjugated DNA probes (20 base each) selectively

hybridize a distinct part of the target DNA. As the size of Streptavidin conjugated DNA probes

(4.5 nm x 4.5 nm)151 is much smaller than the tip diameter of the conical nanopore, so the

Streptavidin conjugated DNA probes can not be detected and be filtered on purpose. The size of

the finally self-assembled complex was double than that of each Streptavidin conjugated DNA

probe. Unspecific DNA will not induce the assembly of the two Streptavidin conjugated DNA

probes. So we can easily distinguish the target DNA from unspecific DNA, using the conical-

shaped nanopore in the polymer membrane.









The analyte was driven electrophoretically through the conical nanopore (from base to tip),

and these translocation events were observed as transient blocks in the ion current. Without the

interference of free Streptavidin conjugated DNA probes, the current-pulse signatures can be

associated with the final assembled complex induced by the target DNA. One of the advantages

of this technique is that it has provided a simple approach without further purification

processes161 and functionalization procedures.147

Experimental

Materials and Methods

12 [m thick poly(ethylene terephthalate) membranes (3 cm in diameter) irradiated with a

single swift heavy ion of 2.2 GeV kinetic energy to create a single damaged track through the

film were obtained from GSI Darmstadt, Germany. Biotin labelled Oligonucleotide probes,

specific and unspecific DNA were purchased from Alpha DNA, Inc. Streptavidin and bis-tris

propane was obtained from Sigma Aldrich. The oligonucleotide sequence for the Biotin labelled

oligonucleotide probe 1 is Biotin-ACACACACACTCATCTGTGA-3, and the oligonucleotide

sequence for probe 2 is 5-AGAGAACCTGGGATATATAT-Biotin. The sequence for target

DNA is 5-ATATATATCCCAGGTTCTCTTCACAGATGAGTGTGTGTGT-3. The sequence

for unspecific DNA is 5-ACACAAAACCTATGTACACATGACAGATGAGTGTGTGTGT-3.

Preparation of the Conical Nanopores

From Figure 4-1, it demonstrates a typical cell for fabricating the conical pore on the ion

tracked PET membrane. One piece of ion-tracked PET membrane was mounted between the

cells; the etching solution (9.0 M NaOH) was placed in one half of the cell and the stopping

solution (1.0 M formic acid plus 1.0 M KC1) in the other half of the cell. Two platinum wire

electrodes were immersed in two cells containing solution and a Keithley 6487 picometer

voltage source (Keithley Instruments, Cleveland, OH) was used to apply a transmembrane









potential difference of 1 V during etching, with polarity such that the anode was in the etch

solution. Etching was terminated after two hours by replacing the solution in the etch half-cell

with stop-etch solution. The membrane was then rinsed with purified water (Barnstead D4641,

E-pure filters). The tip diameter obtained after the first etch was normally in the range of 1 to 7

nm135 after 2 hours of the first step-etch, a second step-etch was applied to modulate the tip

diameter of the conical nanopore. The etching solution (1 M NaOH) was placed on both sides of

the conductivity cell. A platinum electrode was immersed into each half-cell solution, and the

Keithley 6487 picometer voltage source was used to apply a transmembrane potential difference

of 1 V and to measure the nanopore ion current. Etching was terminated at desired current values

by replacing the etching solution in both half cells with the stopping solution. The membrane

remained in the stop etch for at least 30 min and was then rinsed with purified water before

measuring the current-voltage curve.

Assembly of DNA-Protein Complex

100 tl of Streptavidin solution (33 pM in buffer 20 mM bis-tris propane, pH 9, 1 M KC1),

was mixed with 10.7 pl probe 1 (28 tM in buffer 20 mM bis-tris propane, pH 9, 1M KC1) and 25

pl probe 2 (12 tM in buffer 20 mM bis-tris propane, pH 9, 1 M KC1), this mixture was diluted

into 3 ml, and the final concentration for each molecule was 1.1 tM for Streptavidin, 100 nM for

Biotin labelled probe 1 and 100 nM for Biotin labelled probe 2. After 30 minutes reaction carried

out between probes and Streptavidin, the abundance of Streptavidin was monovalent when the

ratio exceeds up to 2.5. In previous paper,153 It was confirmed that if the ratio of Streptavidin to

Biotin-labelled DNA is above 2.5, the majority is monovalent conjugate. Here the ratio (5.5) we

used is far beyond the ratio they used in order to make sure that the main product is monovalent.

For the control experiment in the present study, the unspecific DNA was added into the

Streptavidin conjugated probes solution with a final concentration of 100 nM in 3 ml. For the









present study of target DNA sensing, the target DNA was added into the Streptavidin conjugated

probes solution with the final concentration 100 nM in 3 ml. after the assembly lasts for 5 hours.

The solution was added into the half cell facing the base opening. At pH 9, Streptavidin (pI

~7.0)154 and DNA were highly negatively charged, therefore when applying negative potential on

the electrode in the half cell facing base opening, the assembled complex would be driven from

base to tip.

Current-Pulse Measurements

To measure the currents-pulse, the single pore embedded membrane was mounted in the

cell. Both half cells were filled with -3 ml of 20 mM bis-tris propane buffer solution (pH =9)

that was also 1 M in KC1. An Ag/AgCl electrode ((BAS, West Lafayette, IN) was placed into

each half-cell solution and connected to an axopatch 200B (Molecular Devices Corporation,

Union City, CA) patch-clamp amplifier. The Axopatch was used to apply the desired

transmembrane potential and to measure the resulting ion current flow through the electrolyte-

filled nanotube. The current was recorded in the voltage-clamp mode with a low-pass Bessel

filter at 2 kHz bandwidth. The signal was digitized using a Digidata 1233A analog-to-digital

converter (Molecular Devices Corporation), at a sampling frequency of 10 kHz. Data were

recorded and analyzed using pClamp 9.0 software (Molecular Devices Corporation).

Results and Discussion

Calculation of the Tip Diameter of the Single Conical Nanopore

Three critical parameters including tip diameter and length and base diameter are used to

define the conical-shaped nanopore. The area close to the tip opening is the sensing zone where

the majority of nanopore resistance is located. Electrochemical technique is used to measure the

tip diameters.29 In a typical procedure, the membrane was mounted between two halves of a

conductivity cell, and the half cells were filled with phosphate-buffered saline (100 mM









NaH2PO4, 1M KC1). Keithley 6487 picometer voltage source and Ag/AgCl electrodes immersed

in each solution were utilized to obtain a current-voltage curve for the nanopore. The

experimental slope of this linear I-V curve between -0.2 V and 0.2 V is the ionic conductance, G,

(in siemens S) of the nanopore which is given by157

G = *7J) (4-1)
4L

where o-k is the experimentally measured conductivity of the KCl-based electrolyte (Scm-1), L

is the length of the nanopore (membrane thickness), db is the experimentally measured diameter

of the base opening, and d, is the diameter of the tip opening.

It is challenging to locate a single nanopore embedded in PET membrane using SEM.

Second, a repeatable and accurate data are required to identify accurately both tip and base pore

diameters. We have developed a series of techniques to control the etch rate and a model to

calculate accurately the pore size. From our previous work, the etching rate calculated from

multipore membranes was (2.170.19 nm/min)135 and it was used to obtain the diameter of the

base opening after the first step etching. The average base diameter is 520 45 nm after 2 hrs of

etching.135 The tip diameter obtained after the first etch was always in the range of 1 to 7 nm135

after 2 hours of the first etching. In the present study, we assume the increase of both base

diameter and tip diameter in second step-etch is equal. The final diameter of the base opening is

equal to the summary of the diameter of the tip opening and 520 45 nm. The base diameter for

this experiment is 530 nm. The conductivity of the buffer used for measurement is 117 (S.cm-1),

the ionic conductance of the nanopore, G, calculated from the slope of the linear I-V curves, is

3.59186E-9(S). The calculated tip diameter from equation 4-1 for membrane 1 was 9 nm (Figure

4-2).









Current-Pulses of the Self-Assembled Complex

With buffer solution (20 mM bis-tris propane, 1 M KC1 and 3 mM MgCl2) in both half

cells, a steady-state ion current of -3.7 nA (Figure 4-4A) was observed for the bare conically

shaped nanopore with tip diameter of 9 nm under transmembrane potential -1 V. The current was

slight decreased to -3.5 nA after adding solution which contains 1.1 [tM Streptavidin, 100 nM

probe 1, 100 nM probe 2, and 100 nM unspecific DNA into the half cell facing the base opening

of the nanopore. The current was decreased, which is possibly due to the unspecific absorption of

protein and DNA. No current-pulses were observed. Since the size of the single Streptavidin

conjugated probe (4.5 nm) is much smaller than the tip diameter (9 nm) of conical nanopore and

no link occurs between the two Streptavidin conjugated probes with the presence of unspecific

DNA, no current-pulse was observed in such a condition.

The current-pulse was observed after 100 nM target DNA has been added to the solution

that contained 1.1 pM Streptavidin, 100 nM probe 1 and 100 nM probe 2 in the half cell facing

the base opening of the nanopore. Figure 4-4c depicts a typical currents-pulse that was generated

from target DNA linked Streptavidin dimers. The continuous current-pulses indicate that the

translocation of the target DNA-linked protein dimer. The histogram of current-pulse amplitude

for solution that was 1.1 [tM Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target

DNA shows the average current amplitude (400 pA) (Figure 4-5).

The statistics of the current-pulse duration predicts the distribution of the sizes of the mass

transfer through the pore. A typical histogram currents-pulse duration of solution containing 1.1

tM Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA is depicted in Figure

4-6, where a broadly distributed current-pulse duration was observed. The majority of these

counts of the current-pulse durations are below 100 ms. It is concluded that the current-pulse









below 100 ms is generated from the dimer, and the current-pulse above 100 ms is generated from

multimer. These data are in accordance with previous data.153

The above phenomenon can be explained through the structure of Streptavidin. Streptavidin

has four binding sites available for binding Biotins through which four possible complexes can

be formed: mono-, di-, tri- and tetra- complex. By increasing the ratio of Streptavidin to Biotin-

labelled DNA up to 2.5, the majority of conjugates will be bi-valent complex with less tri-valent

complex. In this project, we use the ratio up to 5.5 to ensure that the majority of the conjugates

are dimers and to minimize trimers.

Scatter plots of current-pulse amplitude, Ai, vs. current-pulse duration, t, are often used to

summarize resistive-pulse data.14'27, 83, 130 The scatter plot for a solution that was 1.1 pM

Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA shows that the majority

of pulses was located below 100 ms and other current-pulses were broadly distributed (Figure 4-

7). These data also confirm the above conclusions that a current-pulse signature can be obtained

for the protein dimer induced by target DNA. In addition, no current pulses were observed for a

control solution containing unspecific DNA. These data proved that unspecific DNA does not

bind protein conjugated probes.

In order to reproduce the results, we etched another conical- shaped nanotube with a tip

diameter of 10 nm. From the scatter plot (Figure 4-8) of a solution that contained 1.1 pM

Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA, data showed the same

trend that we had concluded earlier. Under the transmembrane potential difference -1 V, very

long current pulses of duration lasting for more than 12 s exist. The very long current-pulse

duration event can be stopped by an increase of the voltage to -3 V. The protein mutimers (or

multimers) causing these long current-pulse durations was forced to translocate through the









sensing zone by increasing the trans-membrane potential difference. In order to get the current-

pulses continually without interruption, we increased the voltage to -2 V. The scatter plot (Figure

4-9) of a solution that was 1.1 tM Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM

target DNA reinforce our point that this current pulse was caused by protein dimer or multimer.

Conclusion

We have presented here a new approach to sensing DNA through a conical-shaped

nanopore embedded in PET polymer. The translocation of each protein conjugated probe is

undetectable due to the size much smaller than the tip opening of the bare conical nanopore. On

the contrary, the translocation of target DNA linked complex is detectable because the size of

target DNA linked two components is double the size of each component and also comparable to

the diameter of the tip opening of the nanopore. The sensing of target DNA can be accomplished

by analyzing current-pulses due to translocation of the complex linked by target DNA. The

concept of target analyte inducing self-assembling at the molecular level can be extended to

detect small molecules and proteins based on a nanopore technique.










Electrodes


SClamping
Hscrew

Solution 1.0 cm I
chamber 1 3.5cm





Ion track single pore mbrane
Aluminum frame Poly(chlortrifluorcethylene) cell


Figure 4-1. Scheme of the experimental setup with the conductivity cell. The left compartment
is filled with a stopping solution (1.0 M KC1 and 1.0 M Formic acid), and the right
compartment is filled with a etching solution (9.0 M NaOH).









Z 0.8


pn 1.


-0.1 *(
-0.24-
.,,*" -0.4-


0.1 0.2


Voltage(V)


Figure 4-2. The current-voltage curve of conical pore in 1M KC1 with applied -1.0 V voltage.
The tip opening of the nanopore is 9 nm and the base opening is 530 nm.





















12


Current *
0 .................................
0
+






+


Figure 4-3. Analytical sensor based on conical nanopore embedded in PET membrane. In the
absence of target DNA or in the existence of unspecific DNA, the translocation of
Streptavidin conjugated DNA probes was not detectable from base to tip. The size of
target DNA induced self-assembled DNA-protein complex is double that of
Streptavidin conjugated DNA probes; the translocation of the complex will cause
current-pulses.





A 1is
A
II Al- III


is
*JB



c 1s







Figure 4-4. Current-time transients for a bare conical nanotube sensor with tip diameter =9 nm.
(A) buffer only. (B) Buffer plus 100nM unspecific DNA, 1.1 kM Streptavidin and
100 nM probe 1 and 100 nM probe 2. (C) Buffer plus 100 nM target DNA, 1.1 kM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential for A, B and C was -1000 mV.







50-
45-
40-
35-
30-
25-
o
020-
15-
10-
5-
01M
0. .^


IT'M-M-I


Peak amplitude(pA)

Figure 4-5. Histograms of DNA-protein complex current-pulse-peak amplitude data for
nanotube with tip diameter =9 nm. Buffer plus 100nM target DNA, 1.1 PM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential was -1000 mV.


200-


180-


160.
8 8-
6-
4-
2-
0-


2000 4000 10000 12000


Duration(ms)

Figure 4-6. Histograms of DNA-protein complex current-pulse-duration data for nanotube with
tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 pM Streptavidin and 100
nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV.


f











640-

560-

< 480-
C.
0
a 400-


--
E 320-

| 240-

160-


0






o





0o
0


0
o cb


0 2000 4000 6000 8000 10000 12000


Duration (ms)

Figure 4-7. Scatter plot of current-pulse magnitude (Ai) vs. current-pulse duration (t) for DNA-
protein complex. Tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1
[MStreptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential was -1000 mV.


0 200 400 600 800
Duration(ms)


10oo00 12oo00 1400


Figure 4-8. Scatter plot of current-pulse magnitude (Ai) vs. current-pulse duration (t) for DNA-
protein complex. Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 tM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential was -1000 mV.


450-

400-

350-

S300-

. 250-

200-

0 150-

100-


3u .











1000-
o
800- 0
O0 0 0

600- 0

0 0 o
3 400- o
o





0-


0 2000 4000 6000 8000 10000 12000 14000

Duration(ms)

Figure 4-9. Scatter plot of current-pulse magnitude (Ai) vs. current-pulse duration(t) for DNA-
protein complex. Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 tM
Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane
potential was -2000 mV.









CHAPTER 5
FUNCTIONALIZATION AND DIAMETER CONTROL OF SINGLE CONICAL NANOPORE
IN ION-TRACK PET MEMBRANE VIA LAYER-BY-LAYER METHOD

Introduction

Resistive-pulse105 sensors, which when applied to molecular and macromolecular

analytes14, 17, 19, 24, 27, 29, 79, 81, 82, 94, 105, 114, 121, 122, 142-145 are sometimes referred to as stochastic

sensors,105, 145 use a nanopore in a synthetic or biological membrane as the sensor element. In

resistive pulse sensing, the membrane containing the nanopore is mounted between two

electrolyte solutions, and analytes are driven through the nanopore by applying a transmembrane

potential difference across the pore. The resulting ionic current flowing through the nanopore is

measured and as the analytes translocate the nanopore downward current pulses are produced by

the transient blocking of ion current. The frequency of such current pulses is proportional to the

concentration of the analyte, and the magnitude and duration of the current pulse encodes the

identity of the analyte.

The majority of resistive pulse sensing work has utilized the biological protein nanopore,

a-hemolysin(a-HL), embedded in a supporting lipid-bilayer membrane as the sensing element.

The a-HL nanopore can be made selective by biological or chemical engineering and has been

used to detect numerous different analytes including metal ion,121 DNA,122' 143 proteins,81 and

small molecules.144 However, there is a key impediment to developing practical sensors based on

this biological technology. This problem concerns the fragility of the supporting lipid bilayer

membrane that houses the nanopore, which leads to extremely short lifetimes.145

In order to replace the biological nanopore, artificial nanopores embedded in a

mechanically and chemically robust synthetic membrane30' 89 have been prepared. The common

technique used to create these artificial nanopores is a microlithographic method, using a focused

ion14 or electron17 beam to bear the nanopore into a silicon or Si3N3 membrane. In order to









achieve specific counting and detection of analytes, Nilsson and co-workers148 have locally

functionalized single nanopores by combining controlled silicon oxide growth at the nanopore

entrance with a silicon nitride layer and sliane chemistry. We and others have been exploring an

alternative technology, called the track-etching method,34' 37, 148-150 for preparing nanopores for

resistive-pulse sensors.19 24,27,29,30,89 Biomolecules such as small molecules,24 DNA,19'27

proteins29 and nanoparticles30 can be tested with this device. Furthermore,Virus sensors are

developed based on track-etched nanopores.89 Recent work from our lab has shown that highly

selective sensors can be prepared by biofunctionalization of the conical gold nanotube embedded

within a mechanically and chemically robust polymeric membrane.29

In the present study, the layer-by-layer film-forming method,155 based on the highly

specific binding constant (1015 M-) between Biotin and Streptavidin, was used to modulate the

tip diameter of the conical nanopore and to biofunctionalize the single conical nanopores. In our

lab, the layer-by-layer film-forming method,155 alternating a,co-diorganophosphonate/Zr

chemistry, has been utilized to prepare cylindrical nanotubes with accurately controlled inside

diameter.156, 157 The inner surface of these nanotubes can be further functionalized through the

attachment of DNA.148 Protein-functionalized nanotubes have also been prepared with the

similar alternating strategy 158: the alumina template membrane was alternately exposed to a

solution of desired protein and then to a solution of glutaraldehyde. With this method the inside

surface of the alumina membranes is functionalized with the desired protein. Unlike deposition

of proteins inside the whole cylindrical nanotubes in alumina nanopores,158 the deposition of

proteins onto the sensing zone area of conical-shaped nanopore is the critical part of this work.

Stability of the multilayers in the sensing zone is the prerequisite for further developing these

nanopores into practical sensors. Single conical nanopores are fabricated in ion-tracked PET









membrane by using a two-step etching procedure.135 Multi-Biotin labelled bovine serum

albumin, driven by applying a transmembrane potential difference from the large-diameter (base)

opening to the small-diameter (tip) pore opening, was non-specifically adsorbed onto the inner

surface of the nanopore as a first layer. Streptavidin specifically interacting with multi-Biotin

labelled protein is then deposited as a second layer. Multilayers can be deposited by repeating the

same procedure as that for depositing the second layer. In this way, the diameter of the tip

opening can be adjusted by controlling the number of protein layers; the final layer can be any

Biotin labelled biomolecule, for example, Biotin-labelled antibody, Biotin-labelled aptamer etc.

Experimental

Materials

Poly(ethylene terephthalate) membranes (3 cm in diameter, 12 [tm in thickness) irradiated

with a single swift heavy ion of 2.2 GeV kinetic energy to create a single damaged track through

the film were obtained from GSI Darmstadt, Germany. Multi-Biotin labelled bovine serum

albumin (BSA) and EZ-Link sulfo-NHS-LC-Biotin(sulfosuccinimidyl-6-

(Biotinamido)Hexanoate) were purchased from Pierce. Streptavidin, Biotin labelled IgA and

polylysine(MW70 kDa-150 kDa) were obtained from Sigma Aldrich.

Preparation of the Conical Nanopores

Figure 5-1 demonstrates a typical cell used for fabricating a conical pore on an ion-tracked

PET membrane. One piece of ion-tracked PET membrane was mounted between the cells; the

etching solution (9.0 M NaOH) was placed in one half cell and the stopping solution (1.0 M

formic acid plus 1.0 M KC1) in the other half cell. Two platinum wire electrodes were placed in

the two side solutions and a Keithley 6487 picometer voltage source (Keithley Instruments,

Cleveland, OH) was used to apply a transmembrane potential difference of IV during etching,

with polarity such that the anode was in the etch solution. Etching was terminated after two









hours by replacing the solution in the etch half-cell with stop-etch solution. The membrane was

then rinsed with purified water (Barnstead D4641, E-pure filters). The tip diameter measurement

obtained after the first etch was normally in the range of 1 to 7 nm135 after 2 hours of the first

step-etch, and the second step etch was applied to modulate the tip diameter of the conical

nanopore. Etching solution (1 M NaOH) was placed in both sides of the conductivity cell. A

platinum electrode was immersed into each half-cell solution, and the Keithley 6487 picometer

voltage source was used to apply a transmembrane potential difference of 1 V and measure the

nanopore ion current. Etching was terminated at desired current values by replacing the etching

solution in both half cells with the stopping solution. The membrane remained in the stop etch

for at least 30 min and was then rinsed with purified water before measuring the current-voltage

curve.

Determination of the Diameter of Nanopore

It has been challenging to locate a single nanopore embedded in a PET membrane using

SEM and we have developed a series techniques to control and determine the etch rate. From our

previous work, the etching rate calculated from multipore membranes was (2.170.19

nm/min)135 and was used to obtain the diameter of the base opening after the first step etching.

The average base diameter was 520 45 nm after 2 hrs etching.135 The tip diameter obtained

after the first etch has always been in the range of 1 to 7 nm135 after 2 hours of the first etching.

In the present study, the final diameter of the base opening was equal to the sum of the tip

diameter plus 520 45 nm.

Layer-by-Layer Protein Assembly

Proteins were dissolved in a phosphate buffer (50 mM, pH 7). The layer-by-layer

deposition is illustrated in Figure 5-2. Multi-Biotin labelled BSA (3 [M) was driven by applying

a transmembrane potential difference (1.0 V) from the large-diameter (base) opening to the









small-diameter (tip) pore opening for 1 hour, and the membrane was left in the same BSA

solution overnight. Multi-Biotin labelled BSA was non-specifically adsorbed on the surface of

the nanopore as the first layer. Streptavidin (0.5 [M) filled in both half-cells was driven into the

nanopore by alternately applying voltages of 200 mV and -200 mV for 2 hours. If more than

three layers were deposited, the experimental conditions were the same as those for the second

layer. In experiments where Biotin labelled IgA was used as a final layer, the concentration used

was 200 nM. The conductivity cells were rinsed 3 times with DI water between each step. When

Biotin labelled polylysine has been used for first layer, this step was slightly different. A

0.01(w/v)% polylysine solution filled in both half-cells was driven by applying a voltage (1 V)

from the base opening to tip opening for 1 hour and left in the same solution overnight. After the

conductivity cells were rinsed several times using DI water, NaHCO3 (pH 8.5, 50 mM) buffer

solution containing 50 mM Biotin linker was filled into cells and left to react for 1 hour. The

experimental conditions for additional layers were the same as those described above.

Results and Discussion

Calculation of the Tip Diameter of the Single Conical Nanopore

The tip diameter is measured electrochemically as previously reported. 29 Briefly, the

membrane was mounted between two halves of a conductivity cell, and the half cells were filled

with phosphate-buffered saline (100 mM NaH2PO4, 1 M KC1). Keithley 6487 picometer voltage

source and Ag/AgCl electrodes immersed in each solution were utilized to obtain a current-

voltage curve for the nanopore. The experimental slope of this linear I-V curve between -0.2 V

and 0.2 V is the ionic conductance, G, (in siemens S) of the nanopore which is established by 37


G = ( (5-1)
4L









where o-k is the experimentally measured conductivity of the KCl-based electrolyte (S.cm-1), L

is the length of the nanopore (membrane thickness), db is the experimentally measured diameter

of the base opening, and d, is the diameter of the tip opening.

Controlling Tip Diameter of Single Conical Nanopore

Our lab has developed two methods to control precisely the tip diameter of the conical

nanopore: one method135 is using the two-step etching to control the tip diameter; the second

method13 is using an electroless gold plating in the conical nanopore to adjust the tip diameter. In

the paper29 it has been demonstrated that agents used for the molecular recognition containing

gold concial nanotube can selectively detect proteins, Biotin labelled antibody was immobilized

on the gold nanotube through protein-multilayers construction.

Here we demonstrate that the tip diameter can be modulated by manipulating the layers of

proteins that are based on the strong interaction between Biotin and Streptavidin on the bare

conical nanopore embedded in PET. Mult-Biotin labelled BSA (3 [M) was driven through the

base opening by maintaining a transmembrane potential difference 1 V, It is easier to deposit the

BSA onto the inner wall of the nanopore when driven from the base opening rather than from the

tip opening due to the conical shape of the nanopore. After the membrane had been kept in

protein solution overnight, the I-V curves were measured. The slope of the I-V curves for

nanopore A (starting tip diameter of 33 nm) after non-specific deposition of muti-Biotin labelled

BSA as the first layer had a different slope from that for the bare nanopore (Figure 5-3). The

slope of the I-V curves is equivalent to the conductivity of the nanopore and will be used to

determine the tip diameter (Table 3-1). After first layer deposition, the tip diameter decreased by

7 nm. Comparing the dimensions of BSA159 with the decrease of tip diameter, it is found that the

that deposition of one layer of BSA proteins on the tip area contributes to the decrease of tip









opening. Therefore another different Streptavidin layer will be deposited on the first layer. Then

the tip diameter decreases (6nm) after deposition of Streptavidin (4.5 nm 4.5 nm)151 as the

second layer, which is suggested to be the cause of drop of tip diameter. By controlling the

number of layers of proteins, the tip diameter can be well adjusted to 9nm after deposition of 4

layers of proteins. If the final layer is Streptavidin, we can attach another Biotin-labelled

biochemical molecular-recognition agents and use this single pore for sensing the target analytes.

Multi-Biotin labelled polylysine (or other multi-Biotin labelled molecules) can also be

absorbed on the nanopore wall and employed as the first layer. This was demonstrated by using

bare PET nanopore B with a starting tip diameter of 71nm (Figure 5-4 and Table 5-2). From

Figure 5-4 and Table 5-2, the tip diameter decreased by 1 nm after polylysine, which is

consistent with the thickness between 0.7 nm and 1.3 nm of polylysine deposited on the glass

substrate.160-162 The diameter of the tip opening was successfully decreased to 45 nm after

deposition of 5 layers of protein on the nanopore wall by alternative deposition of multi-Biotin

labelled BSA and Streptavidin.

The deposition of the first layer is very critical. In order to successfully deposit multi-

Biotin labelled protein, a transmembrane voltage difference (1V) was applied to drive the protein

from base to tip in order to increase the physical interaction between multi-Biotin labelled

protein and the conical nanopore wall. The deposition of protein on the pore wall could be

monitored by the change of current. The strong binding affinity between Biotin and Streptavidin

(Kd = 10-15M)155 was used to deposit the next layers for which voltage (200mV) was used to

drive the protein into the tip area. In previous work, it was established that29 even without

applying voltage, Streptavidin could easily react with the Biotin attached on the nanopore wall.









The corresponding current drop through the nanopore could be observed after each layer has

been successfully deposited.

Shown in Figure 5-5 and Table 5-3, shows a final layer of Biotin labelled IgA which was

successfully attached to the second Streptavidin layer in nanopore C. The procedure for the

deposition of the first layer and the second layer remained the same as that used for the

deposition of protein in the nanopore A. From table 5-3, we can see the decrease of tip diameter

after attaching protein IgA up to 5 nm from Table 5-3. Any other Biotin labelled molecular

recognition agent may be attached to the protein nanopore in the same way.

Stability of Protein Nanopore

To investigate the stability of three types of membranes, The tests were conducted lasting

for over a week long. The stability of nanopore A and C was great as illustrated in Figure 5-6.

For nanopore C, the tip diameters in the first day and seventh day showed the same value 8.7 nm.

Nanopore B also has a high stability during the test days. In the paper 157 It has been shown the

multilayer proteins deposition in a cylindrical nanopore, crosslinker(glutaaldehyde) was

however, not necessary in the present situation and rather resulted in a slight decrease of tip

diameter after the application of crosslinker overnight for nanopore B. Nanopore B was

immersed into a glutaradehyde solution (1% in 50mM phosphate buffer, PH 7.4) before storage.

A 5nm decrease of the tip diameter was observed after cross linking. From Figure 5-6 it can be

seen that nanopore B was stable during the test days.

Conclusion

We have presented here a new approach to control the conical pore diameter by applying

layer-by-layer technique to fabricate multilayers of proteins within the conical pore inner

surface. Multilayer constructions were based on the strong interaction between Streptavidin and

Biotin-modified proteins. In addition, we can modify the nanopore with any biochemical









molecular-recognition agents labelled with Biotin. These controllable single nanopores enabled

us to investigate the sensing properties of species biomolecules, such as various sizes and

biofunctional proteins. We believe the stability of this protein nanopore offers great potential for

further practical applications as a biosensor.










Electrodes


SClamping
-H screw

Solution 1.0 cm I
chamber c3.5 cm





Ion track single pore mbrane
Aluminum frame Poly(chlortrifluorcethylene) cell
Figure 5-1. Scheme of the experimental setup with the conductivity cell. During etching the left
compartment is filled with stopping solution (1.0 M KC1 and 1.0 M formic acid), the
right compartment is filled with etching solution (9.0 M NaOH).


Deposit biotin-
labelled protein


Deposit
streptavidin


Deposit biotin-
labelled protein


Figure 5-2. Schematic diagram for Layer-by-layer assembly of proteins on single conical PET
membrane: (1) Bare single conical nanopore embedded in PET membrane, (2) non-
specific deposition of multi-Biotin labelled protein as the first layer, (3) specific
deposition of Streptavidin as the second layer, (4) specific deposition of multi-Biotin
labelled protein as the third layer.





















0.1 0.2
V


Figure 5-3. I-V curves after each assembly step with nanopore A: Black line(square) represents
data for nanopore after second step etch, red line (circle) for nanopore after multi-
Biotin labelled BSA nonspecific absorption, green line (triangle) for nanopore after
Streptavidin adsorption, blue line (triangle) for nanopore after Biotin BSA adsorption,
turquoise (square) for nanopore after Streptavidin adsorption.





























0 1 2 3


Number of protein layers

Figure 5-4. Diameter of tip opening as a function of the number of protein layers within
nanopore B. The first layer is multi-Biotin labelled polylysine, second layer is
Streptavidin, third layer is multi-Biotin labelled BSA, fourth layer is Streptavidin, and
fifth layer is multi-Biotin labelled BSA.


30-

- 28-
E
a 26-
0)
. 24-
C
a. 22-
o
.2 20-
4 1-
o 18-

a 16-
E
e 14-
0


Number of protein layers


Figure 5-5. Diameter of tip opening as a function of different protein layer within nanopore C.
The first layer is multi-Biotin labelled BSA, second layer is Streptavidin, and third
layer is Biotin labelled IgA.


S70-
E
C
S65-
C

0
o
Q.
- 55-
o
L_
S50.
E

o Ar.


4 5












35

30


E 25

a 20
o
o.
15
ca ---- .^ ----- *---
10-

1 2 3 4 5 6 7
Days

Figure 5-6. Diameters of tip opening versus 7 days for three single nanopores. Black circle
represents the tip diameter of nanopore A, green triangle represents that of nanopore
B, blue square represents that of nanopore C.









Table 5-1. Diameter of tip opening and base opening after each protein layer assembly within
nanopore A. DO represents initial pore size, D1,,D2, D3 and D4 represent the pore
size after deposition of Biotin labelled BSA, deposition of Streptavidin, deposition of
Biotin labelled BSA and deposition of Streptavidin respectively.
Diameter of tip opening (nm) Diameter of base opening (nm)
after each laver deposition after each layer deposition


553
546
540
535
529









Table 5-2. Diameter of tip opening and base opening after each protein layer assembly within
nanopore B. DO represents initial pore size, D1,,D2, D3, D4, D5 represent the pore
size after deposition of multi-Biotin labelled polylysine, deposition of Streptavidin,
deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of
mulit-Biotin labelled BSA respectively.
Diameter of tip opening (nm) Diameter of base opening (nm)
after each layer deposition after each layer deposition
DO 71 591
Dl 70 590
D2 61 581
D3 53 573
D4 49 569
D5 45 565









Table 5-3. Diameter of tip opening and base opening after each protein layer assembly within
nanopore C. DO represents initial pore size, D1, D2, D3 represent the pore size after
deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of
Biotin labelled IgA.
Diameter of tip opening (nm) Diameter of base opening (nm)
after each laver deposition after each layer deposition


549
540
538
533









CHAPTER 6
CONCLUSIONS

There is increasing interest in using nanopores in synthetic or biological membranes as

biosensors. In this dissertation, we have demonstrated that track-etched artificial conically

shaped nanopore can be functionalized and tuned by layer-by-layer method and can be used to

selectively sensing drug molecules based on ion-current rectification and DNA linked protein

dimer without probes interference

In chapter 2, a new paradigm making use of the well-known ion-current rectification

phenomenon displayed by conically shaped nanopores is demonstrated. The sensor element in

this case is a single conically shaped nanopore in a polyimide(Kapton) membrane. The sensing

paradigm entails placing electrolyte solutions on either side of the membrane and using

electrodes in each solution to scan the applied transmembrane potential and measure the

resulting ion current flowing through the nanopore. As has been discussed in detail by us and

others, conically shaped nanopores with excess surface charge on the pore walls, and sufficiently

small tip openings, show non-linear current voltage curves; i.e., such pores are ion-current

rectifiers. Because the polyimide nanopores used here have excess anionic surface charge,

rectification is observed at positive applied tranmembrane potential. We have found that when

the nanopore is exposed to a very hydrophobic yet cationic, drug molecule (Hoechst 33258),

adsorption of this molecule on the pore walls neutralizes the excess negative surface charge. As a

result the nanopore does not rectify as strongly, and the magnitude of the decrease in rectification

scales with the concentration of the drug molecule. Ultimately at high concentrations of the drug,

the sign of the excess surface charge switches from net negative to net positive, and the nanopore

rectified at negative applied transmembrane potential. We describe this new nanopore-based

sensing paradigm here.









In chapter 3, we demonstrate the ability of conical nanopore embedded in polymer

membrane to selectively sensing drug molecules based on ion current rectification phenomenon.

As has been pointed out in chapter 2, hydrophobicity is the dominant force which contributes the

absorption of positive drugs to the hydrophobic pore wall of Kapton membrane. This conclusion

paves the foundation for exploration of selectivity based on hydrophobicity. We choose three

positive drugs which have different hydrophobicity. In this chapter, we demonstrate the three

hydrophobic drugs can be be totally discriminated due to the different binding constant. We

believe this powerful sensing ability based ion current rectification can be extended to sense

other interesting biomolecules, for example, DNA and protein.

In chapter 4, we demonstrate promising tool for sensing DNA-linked protein dimmer

which is relevant to biological process, for example, gene expression, DNA degradation and

virus detection. The promising tool is a bare conically shaped nanopore embedded in track-

etched PET membrane. Biotin-labeled DNA probe react with excess Streptavidin to from

Streptavidin conjugated DNA probe. Two Streptavidin conjugated monovalent DNA probes can

bind two distinct segments of target DNA. The size of target DNA linked complex is double that

of each Streptavidin conjugated monovalent DNA probe. By precisely controlling the tip

diameter of conical nanopore embedded in PET polymer, the events due to translocation of the

streptravidin conjugated monovalent DNA probes through the nanopore can be filtered and

undetected on purpose; the current-pulses due to translocation of the target DNA linked complex

can be detected. In order to confirm that two Streptavidin conjuaged DNA probes are linked by

target DNA ,we test if two protein conjugated DNA probes can be linked by multi-mismatched

DNA. The multi-mismatched DNA will not induce the complex formation. The current-pulse

signatures for the self-assembled complex can be used to confirm the existence of target DNA









and DNA linked protein dimer. The concept of size dependent detection of self-assembled

complex on molecule level shows strong promise for detection of biomolecules without

interference of probes.

In chapter 5, we demonstrate a new way to tailor the single conical nanopores embedded in

PET (polyethylene terephthalate) membranes via a layer-by-layer assembly technique, which is

based on strong interaction between Biotin and Streptavidin. Single conical nanopores are

fabricated in ion-tracked PET membranes by using a two-step etch procedure. Multi-Biotin

labeled BSA (or multi-Biotin labeled polylysine) was driven into the tip of the single conical

nanopore from the base of the pore opening by applying a transmembrane potential difference

(1V), and nonspecifically adsorbed onto the inner wall of the nanopore as a first layer.

Streptavidin was then placed on both sides of the nanopore, and specifically interacted with the

multi-Biotin labeled protein and was thus deposited as a second layer by alternately applying a

transmembrane potential difference of 200mV and -200mV. Multilayers were formed by

repeating the same procedure as for depositing the second layer. Most importantly, the diameter

of tip opening can be adjusted by controlling the number of protein layers. The conical nanopore

can also be made selective with this method by depositing any Biotin labeled ligand on the final

layer, which can be used for specifically sensing target analytes. The layer-by-layer assembled

conical protein nanopores have shown great stability and may allow for fabricating practical

biosensors based on these conical nanopores.









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BIOGRAPHICAL SKETCH

JiaHai Wang was born in a beautiful place in China. He spent 4-year undergraduate study

in University of Hui Bei in Hui Bei province and obtained a B.S. in chemical engineering in June

2000. After that, he pursued master's degree in Dalian Institute of Chemical Physics, Chinese

Academy of Science under the guidance of Dr. GuoZhong He and Dr. KeLi Han. In August

2003, after he obtained M.S. in physical chemistry, JiaHai Wang joined Dr. Charles R. Martin's

group in the Department of Chemistry at the University of Florida and continue his Ph.D. study

in the fields ofbio-nano. He completed his research in March 2008, obtaining a Doctor of

Philosophy degree.





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FABRICATION OF ROBUST BIOMIMETIC NANOPORE FOR BIOMOLECULAR AND BIOMEDICAL ANALYSIS By JIAHAI WANG A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2008 1

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2008 JIAHAI WANG 2

PAGE 3

To my family 3

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ACKNOWLEDGMENTS I would like to thank Dr. Charles Martin and the entire Martin group for the opportunity to work with them over the course of my tenure. Dr. Martin was continuously supportive in guidance throughout my scientific development at the University of Florida. Also, I would like to thank Dr. Martin for educating me to become a professional scientist. The Martin group members have been very supportive and terrific examples of ingenuity and perseverance. Dr ShiFeng Hou, Lane Baker, Youngseon Choi, Punit Kohli, Q Trofim and Fatih Buyukserin showed great patience in offering many hours of guidance and helpful ideas. Mario Caicedo, Dooho Park, John Wharton, Fan Xu, Pu Jin, Lindsay Sexton, Lloyd Horne, Kann Kececi and Peng Guo have helped me by giving insightful advice on experiments. I would like to thank my family for their love and encouragement, which gave me great spiritual force. 4

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TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES ...........................................................................................................................7 LIST OF FIGURES .........................................................................................................................8 ABSTRACT ...................................................................................................................................11 CHAPTER 1 INTRODUCTION AND BACKGROUND...........................................................................13 Introduction.............................................................................................................................13 Ion Track-Etch........................................................................................................................15 Formation of Latent Ion Tracks.......................................................................................15 Preferentially Etching of Ion Tracks...............................................................................15 Template Synthesis.................................................................................................................17 Synthetic Strategies in Template Synthesis.....................................................................18 Electroless Deposition.....................................................................................................18 Biological Ion Channels.........................................................................................................20 Voltage-Gated Ion Channel....................................................................................................21 Resistive-Pulse Sensing..........................................................................................................22 Ion-Current Rectification........................................................................................................26 Dissertation Overview............................................................................................................29 2 A NEW DRUG-SENSING PARADIGM BASED ON ION-CURRENT RECTIFICATION IN A CONICALLY SHAPED NANOPORE..........................................38 Introduction.............................................................................................................................38 Experimental...........................................................................................................................39 Materials and Methods....................................................................................................39 Etching the Conical Nanopore in the Tracked Membrane..............................................39 Sensing the Analyte Molecules.......................................................................................41 Results and Discussion...........................................................................................................41 Ion-Current Rectification by the Conical Nanopore.......................................................41 Effect of Hoechst 33258 on Rectification.......................................................................42 Effect of Benzyl and Methyl on Rectification.................................................................43 Langmuir Analysis of the Hoechst 33258 Adsorption Data...........................................44 Conclusions.............................................................................................................................46 3 SELECTIVE DETECTION OF DRUGS BASED ON ION-CURRENT RECTIFICATION IN A CONICALLY-SHAPED NANOPORE.........................................51 Introduction.............................................................................................................................51 5

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Experimental...........................................................................................................................52 Materials and Methods....................................................................................................52 Etching the Conical Nanopore in the Tracked Membrane..............................................52 Sensing the Analyte Molecules.......................................................................................54 Results and Discussion...........................................................................................................55 Ion-Current Rectification by the Conical Nanopores......................................................55 Effect of Hoechst 33342 on Rectification.......................................................................55 Langmuir Analysis of the Hoechst 33342 Adsorption Data...........................................57 Effect of Amitriptyline and Bupivacaine on Rectification..............................................58 Summary and Future work.....................................................................................................58 4 INVESTIGATION OF SELF-ASSEMBLED PROTEIN DIMERS THROUGH AN ARTIFICAL ION CHANNEL FOR DNA SENSING...........................................................67 Introduction.............................................................................................................................67 Experimental...........................................................................................................................69 Materials and Methods....................................................................................................69 Preparation of the Conical Nanopores.............................................................................69 Assembly of DNA-Protein Complex...............................................................................70 Current-Pulse Measurements...........................................................................................71 Results and Discussion...........................................................................................................71 Calculation of the tip Diameter of the Single Conical Nanopore....................................71 Current-Pulses of the Self-Assembled Complex.............................................................73 Conclusion..............................................................................................................................75 5 FUNCTIONALIZATION AND DIAMETER CONTROL OF SINGLE CONICAL NANOPORE IN ION-TRACK PET MEMBRANE VIA LAYER-BY-LAYER METHOD...............................................................................................................................81 Introduction.............................................................................................................................81 Experimental...........................................................................................................................83 Materials..........................................................................................................................83 Preparation of the Conical Nanopores.............................................................................83 Determination of the Diameter of Nanopore...................................................................84 Layer-by-Layer Protein Assembly..................................................................................84 Results and Discussion...........................................................................................................85 Calculation of the Tip Diameter of the Single Conical Nanopore..................................85 Controlling tip Diameter of Single Conical Nanopore....................................................86 Stability of Protein Nanopore..........................................................................................88 Conclusion..............................................................................................................................88 6 CONCLUSIONS....................................................................................................................97 LIST OF REFERENCES.............................................................................................................100 BIOGRAPHICAL SKETCH.......................................................................................................108 6

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LIST OF TABLES Table page 2-1 Rectification ratio in various concentration of Hoechst 33258 at transmembrane potential difference of 6V..................................................................................................49 2-2 Current values in various concentration of Hoechst 33258 at transmembrane potential -6V......................................................................................................................50 3-1 Rectification ratio in various concentration of Hoechst 33342 at transmembrane potential difference of 2 V................................................................................................64 3-2 Rectification ratio in various concentration of Amitriptyline at transmembrane potential difference of 2 V................................................................................................65 3-3 Rectification ratio in various concentration of Bupivacaine at transmembrane potential difference of 2 V.................................................................................................66 5-1 Diameter of tip opening and base opening after each protein layer assembly within nanopore A. D0 represents initial pore size, D1, D2, D3 and D4 represent the pore size after deposition of Biotin labelled BSA, deposition of Streptavidin, deposition of Biotin labelled BSA and deposition of Streptavidin respectively.....................................94 5-2 Diameter of tip opening and base opening after each protein layer assembly within nanopore B. D0 represents initial pore size, D1,,D2, D3, D4, D5 represent the pore size after deposition of multi-Biotin labelled polylysine, deposition of Streptavidin, deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of mulit-Biotin labelled BSA respectively.............................................................................95 5-3 Diameter of tip opening and base opening after each protein layer assembly within nanopore C. D0 represents initial pore size, D1, D2, D3 represent the pore size after deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of Biotin labelled IgA.............................................................................................................96 7

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LIST OF FIGURES Figure page 1-1 (A) The heavy ion beam forms a latent ion track in the dielectic membrane. (B) Chemically etching will selectively remove the latent track and form a cylindrical shape..................................................................................................................................32 1-2 Definition of cone half-angle bulk etch rate V B and track etch-rate V T ........................32 1-3 Scanning electron microscopic images of different nanoporous materials developed by ion-track-etching process..............................................................................................33 1-4 Scanning electron microscopic images of different template............................................33 1-5 Schematic diagram of Au electroless plating procedure....................................................34 1-6 Schematic illustration of Au nanotubes obtained from electroless gold deposition..........34 1-7 Schematic illustration of open and close state of K + channel............................................35 1-8 Schematic illustration of resistive-pulse sensing...............................................................35 1-9 Protein channel embedded in lipid bilayer.........................................................................36 1-10 (A) I-V curve and current rectification for nanopore without charge. (B) I-V curve and current rectification for nanopore with negative charge. (C) I-V curve and current rectification for nanopore with positive charge.....................................................36 1-11 (A) Scheme of an axial cut of a conical pore; (B) profile of electrical potential,V(z), inside a tapered-cone pore, calculated from Eq. 1.............................................................37 1-12 Ratchet model for ion current recification in a conical nanopore with excess negative surface charge on pore wall...............................................................................................37 2-1 Molecular structure of different drug molecules and polymer..........................................47 2-2 I-V curves for a conical nanopore sensor (tip diameter =67 nm, base diameter 1.43 m) in the presense of the following concentrations of Hoechst 33258: 0 nM (black square), 1.25 M (red circle), 2.5 M (green triangle), 5 M (blue triangle), 10 M (cyan square), 15 M (magenta), 25 M (yellow)............................................................47 2-3 I-V curve for conical nanopore in Kapton membrane (tip diameter 48 nm, base diameter 2.0 m) with different molecules: 2.3 mM benzyl viologen (cyan square), 1mM benzyl viologen (blue triangle), control buffer (black square), 1 mM methyl viologen (red circle), 2.3 mM methyl viologen (green triangle).......................................48 2-4 Plot of surface coverage (theta ) versus concentration of Hoechst 33258.........................48 8

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3-1 Molecular structure of different drug molecules...............................................................60 3-2 I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21 m) in the presense of the following concentrations of Hoechst 33342: 0 nM (black square), 5.3 M (red circle), 15 M (green triangle), 2.3 mM (blue triangle)..................60 3-3 Plot of surface coverage (theta) versus concentration of Hoechst 33342.........................61 3-4 I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21 m) in the presense of the following concentrations of Amitriptyline: 0 nM (black square), 90 M (red circle), 390 M (green triangle), 11.2 mM (blue triangle)...............61 3-5 Plot of surface coverage (theta) versus concentration of Amitriptyline............................62 3-6 I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21 m) in the presense of the following concentrations of Bupivacaine: 0 nM (black square), 0.67 mM (red circle), 2 mM(green triangle), 11.6 mM (blue triangle)................62 3-7 Plot of surface coverage (theta) versus concentration of Bupivacaine..............................63 4-1 Scheme of the experimental setup with the conductivity cell. The left compartment is filled with a stopping solution (1.0 M KCl and 1.0 M Formic acid), and the right compartment is filled with a etching solution (9.0 M NaOH)...........................................76 4-2 The current-voltage curve of conical pore in 1 M KCl with applied -1.0 V voltage. The tip opening of the nanopore is 9nm and the base opening is 530 nm.........................76 4-3 Analytical sensor based on conical nanopore embedded in PET membrane. In the absence of target DNA or in the existence of unspecific DNA, the translocation of Streptavidin conjugated DNA probes was not detectable from base to tip. The size of target DNA induced self-assembled DNA-protein complex is double that of Streptavidin conjugated DNA probes; the translocation of the complex will cause current-pulses.....................................................................................................................77 4-4 Current-time transients for a bare conical nanotube sensor with tip diameter =9 nm.......77 4-5 Histograms of DNA-protein complex current-pulse-peak amplitude data for nanotube with tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV.....................................................................................................78 4-6 Histograms of DNA-protein complex current-pulse-duration data for nanotube with tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV.......78 4-7 Scatter plot of current-pulse magnitude (i) vs. current-pulse duration(t) for DNA-protein complex Tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 M 9

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Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV.....................................................................................................79 4-8 Scatter plot of current-pulse magnitude (i) vs. current-pulse duration(t) for DNA-protein complex Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV.....................................................................................................79 4-9 Scatter plot of current-pulse magnitude (i) vs. current-pulse duration(t) for DNA-protein complex Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -2000 mV.....................................................................................................80 5-1 Scheme of the experimental setup with the conductivity cell. During etching the left compartment is filled with stopping solution ( 1.0 M KCl and 1.0 M formic acid), the right compartment is filled with etching solution ( 9.0 M NaOH)....................................90 5-2 Schematic diagram for Layer-by-layer assembly of proteins on single conical PET membrane...........................................................................................................................90 5-3 I-V curves after each assembly step with nanopore A: Black line (square) represents data for nanopore after second step etch, red line (circle) for nanopore after multi-Biotin labelled BSA nonspecific adsorption, green line (triangle) for nanopore after Streptavidin adsorption, blue line (triangle) for nanopore after Biotin BSA adsorption, turquoise (square) for nanopore after Streptavidin adsorption.......................91 5-4 Diameter of tip opening as a function of the number of protein layers within nanopore B. The first layer is multi-Biotin labelled polylysine, second layer is Streptavidin, third layer is multi-Biotin labelled BSA, fourth layer is Streptavidin, and fifth layer is multi-Biotin labelled BSA......................................................................92 5-5 Diameter of tip opening as a function of different protein layer within nanopore C. The first layer is multi-Biotin labelled BSA, second layer is Streptavidin, and third layer is Biotin labelled IgA................................................................................................92 5-6 Diameters of tip opening versus 7 days for three single nanopores. Black circle represents the tip diameter of nanopore A, green triangle represents that of nanopore B, blue square represents that of nanopore C....................................................................93 10

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Abstract of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy FABRICATION OF ROBUST BIOMIMETIC NANOPORE FOR BIOMOLECULAR AND BIOMEDICAL ANALYSIS By JiaHai Wang May 2008 Chair: Charles R. Martin Major: Chemistry The goal of this research is to develop new methods based on robust nanopores for sensing biomolecules and drug molecules. The first part of this work is to sense a cationic hydrophobic drug based on ion-current rectification phenomenon observed for conically-shaped nanopores. The nanopore walls in the Kapton membrane are hydrophobic and have fixed carboxylate groups that give the walls a net negative charge. The analyte drug molecule, Hoechst 33258, is cationic yet also hydrophobic. When the membrane is exposed to this molecule, the molecule adsorbs to the pore walls and neutralizes the anionic surface charge, thus lowering the extent of ion-current rectification. The change in rectification is proportional to the concentration of the drug. This nanopore sensor is selective for hydrophobic cations relative to anions, neutral molecules, and less hydrophobic cations. The second part focuses on improving the selectivity and sensitivity of the above-mentioned sensor described in the first part. We have selected three positive drugs with different hydrophobicity. We can successfully discriminate these drugs. The highest binding constant was obtained for the drug with highest hydrophobicity. Another interesting result is that the detection limit for the drug with the highest binding constant shifts to submicromole. 11

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The third part of this dissertation presents a new approach to sensing DNA through a conically-shaped nanopore embedded in PET polymer. The translocation of each protein conjugated probe is undetectable because the size is much smaller than the tip opening of a bare conical nanopore. The translocation of the protein dimer linked by target DNA is detectable because the size of the target DNA linked protein dimer is double the size of each component and also comparable to the diameter of the tip opening of the nanopore. The control DNA will not induce the assembly of two protein conjugated probes; no events will be observed. By this way, we can detect the target analyte without interference of probes. The fourth part of this work presents a new approach to control the conical pore diameter by applying a layer-by-layer technique to fabricate multilayers of proteins within the inner surface of the conical nanopore. Multilayer constructions were based on the strong interaction between Streptavidin and Biotin modified protein. In addition, we can modify the nanopore with any biomolecular-recognition agents labelled with Biotin. These controllable single nanopores enable us to investigate the sensing properties of biomolecules, such as various sizes and biofunctional proteins. 12

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CHAPTER 1 INTRODUCTION AND BACKGROUND Introduction In the past decades, nanomaterials have been the subject of tremendous interest. These materials which have specific feature size have great potential for application in biomedicine, chemistry, and electronics. 1-10 Nanomaterials can be ceramics, metal, polymeric materials, or composite materials. The defining feature for these materials is the size in the range of 1-100 nanometers (nm). Nanomaterials are not simply another step in miniaturization, but a totally different field. At the nanomaterial level, some material properties behave by the laws of atomic physics, rather than behave as traditional bulk. Although nanomaterials were of widespread interest, the concept was raised over 40 years ago by physicist Richard Feynman who delivered a talk in 1959 entitled Theres plenty of Room at the Bottom. 11 Among the nanomaterials, nanopores play a very important role. Molecular transporting through nanopores has attracted a very large scientific interest because of its relevance to those issues in biology and biotechnology. Biological nanopores such as channels and pores in biomembranes of cells are involved in almost all physiological processes of a living organism. These channels and pores are the principal nanodevices mediating the communication of a cell with other cells via exchange of ions and neutral molecules. Biological channels perform various physiological functions. Inspired by the studies of biological nanopores, there has been intense interest in artificial nanopores. Given the fact that solid-state nanopores are highly stable over a wide range of pH values, salt conditions, temperature, and bias voltages, and are highly portable, it will be promising to continue to explore potential applications of nanopores. On the other hand, we can 13

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do something beyond the biological nanopore: change the size of nanopores by well controlling the experimental conditions; Sense different analytes unreachable by biological ion channel. Nanoporous materials can be synthesized by using many different techniques using different materials. The template-based synthesis pioneered by the Martin research group and others is a general method for preparing nanomaterials. 12, 13 This method entails the synthesis or deposition of a desired material within the pores of a nanopore membrane that serves as a template. These template membranes contain uniform pores that are typically cylindrical in geometry, and the pore diameter can be varied at will from tens of nanometers to tens of microns. Since typical pore geometries are cylindrical, correspondingly cylindrical nanostructures are usually synthesized via the template method; these nanotube membranes have been widely used for biomolecular analysis and batteries. Recently, our research team and others have become interested in conically-shaped nanopores. 14-23 A number of applications can potentially benefit from conical pore geometry. For instance, it has been shown that such conically-shaped nanopores can be used as the sensing element for new types of small molecule, 24 DNA, 25, 26, 27, 28 protein, 29 and particle 30 sensors. Conically-shaped gold nanotubes deposited within such pores can also act as mimics of voltage gated ion channels. 31 Membranes used for separations might also benefit from a highly asymmetric pore structure. Finally, in addition to sensing and separations platforms, conical nanostructures prepared by more conventional methods have been proposed for use as cathodes in field-emission displays. 32 In this dissertation, several techniques and knowledge have been used: Ion track-etch process, template synthesis, biological ion channel, resistive-pulse sensing, and ion rectification. 14

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Ion Track-Etch The ion track etch process 33-34 based on the availability of accelerated heavy ions enables one to prepare nanoand micro-pores with a high aspect ratio and various shapes in many dielectric solids. Polymers and mica due to their mechanical and chemical strength, and their high susceptibility for selective ion track etching are suitable for practical application. Formation of Latent Ion Tracks Heavy ion accelerators create ion beams of defined isotopic mass and energy suited for a well-defined generation of ion tracks. Every ion hitting and potentially penetrating the polymer leads to a permanent modification of its chemical and physical properties along its path. The result of this modification is latent ion track. The strength of the modification depends on the radiation sensitivity of the material, on the deposited energy density, and on the storage conditions of the polymer after the ion irradiation, such as temperature, environmental gases, and illumination conditions. Preferentially Etching of Ion Tracks Chemical etching can preferentially remove latent ion tracks (Figure. 1-1). The resulting shape of the etched track depends on the type of material, the concentration of the etchant, and the temperature of the etch bath. As the density of the material in the track core is lower than the density of pristine polymer, 35 the selective etching of the track core can be attributed to its increased free volume 36 corresponding to nanovoids with increased freedom for rearrangements of the chain segments. The increased free volume facilitates chain rupture under chemical attack. Preferential etching can be impeded by a cross-linked zone around the track core. After removal of the cross-linked zone, the track radius grows linear in time. The result is an etch trough, pore, or channel that can be used as a selective gate for ions or fluid-suspended particles or may be used as a template for deposition of other materials. 15

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For large track etch velocities, the etch cone transforms into a cylinder. In general, heavier ions induce a stronger modification, improving the local definition of the modified zone and the selectivity of the etch process. After selective removal of the strongly modified ion track core, etching can be retarded by a polymerized zone. Further etching proceeds at bulk etch velocity, i.e., the track radius increases linear in time at the same rate as the polymer surfaces recede. The etch process is finally interrupted by replacing the etchant with water or with a dilute acid. The interruption can be induced at a chosen time or at a chosen electrolytical conductivity across the membrane. 37 The cone half-angle is defined by the relation sin =V B /V T (Figure 1-2). For the high track etch ratio, sin can be replaced by The track-etch-ratio is usually treated as constant as long as the ion range exceeds the thickness of the material. It depends on the energy density along the ion path, the radiation sensitivity, and the selectivity of the etch process, i.e., its ability to differentiate between irradiated and pristine material. The central figure of merit for ion track etching is the selectivity of the track-etch process. It is given by the ratio of the etch velocity along the ion track,V T and the etch velocity of the removing the bulk material,V B the so-called track etch ratio,V T /V B The track etch ratio is also responsible for the shape of the porous structure. The shape is defined as a self-organized process given by the energy deposition density, the direction of etch attach, the material used, the etch medium, the etch time, and the etch temperature. The rate of etching can be increased by raising the temperature, for example, in high throughput development which is used in industrial applications. Also, the concentration of the etchant influences its bulk etch rate V B, and its track-etch rate, and the selectivity s=V T /V B There are many different materials which are ideal candidates for preparing high aspect ratio ion track-etch pores in a free standing membrane. 16

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These materials include PC (polycarbonate), PET ( polyethylene terephthalate), PP (polypropylene), PVDF (polyvinylidenefluoride), PI (polyimide), and CR 39 (polydiethyleneglycolbisallylcarbonate). The use of ion track-etching technology allows the opportunity for the production of many different type of nanoporous material which is illustrated in Figure 1-3. 33, 34 These different materials can then be used as templates for the development of a variety of other nanostructured materials. One technique which entails the use of a template to produce the production of nanostructure materials is a process called template synthesis. Template Synthesis In recent years, the Martin group has pioneered a general method for the preparation of nanostructured materials called template synthesis. 1, 3, 38 In the template synthesis method, the material of interest is deposited within the nanoporous material of a host solid. The size and shape of the nanomaterial depend on the dimensions of the nanocavities within the host template. Membrane-based template synthesis entails deposition of desired materials within the pores of a host solid. Depending on the membrane and synthetic method used, the obtained nanostructured material can be solid nanofibers or hollow nanotubes. There are a variety of interesting and useful characteristics associated with template synthesis. One of the most useful features of the method is that it is very general with regards to the type of materials that can be prepared. This method has been used to prepare nanofibers and nanotubes composed of metals, 39, 40-46 polymer, 47-50 carbon, 51-53 and semiconductors. 54, 55 Also, it is possible to prepare composite nanostructured materials both concentric tubular composites 56, 57 and segmental composite nanowires. 58 This method has also been used to prepare materials with a very small diameter, such as, conductive polymer nanofibers with diameters of 3nm have been prepared. 59 17

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Finally, template synthesized nanostructured materials can be assembled into a variety of different architectures. For example, the nanostructured material can remain inside the pores of the template membrane; or they can be freed from the template membrane and collected by filtration. Alternatively, if the nanostructure-containing membrane is attached to a surface and the membrane is removed, an ensemble of nanostructures can protrude from the surface like the bristle of a brush. Synthetic Strategies in Template Synthesis There are two commonly used templates; organic ion track-etched polycarbonate membranes and inorganic Al 2 O 3 membranes (Figure 1-4). There are a variety of different synthetic strategies adapted from the preparation of bulk materials including chemical and electrochemical polymerization, and sol-gel chemistry. Electroless Deposition The electroless deposition method involves the use of a chemical reducing agent to plate a metal from a solution onto a surface. Unlike electrochemical deposition, a conductive surface is not necessary. The key requirement of electroless deposition is arrangement of the chemistry such that the kinetics of homogeneous electron transfer from the reducing agent to metal ions is slow. This is extremely important because otherwise the metal ions would simply be reduced in the bulk solution. One caveat of electroless deposition is that a catalyst is needed on the pore walls so that the reduction of the metal ion will only occur at the pore surface. Figure 1-5 shows the schematic representation of the electroless deposition chemisty that was used to prepare gold nanowires and nanotubes within polycarbonate track-etched membranes. The polycarbonate membrane is first exposed to a sensitizer (Sn 2+ ). This is accomplished by simply immersing the membrane for 45 minutes in a solution that is 0.026 M in SnCl 2 and 0.07 M in trifluoroacetic acid in 50/50 methanol/water. The sensitizer binds to the pore walls and the membrane surfaces 18

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via complexation with amine, carboxyl and hydroxyl groups. 60 After sensitization of ammoniac silver nitrate (0.029 M Ag(NH 3 ) 2 + ) for 5 minutes, a redox reaction occurs in which the surface bound tin(II) is oxidized to tin(IV) and the Ag + is reduced to elemental Ag. As a result, the pore walls and the membrane surface becomes coated with nanoscopic Ag particles. The membrane is again thoroughly rinsed with methanol. The silver coated membrane is then immersed into a gold plating bath that is 7.9x 10 -3 M in Na 3 Au(SO 3 ) 2 0.127 M Na 2 SO 3 and 0.625 M in formaldehyde at 4 0 C. The Au galvanically displaces the Ag particles because the reduction potential Au is more positive than that of Ag. As a result, the pore walls and surface become coated with Au particle. These particles are excellent catalytic sites for the oxidation of formaldehyde and the concurrent reduction of Au(I) to Au(0). 60 Without a catalyst, the kinetics of the electron transfer from the reducing agent(formaldehyde) to Au(I) is slow; therefore, the gold plating continues on the gold particle instead of in bulk solution. The reaction can be represented as follows: 2Au(I) + HCHO + 3OH =HCOO +2H 2 O +2Au(0) (1-1) This method yields Au nanowires or nanotubes within pores plus a Au surface layer on both faces of the membrane. These structures run through the entire thickness of the template membrane (Figure 1-6). By controlling the plating time, the inside diameter of the nanotubes can be varied because the thickness of both the Au surface films and the nanotube walls increase with plating time. By controlling the plating time, the inside diameter (ID) of the nanotubes can be varied, even as low as 1 nm in diameter. 48 As a result, these membranes can be used in a simple membrane permeation experiment to cleanly separate thiols to an Au nanotube walls based on the well known gold thiol chemistry, the Au nanotube membrane can be made to preferentially transport cation vs. anions and hydrophobic vs. hydropholic molecules. 40, 44, 45, 61 In addition, the 19

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Au nanotube membrane is electronically conductive and can be charged electrostatically in an electrolyte solution. 40 This introduced ion-transport selectivity, allows the Au nanotube membranes to be electromodulated between ideal-cation and ideal-anion transport states. 40 Thus these Au nanotube membranes are ideal model systems for studying how pore size, chemistry, and charge affect the transport selectivity at the nanometer scale. The electroless gold deposition method has also been used in the study of ion current rectification within single nanopore track-etched membranes. 62 These systems can be used as robust synthetic systems for the study of voltage-gating and ion current rectification which is present in the biological voltage-gated ion channel. 20-23 These systems have the potential of offering a greater understanding of the different functional mechanisms which are present within biological ion channels. Biological Ion Channels Biological ion channels enable the functioning of a living organism and mediate the communication of a cell with other cells via ion transport, 63 Three types of ion channels were studied before: The ligand gated channel, the mechanically gated channel, and the voltage-gated channel. 63 The ligand gated channel is unique in that it will open and close in response to the binding or unbinding of a particular ligand or molecule. The mechanical gated ion channel open and closes by the mechanical deformation of the cells of stretch receptors. The voltage-gated channel is very unique in that it will open and close in response to the change in the transmembrane potential. The voltage-gated ion channels also control the excitability of nerve, muscle, and endocrine and other cell types, thereby regulating a broad spectrum of cellular processes. 20

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Voltage-Gated Ion Channel The ion channel conducting potassium across the cell membrane down the electrochemical gradient for K + underlies many different cellular processes including cell volume regulation, hormone secretion, and electrical impulse formation in electrically excitable cells. 63 All known K + channels are related members of a single protein family. They are found in bacterial, archeal, and eukaryotic cells both plant and animal and their amino acid sequences are very easy to recognize because the potassium channels contain a highly conserved segment called the K + channel signature sequence. 64 The sequence forms a structural element 65, 66 known as the selectivity filter (Figure 1-7), which prevents the passage of Na + ions but allows K + ions to conduct across the membrane at rates approaching the diffusion limit. This is the hallmalk of K + channels: nearly perfect selectivity for K + ions over Na + ions in the setting of very high K + conduction rates. Determination of the molecular sequence and primary structure of many of their protein components has put new insights into the physiological functions and biophysical properties of these channels. Yet the mechanism by which these proteins sense changes in membrane potential has remained elusive. Now, YouXing Jiang and Roderick MacKinnon and colleages have published the crystal structure of a full-length voltage dependent K + channel. 67 Their findings reveal an unexpected and surprisingly simple design in the voltage sensor. The functional unit of a voltage-gated ion channel is tetramer. Each of the four subunits of the tetramer is a protein with six transmembrane domains. Reasoning dictates that the voltage sensor would be a charged sequence located within the cell membrane that would move from one side to the other in response to changes in potential across the membrane. The fourth transmembrane domain, known as S4, is a likely candidate for the voltage sensor because of two properties. First, it is hydrophobic, which indicates that it should be located within the lipid layer of the membrane or 21

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embedded within the interior of a protein. Second, S4 contains four to seven positive charges, depending on the channel type, which would confer voltage sensitivity to this segment of the protein. For these seasons S4 has been the focus of numerous studies on voltage sensing in ion channels. 68 One of the main characteristics of the potassium voltage-gated ion channel is that it is an ion current rectifier. Rectifier is a term that comes from electronics, referring to devices that conduct electrons only in one direction. These potassium voltage-gated ion channels show a nonlinear current-voltage characteristic which says that they are ion current rectifiers. Ion current rectification suggests that there is a preferential flow of ions through these ion channels. Although the structure of these channels are known, 68-71 there are still many aspects of ion transport that are not yet well understood. The phenomenon of ion current fluctuations is one of the unsolved puzzles. 72 Also, there are open questions regarding ion current rectification and pumping within these channels. These questions have motivated researchers to design biosensors and learn more about ion transport with nanochannels. To design biosensors and learn about ion transport in nanochannels, it would be very helpful to have a synthetic, robust system that is much easier to understand and describe. This would also allow researchers to perform experimental studies not applicable to biological channels due to their fragile nature. First however, we have to determine whether it would be possible with synthetic pores in a synthetic film of dimensions similar to those biological channels, to observe similar transport properties, such as, ion current fluctuations, rectification, and pumping. Resistive-Pulse Sensing It has been shown that a protein nanopore (for example, the -hemolysin channel) can function as a biosensor for the detection of biomolecules, for example, DNA. 73 The sensing procedure used is based on a technique called resistive-pulse sensing. In the simplest terms, this 22

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method is based on an electrochemical cell in which a small aperture separates two ionically-conductive salt solutions. Within each side of the cell an electrode is placed and an ionic current is passed through the aperture. A charged analyte species with a diameter that is comparable to that of the inside diameter of the single aperture is electrophoretically driven through the aperture. When the analyte species enter the aperture the channel pathway is partially obstructed. This change in ionic current can be used to determine the size, identity, surface charge and even the concentration of the analyte species present within the system. Figure 1-8 shows a schematic representation of how this process works. Because many biomolecules are charged, this detection method can potentially be very widely applied and does not require any chemical pretreatment of the molecules, which is a big advantage over other detection techniques. The classic example of a resistive-pulse sensor is the coulter counter (Beckman Coulter, Fullerton, CA), a commercially available device used to count and size biological cells and colloidal particles. 74-76 The Coulter counter uses a small diameter aperture (from 20m to as large as 2mm) separated by two electrolyte solutions and a constant ionic current is passed through this aperture. The aperture is typically fabricated through a man-made sapphire, the thickness of which is comparable to the diameter of the aperture. An electrolyte solution is placed on each side of the aperture. The suspended biological cells (or other particles) to be counted are introduced on one side of the aperture. This solution is then forced to flow through the aperture. Flow of the solution is driven by a pressure gradient across the aperture, and with modern instruments, the volume of liquid sampled can be precisely controlled. 76 When a particle enters the aperture it effectively displaces a volume element of electrolyte solution equivalent to the particle volume. As a result, the resistance through the aperture increases during the obstructed time of the particle within the aperture. This transient increase in 23

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the aperture resistance is monitored via the corresponding increase in voltage drop across the aperture. The number of such voltage pulses provides a count of the particles suspended in the electrolyte. The height of the pulse is proportional to the volume of the particle within the aperture. Therefore, from this information, particle size information can be obtained. Also, the distribution of pulse amplitudes reflects the relative distribution of the volumes of the particles counted. 75 This process can be used to size several thousand particles per second. Commercially available instruments can measure particles with diameters ranging from as small as 400nm to as large as 1mM. 74-76 The diameter of the particle to be counted determines the diameter of the aperture used in the instrument. As would be expected, the smaller the particles to be counted, the smaller the aperture used. Therefore, to detect smaller analyte species smaller aperture systems are needed. The model system to date which is used in the stochastic sensing of individual analytes is the use of a bioengineered -hemolysin protein channel (Figure 1-9). 77, 78, 79 These channels have been used in the detection of divalent metal ions, 80, 81 organic analytes, 82 proteins, 83, 84 polymers, 85 DNA, 86-90 and peptides. 91 Even though these channel proteins have proven to be an instrumental tool in the development of a molecular stochastic sensor they still possess limitations which need to be overcome for future applications. The biggest limitation of this protein channel system is the stability of the biological support system (lipid bilayer membrane). This limitation has sparked an increased interest for researchers to develop a synthetic nanopore system which has similar sensing capabilities but overcomes the stability limitations encountered by biological systems. There has been a significant amount of effort focused toward the development of a synthetic single aperture system which would be able to analyze individual analytes at the molecular level. The first system was demonstrated by DeBlois and Bean. 91-94 They used a 24

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system which incorporated a 500 nm diameter single pore within a track-etched polycarbonate membrane. Because of the smaller aperture, this device could detect particles with diameters as small as 60 nm. For example,Virus particles were detected with this device. 92 Also, Li and Crooks developed a single nanopore device which was made up of a single carbon nanotube embedded within a support material. 95, 96 These single nanotube systems had an aperture diameter of -60nm and a path length of 1.0 m. These systems have been used for analysis of nanoparticles. There have been several single nanopore systems developed from inorganic solid-state materials. One such system employs the use of a feedback-controlled sputtering system, based on irradiating the materials with ion beams. 14, 97 This technique allowed the preparation of a single nanopore in a Si 3 N 4 support with diameter down to 1.8nm. Another method used to produce pores in silicon oxide with an aperture diameter of several nanometers was developed in the group of Dees Dekker. The pores are manufactured by electron beam lithography and anisotropic etching in combination with high-energy beam in transmission electron microscope. 98 There is also a technique which uses classical lithographic methods combined with micromolding of poly(dimethylsiloxane). This approach produces larger channels of approximately 200 nm in diameter, 15, 16 Finally, the track-etching process has been used to produce single nanopore membranes in polyamide ( kapton 50 HN, DuPont). 19 All of these systems have been used in the detection or discrimination of biomolecules. Within this dissertation we will discuss application of the single conical nanopore within a PET (polyethylene terephthalate) film which is not currently available within the present synthetic single nanopore systems. The first advantage is that we are able to control the diameter of the nanopore over a very large diameter range. We have demonstrated that we can make 25

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single nanopores with diameters > 200nm and diameters as small as 1.9nm. Also, the length of the nanopore can be systematically altered for each desired experimental setup. By using the track-etch process to fabricate single nanopore systems, the effective length of the nanopore can be changed from a large effective length of 12 m to a value of <100 nm. This flexibility offers one the control over a very important parameter within single nanopore systems which is the effective detection zone within the channel. This detection zone is the area within the channel in which the particular analyte is detected. By reducing the length of this zone you are able to then in turn detect smaller analytes. The practical side of this system is that it allows the researcher the ease of preparation. With the track-etch process there is no need for expensive equipment in which a highly experienced technician is needed to perform the task. This allows for a more stream line process which is very important in future directions of mass production of these single nanopore membranes. This system also has an advantage in characterizing the nanopore. There has been a large amount of research directed at studying the nanopore track-etched membrane within Martin group. Ion Current Rectification Conical nanopores in polymer films and glass have attracted increasing attention due to their application as biomimetic systems for models of biological channels and as biosensors. 99 One particular transport phenomenon has been observed in this kind of conically-shaped nanopore, which is due to the nanometer-sized opening. It has been found that these asymmetric nanopores and nanocapillaries rectify ion current, although the concentration and pH of the electrolyte in contact with pore openings are the same. The rectification is observed as an asymmetric current-voltage (I-V) curve, with the current recorded for one voltage polarity higher than the current recorded for the same absolute value of voltage but different polarity. 26

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The ion current rectification is dependent on the electrolyte concentration, pH value, and voltage, nanopore diameter and surface charge density of the nanopore. Conical nanopores rectify ion current only when the pore walls possess an excess surface charge. Chemically etching polymeric materials (PET and Kapton) result in the formation of carboxylate groups on the pore wall. The density of carboxylate groups has been estimated to be 1.5 groups nm -2 100 A direct consequence of the presence of carboxylate groups is the possibility that the surface charge can be defined by immersing the membranes into the electrolytes with various pH values. For example, at neutral and basic conditions, the carboxylate groups are deprotonated and the net surface charge is negative. Lowering the pH to values close to the isoelectric point of the track-etched surface neutralizes the surface charge. 22 Several mechanisms have been suggested to explain the ion-current rectification effect observed in synthetic nanoporous systems. Here is a explanation of one ratchet model introduced by Swiy et al. 101-103 The ratchet model has been formed on the basis of experimental observation of conditions at which the nanoporous systems rectify ion current. The main experimental observations were summarized: i) the opening diameter of the tip is comparable to the thickness of the electrical double layer, ii) there is an excess surface on the pore walls, and iii) the interactions of ions with the pore walls, induced either by the size of the openings or surface charge, are asymmetric at the two entrances of the pores. It has been shown that the sign of the surface charge determines the direction of ion-current rectification (Figure 1-10): Rendering the surface charge positive or negative makes the nanotubes rectify in opposite directions. This observation provides evidence that the rectification effect originated from electrostatic interactions between the ions passing through the nanopore and the pore wall. Interaction of ions 27

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with the pore wall is the basis of pore selectivity, because excess negative surface charge allows mainly cations to enter the pore, while anions are rejected. 40, 104 When the cation moves along the nanopore, the interaction between cation and the negatively charged pore wall was assumed to be a Debye-type interaction. The interaction between passing ions and the surface charges occur only if the pore is sufficiently narrow, with a diameter comparable to the thickness of the electrical double layer. This is caused by the short-range character of electrostatic interactions in an electrolyte solution, resulting from a strong screening induced by the presence of other ions. 104 To calculate the electrical potential of a cation at a given position z at the pore axis, they used the following formula 101-103 )',(/)'('2)(0)',(zzRezhdzzVLzzR (1-2) where p is the surface-charge density at the pore wall, R is the distance between the cation on the pore axis and negative charges on the pore walls (Figure 1-11), L stands for length of the pore, h(z) is the radius of the pore at point z and indicates the inverse screening length related to the thickness of the electrical double layer. The integration indicates that the potential of a cation at a given position z results from interactions with carboxylate groups on the entire surface of the pore. The problem has been treated in two-dimensional and three-dimensional space. 107 For conical nanopores, without any voltage applied from outside, the shape of the internal potential has been shown to be asymmetric and toothlike, reminiscent of the shape of a ratchet potential. The potential minimum is situated at the tip of a conical nanopore. Assuming a simple superposition of the externally applied voltage with the internal electrical field, one can obtain the resultant potential profiles for the two polarities of the applied voltage. Figure 1-12 shows that for positive voltages, a trap of electrostatic origin is created, 28

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causing an off state of the pore, i.e., low conductivity. Applying voltage of the opposite polarity does not lead to formation of the trap and the ion currents are higher. Dissertation Overview The main focus of my research is to develop a new method which can be used to improve the quality of nanopore membranes and to create new approaches for sensing drug molecules, DNA and proteins based on track-etched conical nanopore embedded in polymer membrane. The previous part of chapter 1 has reviewed the background information for this dissertation including the ion track-etch process, membrane based template synthesis, biological ion channel, potassium-gated ion channels, stochastic chemical sensing, and ion current rectification. In chapter 2, a new paradigm making use of the well-known ion-current rectification phenomenon displayed by conically-shaped nanopores is demonstrated. The sensor element in this case is a single conically-shaped nanopore in a polyimide (Kapton) membrane. The sensing paradigm entails placing electrolyte solutions on either side of the membrane and using electrodes in each solution to scan the applied transmembrane potential and measure the resulting ion current flowing through the nanopore. As has been discussed in detail by us and others, conically-shaped nanopores with excess surface charge on the pore walls, and sufficiently small tip openings, show non-linear current voltage curves; i.e., such pores are ion-current rectifiers. Because the polyimide nanopores used here have excess anionic surface charge, rectification is observed at positive applied transmembrane potential. We have found that when the nanopore is exposed to a very hydrophobic yet cationic, drug molecule (Hoechst 33258), adsorption of this molecule on the pore walls neutralizes the excess negative surface charge. As a result, the nanopore does not rectify as strongly, and the magnitude of the decrease in rectification scales with the concentration of the drug molecule. Ultimately at high concentrations of the drug, the sign of the excess surface charge switches from net negative to 29

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net positive, and the nanopore rectified at negative applied transmembrane potential. We describe this new nanopore-based sensing paradigm here. In chapter 3, we demonstrate the ability of a conical nanopore embedded in a polymer membrane to selectively sense drug molecules based on ion current rectification phenomenon. As has been pointed out in chapter 2, hydrophobicity is the dominant force which contributes to the absorption of positive drugs to the hydrophobic pore wall of the Kapton membrane. This conclusion paves the foundation for exploration of selectivity based on hydrophobicity. We choose three positive drugs which have different hydrophobicity. In this chapter, we demonstrate that three hydrophobic drugs can be be totally discriminated due to different binding constant. We believe that this powerful sensing ability based on ion current rectification can be extended to sense other interesting biomolecules, for example, DNA and proteins. In chapter 4, we demonstrate a promising tool for sensing DNA-linked protein dimmers which are relevant to a biological process, for example, gene expression, DNA degradation, and virus detection. The sensing device investigated is a bare conically-shaped nanopore embedded in track-etched PET membrane. A Biotin-labelled DNA probe reacts with excess Streptavidin to form a Streptavidin conjugated DNA probe. Two Streptavidin conjugated monovalent DNA probes can bind two distinct segments of target DNA. The size of the target DNA linked complex is double that of each Streptavidin conjugated monovalent DNA probe. By precisely controlling the tip diameter of the conical nanopore embedded in PET polymer, the events due to the translocation of the streptravidin conjugated monovalent DNA probes through the nanopore can be filtered and undetected on purpose; the current-pulses due to translocation of the target DNA linked complex can thus be detected. In order to confirm that the two Streptavidin conjuaged DNA probes are linked by target DNA ,we test if the wo protein conjugated DNA 30

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probes can be linked by multi-mismatched DNA. The multi-mismatched DNA will not induce the complex formation. The current-pulse signatures for the self-assembled complex can be used to confirm the existence of target DNA and DNA linked protein dimer. The concept of size dependent detection of self-assembled complexes on the molecule level shows strong promise for detection of biomolecules without interference of probes. In chapter 5, we demonstrate a new way to tailor the single conical nanopores embedded in PET (polyethylene terephthalate) membranes via a layer-by-layer assembly technique, which is based on strong interaction between Biotin and Streptavidin. Single conical nanopores are fabricated in ion-tracked PET membranes by using a two-step etch procedure. Multi-Biotin labelled BSA (or multi-Biotin labelled polylysine) were driven into the tip of the single conical nanopore from the base of the pore opening by applying a transmembrane potential difference (1V), and nonspecifically adsorbed onto the inner wall of the nanopore as a first layer. Streptavidin was then placed on both sides of the nanopore, and specifically interacted with the multi-Biotin labelled protein and was thus deposited as a second layer by alternately applying a transmembrane potential difference of 200mV and -200mV. Multilayers were formed by repeating the same procedure for depositing the second layer. Most importantly, the diameter of the tip opening can be adjusted by controlling the number of protein layers. The conical nanopore can also be made selective with this method by depositing any Biotin labelled ligand on the final layer, which can be used for specifically sensing target analytes. The layer-by-layer assembled conical protein nanopores have shown great stability and may allow for fabricating practical biosensors based on these conical nanopores. 31

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Figure 1-1. (A) The heavy ion beam forms a latent ion track in the dielectic membrane. (B) Chemically etching will selectively remove the latent track and form a cylindrical shape. Figure 1-2. Definition of cone half-angle bulk etch rate V B and track etch-rate V T 32

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Figure 1-3. Scanning electron microscopic images of different nanoporous materials developed by ion-track-etching process. (A) Kapton (B) PC (C) PET (D) Mica. Figure 1-4. Scanning electron microscopic images of different template. (A) Polycarbonate membrane and (B) Alumina membrane. 33

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Figure 1-5. Schematic diagram of Au electroless plating procedure. Figure 1-6. Schematic illustration of Au nanotubes obtained from electroless gold deposition. 34

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Figure 1-7. Schematic illustration of open and close state of K + channel.[Adapted from Long, S. B.; Campbell, E. B.; MacKinnon, R. Science 2005, 309, 897-903.] Figure 1-8. Schematic illustration of resistive-pulse sensing. 35

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Figure 1-9. Protein channel embedded in lipid bilayer. Figure 1-10. Current-voltage curve for conical nanopore with different charge, the voltage scan from positive potential in base side to negative potential in based side: (A) I-V curve and current rectification for nanopore without charge. (B) I-V curve and current rectification for nanopore with negative charge. (C) I-V curve and current rectificationfor nanopore with positive charge. 36

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Figure 1-11. (A) Scheme of an axial cut of a conical pore; (B) profile of electrical potential,V(z), inside a tapered-cone pore, calculated from Eq. 1-2. [Adapted from Siwy, Z. Adv. Funct. Mater. 2006, 16, 735-746.] Figure 1-12. Ratchet model for ion current recification in a conical nanopore with excess negative surface charge on pore wall: (A) schematic representation of the electric potential for cation inside a nanopore without external voltage; (B) solution voltage drop for cations, left: positive voltage, right; negative voltage; (C) profile of the electric potential resulting from superposition of the profile shown in (A) with the two profiles from (B). Appling positive voltages results in formation of an electrostatic trap and consequently lower ion current. [Adapted from Siwy, Z. Adv. Funct. Mater. 2006, 16, 735-746.] 37

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CHAPTER 2 A NEW DRUG-SENSING PARADIGM BASED ON ION-CURRENT RECTIFICATION IN A CONICALLY SHAPED NANOPORE Introduction There is increasing interest in using nanopores in synthetic 14-17, 92-94, 105-118 or biological 77, 79-80, 83-86, 119-129 membranes as biosensors. Perhaps the most popular nanopore-based sensing paradigm is the well-known resistive-pulse, or stochastic-sensing, method which entails counting individual analyte molecules as they are driven through the nanopore sensor element. 105-129 Prototype sensors for analyte species as diverse as proteins 114 DNA 109 and small molecules 110 have been described. While we too are exploring resistive-pulse sensors, 109-110, 130 we have also been investigating other sensing paradigms based on artificial nanopores 107 One such paradigm makes use of the well-known ion-current rectification phenomenon displayed by conically shaped nanopores. 21, 26, 31, 37, 130-134 The sensor element in this case is a single conically shaped nanopore in a polyimide (Kapton) membrane. 37, 110 The sensing paradigm entails placing electrolyte solutions on either side of the membrane and using electrodes in each solution to scan the applied transmembrane potential and measure the resulting ion current flowing through the nanopore. As has been discussed in detail by us 26, 62 and others 21, 31, 131-133 conically shaped nanopores with excess surface charge on the pore walls, and sufficiently small tip openings, show non-linear current voltage curves; i.e., such pores are ion-current rectifiers. Because the polyimide nanopores used here have excess anionic surface charge, rectification is observed at positive applied transmembrane potential. 31 We have found, however, that when the nanopore is exposed to a very hydrophobic, yet cationic, drug molecule (Hoechst 33258, Figure 2-1), adsorption of this molecule on the pore walls neutralizes the excess negative surface charge. As a result the nanopore does not rectify as 38

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strongly, and the magnitude of the decrease in rectification scales with the concentration of the drug molecule. Ultimately at high concentrations of the drug, the sign of the excess surface charge switches from net negative to net positive, and the nanopore rectifies at negative applied transmembrane potential. 62 We describe this new nanopore-based sensing paradigm here. Experimental Materials and Methods Polyimide (Kapton, Scheme 1) membranes (diameter = 3 cm, thickness = 12 m) that had been irradiated with a heavy ion of 2.2 GeV kinetic energy to create a single damage track through the membrane were obtained from GSI, Darmstadt, Germany. 37, 110 We refer to these as-received membranes as the tracked membranes. Hoechst 33258, methyl viologen dichloride hydrate, benzylviologen and sodium hypochlorite (13% active chloride) were purchased from Sigma-Aldrich and used as received. Bis-Tris propane, used to prepare the buffer solutions, was also obtained from Aldrich. All other chemicals were used as received. Purified water was prepared by passing house-distilled water through a Millipore Milli-Q water purification system. Etching the Conical Nanopore in the Tracked Membrane We have recently described a two-step etching procedure for reproducibly preparing conically shaped nanopores in tracked poly(ethylene terphthalate membranes). 135 A variant of that method was used to etch the conical nanopores in the tracked Kapton membranes used for these studies. The tracked Kapton membrane was irradiated under UV light (320 nm) for 15 hours, and then mounted in a two-compartment cell 135 such that electrolyte solution could be placed on either side of the tracked membrane. The first etch step, developed by Apel, et al., 37 entailed placing a solution that etched the damage track (13% NaOCl, pH =12.6) on one side of the membrane and a solution that neutralizes the etchant (2 M KI, the stop solution) on the other side. 110 The temperature during 39

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etch was 50 o C. Each half cell contained a Pt wire (dia = 0.2 cm, length ~7.6 cm), and a Keithley 6487 picoammeter/voltage-source (Keithley Instruments, Cleveland, OH) was used to apply a transmembrane potential of 1V, during etching and measure the resulting current ionic flowing through the nascent nanopore. The current was initially zero but increased suddenly when the etch solution broke through to the stop solution. This first etch step was terminated when the current increase up to 0.1 nA. At this point, stop solution was placed in both half cells to quench the etch. As per our prior work, 110 the diameter of the base opening after the first etch step was determined by obtaining scanning electron micrographs of the base side of multi-track Kapton membranes etched in the analogous way. Multi-track membranes (1*10 6 tracks cm -2 also from GSI) were used because it is difficult to find the base openings by electron microscopy in etched single-track membranes. These studies yielded an etch rate of 8.3 nm min -1 in close agreement to the value of 7.0 nm min -1 obtained by Siwy et al. 23 Our studies with PET membranes showed that by varying the etch time (or final etch current) or the transmembrane voltage applied during etching, the base diameter can be reproducibly controlled during this first etch step. 135-136 We found, however, that it is difficult to reproducibly control the tip diameter. This led us to subject the membrane to a second etch step which allows us to control and fine-tune the tip diameter. 135 The second etch step entailed placing the NaOCl etch solution on both sides of the membrane. A transmembrane potential of 200 mV was applied, and again the transmembrane current was monitored during the etch. The key innovation is that this etch is stopped at a prescribed value of the transmembrane current rather than at a prescribed time. 135 We have found that this allows for excellent reproducibility in both tip and base diameter. 135 The base and tip diameters after the second etch were measured using the electrochemical method described in 40

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detail previously. 135 Membranes with two different base and tip diameters were used for these studies. The first had base diameter of 1.43 m and tip diameter of 67 nm. The second had base diameter of 2.0 m and tip diameter of 48 nm. Sensing the Analyte Molecules The membrane containing the conically shaped nanopore was mounted in the two-compartment cell, 135 and a solution containing the desired analyte molecule (Figure 2-1) was placed on the side on the membrane containing the tip opening. This solution was prepared in 10mM Bis-tris propane (pH = 7.0) that was also 3 mM in MgCl2, and the same buffer solution, devoid of the analyte, was placed on the opposite side on the membrane. A Ag/AgCl electrode was placed into each solution, and the Keithley 6487 was used to obtain a current-voltage (I-V) curve associated with ion transport through the nanopore. The working Ag/AgCl electrode was in the half-cell facing the base opening, and the potential of this electrode was controlled relative to the counter Ag/AgCl electrode in the opposite solution. The I-V curve was obtained by stepping the potential in 300 mV steps through desired potential range. The sign convention used here is the same as used in our prior studies, 62 negative transmembrane potentials mean that the cathode is in the solution facing the base opening and the anode is in the solution facing the tip opening. Results and Discussion Ion-Current Rectification by the Conical Nanopore Figure 2-2 shows I-V curves for a conical nanopore in a Kapton membrane with and without the analyte drug molecule Hoechst 33258. In the absence of this drug, the I-V curve is non-linear, indicating that the nanopore strongly rectifies the ion current flowing through it. 21, 31, 62, 131-134 There seems to be some disagreement in the literature as to the precise mechanism by which conical nanopores rectify the ion current. All extant theories agree on the following: 41

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Rectification requires that excess charge density be present on the pore walls and that the diameter of the tip opening be comparable to the thickness of the electrical double layer extending from the pore wall. The ion-current rectification phenomenon can be described by defining on and off states for the nanopore rectifier. 62 In agreement with previous results for conically shaped Kapton nanopores, Figure 2-2 shows that in the absence of Hoechst 33258, the on state occurs at negative potentials and the off state at positive potentials. 62 This indicates that rectification is caused by fixed anionic (carboxylate) groups on the pore wall. 23, 31 The extent of rectification can be quantified by the rectification ratio 26, 62 defined here as the current at -6.0 V divided by the current at +6.0 V (Table 2-1). Effect of Hoechst 33258 on Rectification The key experimental observations of these studies are: 1. As Hoechst 33258 is added, the extent of rectification decreases (Figure 2-2). 2. The extent of rectification scales inversely with the concentration of Hoechst 33258 (Table 2-1). 3. Ultimately at high drug concentrations, the rectification is reversed (Figure 2-2). This reversal in rectification is signaled by the fact that at high drug concentrations the on state is at positive potentials and the off state is at negative potentials. Rectification with this polarity causes the rectification ratio to be less than unity (Table 2-1). We have shown that rectification with this polarity requires excess positive charge on the pore walls. 62 At pH = 7.0 Hoechst 33258 is cationic with a net charge of +1, 137 due to protonation of the methyl-substituted piperdine-like N. In addition, this drug is quite hydrophobic, as is Kapton polyimide, dielectric constant = 3.4. We have shown that such hydrophobic cationic drug molecules can adsorb to hydrophobic surfaces and impart positive charge to the surface. 138 These prior studies provide a simple explanation for the results in Figure 2-2. Exposure of the 42

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hydrophobic Kapton membrane to the cationic and hydrophobic Hoechst 33258 causes this molecule to adsorb to the pore wall, thus neutralizing the surface-carboxylate sites, and this neutralization of the negative surface charge causes the observed decrease in ion current rectification (Table 2-1). The reversal of polarity at high drug concentrations (Figure 2-2), and concomitant less-than-unity rectification ratios (Table 2-1), indicate that ultimately the quantity of adsorbed cationic charge due to the drug exceeds the quantity of fixed negative charge due to the carboxylates. This reversal in the sign of the surface charge illustrates an interesting chemical point. At low drug concentrations where the net surface charge is negative, there is no question that part of the interaction between the drug and the surface is electrostatic the surface needs a charge balancing cation and it chooses the hydrophobic drug over the inorganic cations present in the solution. However, this electrostatic component is augmented by the hydrophobic component, as indicated by the fact that when the net surface charge becomes positive at high drug concentrations, the drug continues to adsorb. For example the less-than-unity rectification ratio for 25 M drug (Table 2-1) indicates that the surface has net positive charge when the membrane is exposed to this drug concentration. Effect of Benzyl and Methyl on Rectification To explore the surface chemical interactions further, we obtained analogous data for two other relatively hydrophobic cationic molecules methyl and benzyl viologen (Scheme 1). Current voltage curves for a conical nanopore sensor before and after exposure to these molecules are shown in Figure 2-3. The black curve was obtained in the absence of the viologens, and as before, shows the strong surface-carboxylate-induced rectification phenomenon. In analogy to Hoechst 33258 the more hydrophobic benzyl viologen engenders a concentration dependent decrease in the extent of rectification. However, the concentrations 43

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required to produce a measurable change are about three orders of magnitude higher than the concentration needed for Hoechst 33258. This clearly shows that benzyl viologen adsorbs much more weakly to the Kapton surface than Hoechst 33258. This observation helps us understand the relative contributions of hydrophobicity vs. molecular charge to the interaction of the adsorbing molecule with the Kapton surface. Recall first that benzyl viologen is a divalent cation, whereas Hoechst 33258 is monovalent. If the interaction between the adsorbing molecule and the Kapton surface was dominated by electrostatics, then benzyl viologen would adsorb much more strongly, and this is not what is observed experimentally. Hence it is clear that the hydrophobic effect is the dominant force that causes adsorption to the Kapton surface. This is in agreement with our early observation that cationic Hoechst 33258 continues to adsorb even after the Kapton surface has net positive charge. The dominance of the hydrophobic effect is also strongly reinforced by the methyl viologen data in Figure 2-3. Methyl viologen retains the 2+ charge of benzyl viologen, but because it lacks the two benzene rings, it is much less hydrophobic. As a result, no evidence for methyl viologen adsorption is observed in Figure 2-3. A slight increase in current, relative to the I-V curve obtained in the absence of adsorbing molecule, is observed because at the 1mM and higher concentrations used, the divalent methylviologen makes a measurable contribution to the bulk conductivity of the electrolyte. Langmuir Analysis of the Hoechst 33258 Adsorption Data We can write the following general equation for Langmuir adsorption of a molecule to a surface 138 = KC/(1 + KC) (2-1) 44

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where is the fractional coverage of the molecule on the surface, K is the binding constant with units of L mol -1 and C is the concentration of the drug in the contacting solution phase. is also given by = mole D,i / mole D,max (2-2) where mole D,i is the moles of molecule on the surface when the surface is exposed to some concentration of drug i and mole D,max is the maximum adsorption capacity of the surface obtained at some very high concentration of the molecule. Table 2-2 shows values of the ion current, at 6.0 V, for a conical nanopore sensor at high concentrations of Hoechst 33258. We see that the current decreases to a minimum and then increases again at concentrations above about 1 mM. This increase at high concentration results because the drug concentration is comparable to the electrolyte concentration and the drug begins to contribute to the bulk conductivity of the electrolyte. Based on these results, we assume that mole D,max occurs for a solution drug concentration, and we call the current obtained I min If we call the current obtained in the absence of drug I 0 then mole D,max is proportional to the difference I 0 I min Likewise, if we call the current observed at some intermediate drug concentration, i, I i then mole D,i is proportional to the difference I 0 I i This allows us to calculate for any concentration of drug, I, via = (I 0 I i )/ (I 0 I min ) (2-3) equating these values to the corresponding concentration values (Equation 2-1) allows us to plot out the Langmuir isotherm, and by fitting the experimental data to Equation 2-1, the value of the binding constant K can be obtained. Figure 2-4 shows the experimental and calculated 45

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plots and a value of K = 2x10 5 L/Mol was obtained from the best fit. This K quantifies what the experimental data already taught us Hoechst 33258 binds very strongly to the Kapton surface. Conclusions The sensor described here is reminiscent of much ealier work on ion-selecitive electrode. Potentiometric sensors, for hydrophobic drug molecules. 139-140 Both sensors use a hydrophobic membrane with fixed negative charge to extract hydrophobic cations into the membrane. In both cases, the sensor has greater selectivity for hydrophobic analytes relative to more hydrophilic analytes. In the case of the ion-selective electrode, this was quantified by investigating the response of the device to a homologous series of alkyl ammonium ions. 140 We are currently conducting studies of this type for the sensor described here. The disadvantage of this hydrophobic-based selectivity paradigm is that the device can not discriminate between analytes of similar mass and charge. In successful (commercially available) ion-selective electrodes, this problem is solved by incorporating a highly selective ionophore in to the membrane. This could be accomplished with the sensor described here by simply attaching the ionophore to the pore wall. Finally, it is important to point out that with our current sensor design; the drug molecule binds not only to the pore walls but also to the faces of the membrane. This is because the pore walls and membrane faces are chemically identical. If adsorption to the membrane faces could be blocked, then a much smaller number of sites, only those along the pore walls, would be available for analyte adsorption. This would shift the isotherm to much lower analyte concentrations, and lower detection limits would be achieved. This could be accomplished by attaching a neutral and hydrophilic chemical species to the membrane faces. 46

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Figure 2-1. Molecular structure of different drug molecules and polymer. Figure 2-2. I-V curves for a conical nanopore sensor (tip diameter =67 nm, base diameter 1.43 m) in the presence of the following concentrations of Hoechst 33258: 0 nM (black square), 1.25 M (red circle), 2.5 M (green triangle), 5 M (blue triangle), 10 M (cyan square), 15 M (magenta), 25 M (yellow). 47

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Figure 2-3. I-V curve for conical nanopore in kapton membrane (tip diameter 48 nm, base diameter 2.0 m) with different molecules: 2.3 mM benzyl viologen (cyan square), 1 mM benzyl viologen (blue triangle), control buffer (black square), 1 mM methyl viologen (red circle), 2.3 mM methyl viologen (green triangle). 05101520250.00.20.40.60.81.0 ThetaConcentration (M) Figure 2-4. Plot of surface coverage (theta) versus concentration of Hoechst 33258. 48

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Table 2-1. Rectification ratio in various concentration of Hoechst 33258 at transmembrane potential difference of 6V. Concentration (M) 0 2.5 5 10 15 25 Rectification ratio 19.58 10.84 4.91 1.86 1.24 0.672 49

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Table 2-2. Current values in various concentration of Hoechst 33258 at transmembrane potential -6V. Concentration (M) 0 2.5 5 10 15 25 500 1000 1500 Current value (nA) -21.90 -14.8 -9.75 -6.96 -5.43 -3.60 -4.60 -5.99 -6.06 50

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CHAPTER 3 SELECTIVE DETECTION OF DRUGS BASED ON ION-CURRENT RECTIFICATION IN A CONICALLY-SHAPED NANOPORE Introduction There is increasing interest in using nanopores in synthetic 14-17, 92-94, 105-118 or biological 77, 79-80, 83-86, 119-129 membranes as biosensors. Perhaps the most popular nanopore-based sensing paradigm is the well-known resistive-pulse, or stochastic-sensing, method which entails counting individual analyte molecules as they are driven through the nanopore sensor element. 1105-129 Prototype sensors for analyte species as diverse as proteins, 114 DNA, 109 and small molecules 110 have been described. While we too are exploring resistive-pulse sensors, 109-110, 130 we have also been investigating other sensing paradigms based on artificial nanopores. 107 One of these paradigms makes use of the well-known ion-current rectification phenomenon displayed by conically-shaped nanopores. 21, 26 31, 37, 130-134 The sensor element in this case is a single conically-shaped nanopore in a polyimide (Kapton) membrane. 37, 110 The sensing paradigm entails placing electrolyte solutions on either side of the membrane and using electrodes in each solution to scan the applied transmembrane potential and measure the resulting ion current flowing through the nanopore. As has been discussed in detail by us 26, 62 and others, 21, 31, 131-133 conically-shaped nanopores with excess surface charge on the pore walls, and sufficiently small tip openings, show non-linear current voltage curves, i.e., such pores are ion-current rectifiers. Because the polyimide nanopores used here have excess anionic surface charge, rectification is observed at positive applied transmembrane potential. 31 We have reported 141 that when the nanopore is exposed to a very hydrophobic, yet cationic, drug molecule (Hoechst 33258), adsorption of this molecule on the pore walls neutralizes the excess negative surface charge. As a result the nanopore does not rectify as strongly, and the 51

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magnitude of the decrease in rectification scales with the concentration of the drug molecule. Ultimately at high concentrations of the drug, the sign of the excess surface charge switches from net negative to net positive, and the nanopore rectifies at negative applied transmembrane potential. 62 In the previous report, 141 selectivity has not been explored. Here we have clearly demonstrated that the conical-shaped nanopore embedded in the Kapton membrane can be used to selectively discriminate cationic hydrophobic drugs based on ion-current rectification and three drugs including Hoechst 33342, Amitriptyline and Bupivacaine were chosen to explore this powerful ability. Hoechst 33342 is a more hydrophobic analog of Hoechst 33258, and Amitriptyline and Bupivacaine are less hydrophobic. Experimental Materials and Methods Polyimide (Kapton, Scheme 1) membranes (diameter = 3 cm, thickness = 12 m) that had been irradiated with a heavy ion of 2.2 GeV kinetic energy to create a single damage track through the membrane were obtained from GSI, Darmstadt, Germany. We refer to these as-received membranes as the tracked membranes. Hoechst 33342, Amitriptyline, Bupivacaine and sodium hypochlorite (13% active chloride) were p 37, 110 urchased from Sigma-Aldrich and used as received. Bis-Tris propane, used to prepare the buffer solutions, was also obtained from Aldrich. All other chemicals were used as received. Purified water was prepared by passing house-distilled water through a Millipore Milli-Q water purification system. Etching the Conical Nanopore in the Tracked Membrane We have recently described a two-step etching procedure for reproducibly preparing conically-shaped nanopores in tracked poly(ethylene terphthalate membranes). A variant of that method was used to etch the conical nanopores in the tracked Kapton membranes used for 135 52

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these studies. The tracked Kapton membrane was irradiated under UV light (320 nm) for 15 hours, and then mounted in a two-compartment cell 135 such that electrolyte solution could be placed on either side of the tracked membrane. The first etch step, developed by Apel, et al., 37 entailed placing a solution that etched the damage track (13% NaOCl, pH =12.6) on one side of the membrane and a solution that neutralizes the etchant (2 M KI, the stop solution) on the other side. 110 The temperature during etch was 50 o C. Each half cell contained a Pt wire (dia = 0.2 cm, length ~7.6 cm), and a Keithley 6487 picoammeter/voltage-source (Keithley Instruments, Cleveland, OH) was used to apply a transmembrane potential of 1V, during etching and to measure the resulting ionic current flowing through the nascent nanopore. The current was initially zero but increased suddenly when the etch solution broke through to the stop solution. This first etch step was terminated when the current increased up to 0.1 nA. At this point, stop solution was placed in both half cells to quench the etch. As in our prior work, the diameter of the base opening after the first etch step was 110 determined by obtaining scanning electron micrographs of the base side of the multi-track Kapton membranes etched in the analogous way. Multi-track membranes (1*10 6 tracks cm -2 also from GSI) were used because it is difficult to find the base openings by electron microscopy in etched single-track membranes. These studies yielded an etch rate of 8.3 nm min -1 in close agreement to the value of 7.0 nm min -1 obtained by Siwy et al. 23 Our studies with PET membranes showed that by varying the etch time (or final etch current) or the transmembrane voltage applied during etching, the base diameter can be reproducibly controlled during this first etch step. 135-136 We found, however, that it is difficult to reproducibly control the tip diameter. 53

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This led us to subject the membrane to a second etch step which allows us to control and fine-tune the tip diameter. 135 The second etch step entailed placing the NaOCl etch solution on both sides of the membrane. A transmembrane potential of 200 mV was applied, and again the transmembrane current was monitored during the etch. The key innovation is that this etch is stopped at a prescribed value of the transmembrane current rather than at a prescribed time. 135 We have found that this allows for excellent reproducibility in both tip and base diameters. 135 The base and tip diameters after the second etch were measured using the electrochemical method described in detail previously. 135 Membranes with a base diameter of 1.21 m and tip diameter of 57 nm were used for these studies. Sensing the Analyte Molecules The membrane containing the conically-shaped nanopore was mounted in the two-compartment cell, 135 and a solution containing the desired analyte molecule (Figure 3-1) was placed on the side of the membrane containing the tip opening. This solution was prepared in 10mM Bis-tris propane (pH = 7.0) that was also 3 mM in MgCl 2 and the same buffer solution, devoid of the analyte, was placed on the opposite side on the membrane. A Ag/AgCl electrode was placed into each solution, and the Keithley 6487 was used to obtain a current-voltage (I-V) curve associated with ion transport through the nanopore. The working Ag/AgCl electrode was in the half-cell facing the base opening, and the potential of this electrode was controlled relative to the counter Ag/AgCl electrode in the opposite solution. The I-V curve was obtained by stepping the potential in 300 mV steps through desired potential range. The sign convention used here is the same as used in our prior studies, 62 negative transmembrane potentials mean that the cathode is in the solution facing the base opening and the anode is in the solution facing the tip opening. 54

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Results and Discussion Ion-Current Rectification by the Conical Nanopores Figure 3-2 shows I-V curves for a conical nanopore in a Kapton membrane with and without the analyte drug molecule Hoechst 33342. In the absence of this drug, the I-V curve is non-linear, indicating that the nanopore strongly rectifies the ion current flowing through it. 21, 31, 62, 131-134 While there is currently some disagreement in the literature as to the precise mechanism by which conical nanopores rectify the ion current. All extant theories agree on the following: Rectification requires that excess charge density be present on the pore walls and that the diameter of the tip opening be comparable to the thickness of the electrical double layer extending from the pore wall. The ion-current rectification phenomenon can be described by defining on and off states for the nanopore rectifier. 62 In agreement with previous results for conically-shaped Kapton nanopores, Figure 3-2 shows that in the absence of Hoechst 33342, the on state occurs at negative potentials and the off state at positive potentials. 62 This indicates that rectification is caused by fixed anionic (carboxylate) groups on the pore wall. 23, 31 The extent of rectification can be quantified by the rectification ratio 26, 62 defined here as the current at -2.0 V divided by the current at +2.0 V (Table 3-1). Effect of Hoechst 33342 on Rectification The key experimental observations for studies 41 with Hoechst 33258 can be reproduced by Hoechst 33342 which is one more hydrophobic analog of Hoechst 33258, which are: 1. As Hoechst 33342 is added, the extent of rectification decreases (Figure 3-2). 2. The extent of rectification scales inversely with the concentration of Hoechst 33342 (Table 3-1). 3. Ultimately at high drug concentrations, the rectification is reversed (Figure 3-2). This reversal in rectification is signaled by the fact that at high drug concentrations the on state is at positive 55

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potentials and the off state is at negative potentials. Rectification with this polarity causes the rectification ratio to be less than unity (Table 3-1). We have shown that rectification with this polarity requires excess positive charge on the pore walls. 62 At pH = 7.0 Hoechst 33342 is cationic with a net charge of +1, 137 due to protonation of the methyl-substituted piperdine-like N. In addition, this drug is quite hydrophobic, as is Kapton polyimide, dielectric constant = 3.4. We have shown that such hydrophobic cationic drug molecules can adsorb to hydrophobic surfaces and impart positive charge to the surface. 138 These prior studies provide a consistent explanation for the results in Figure 3-2. Exposure of the hydrophobic Kapton membrane to the cationic and hydrophobic Hoechst 33342 causes this molecule to adsorb to the pore wall, thus neutralizing the surface-carboxylate sites, and this neutralization of the negative surface charge causes the observed decrease in ion current rectification (Table 3-1). The reversal of polarity at high drug concentrations (Figure 3-2), and concomitant less-than-unity rectification ratios (Table 3-1), indicate that ultimately the quantity of adsorbed cationic charge due to the drug exceeds the quantity of fixed negative charge due to the carboxylates. The similarity of molecular structures between Hoechst 33258 and Hoechst 33342 tell us that the interaction of Hoechst 33342 and nanopore wall in Kapton can also be explained by hydrophobicity which was used to explain the interaction mechanism between Hoechst 33258 and the nanopore wall in the kapton. 41 Similar to analysis of Hoechst 33258, electrostatic force was not the dominant force since Hoechst 33342 continues to adsorb to the nanopore wall after excess positive charge exists on the surface. For example the less-than-unity rectification ratio for 15 m drug (Table 3-1) indicates that the surface has net positive charge when the membrane 56

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is exposed to this drug concentration; yet the smaller ratio observed at 2.3 mM drug indicates that additional drug adsorbed after exposure to this higher drug concentration. The Hoechst 33342 was expected to adsorb to the nanopore wall of the Kapton stronger than Hoechst 33258. This can be confirmed by the binding constant 2.27x10 5 obtained by fitting the experimental data with equation 3-1 (Figure 3-2). Langmuir Analysis of the Hoechst 33342 Adsorption Data We can write the following general equation for Langmuir adsorption of a molecule to a surface 55 = KC/(1 + KC) (3-1) where is the fractional coverage of the molecule on the surface, K is the binding constant with units of L mol -1 and C is the concentration of the drug in the contacting solution phase. is also given by = moles s,i / moles s,max (3-2) where moles s,i is the moles of molecule on the surface when the surface is exposed to some concentration of drug i and moles s,max is the maximum adsorption capacity of the surface obtained at some very high concentration of the molecule. We assume that moles s,max occurs for a solution drug concentration, and we call the current obtained I min If we call the current obtained in the absence of drug I 0 then moles s max is proportional to the difference I 0 Imin. Likewise, if we call the current observed at some intermediate drug concentration, i, I i then moles s,i is proportional to the difference I 0 I i This allows us to calculate for any concentration of drug, I, via = (I 0 I i )/ (I 0 I min ) (3-3) 57

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Equating these values to the corresponding concentration values (Equation 3-1) allows us to plot out the Langmuir isotherm, and by fitting the experimental data to Equation 3-1, the value of the binding constant K can be obtained. Figure 3-3 shows the experimental and calculated plots and a value of K = 2.27x10 5 L/Mol was obtained from the best fit. This K quantifies what the experimental data already taught us Hoechst 33342 binds very strongly to the Kapton surface. Effect of Amitriptyline and Bupivacaine on Rectification Hydrophobicity of Amitriptyline and Bupivacine are much weaker compared to Hoechst 33342. The first and second key experimental observations for Hoechst 33342 and 33258 can be reproduced with Amitriptyline and Bupivacine (Figures 3-4 and 3-6). As either Amitriptyline or Bupivacine was added, rectification was decreased; the rectification scales inversely with the concentration of Amitriptyline or Bupivacine. The rectification was not reversed and remain above unity even when the concentration of Amitriptyline or Bupivacine was beyond 10 mM (Table 3-2 and Table 3-3). This means that the surface charge of the Kapton membrane has not been reversed even when the maximum coverage of the drug was reached. Amitriptyline was much more hydrophobic than Bupivacaine even there is only a 3% difference in the molecular weights of Amitriptyline and Bupivacaine. Bupivacaine presents two additional opportunities for hydrogen bonding with water: the lone pairs on the carbonyl group and the lone pair of the nonprotonated nitrogen. It was expected that Bupivacaine will be the most poorly detected of the three drugs. The bind constant (6.3x10 2 L/Mol, Figure 3-7) for Bupivacaine to the nanopore wall in the Kapton membrane is lower than that for Amitriptyline ( 3.97x10 3 L/Mol, Figure 3-5) and that for Hoechst 33342 ( 2.27x10 5 L/Mol, Figure 3-3) Summary and Future Work The sensor we developed here has great selectivity toward hydrophobic cationic drugs. More hydrophobic cationic drug can be easily discriminated from those less hydrophobic 58

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cationic drugs. The highest binding constant of Hoechst 33342 toward the nanopore wall in the Kapton membrane offers the lowest detection limit. In future work, we will focus on extending the application of an ion-current rectification based Sensor, for example, immobilze a negative(or positive) charged molecular recognition agent onto the pore wall of a conical nanotube for sensing positive (or negative) analyte. 59

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Figure 3-1. Molecular structure of drug molecules. -2-1012-25-20-15-10-505 Current (nA)Transmembrane Potential (V) Figure 3-2. I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21 m) in the presense of the following concentrations of Hoechst 33342: 0 nM (black square), 5.3 M (red circle), 15 M (green triangle), 2.3 mM (blue triangle). \ 60

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0501001502002500.00.20.40.60.81.0 Surface CoverageConcentration(M) Figure 3-3. Plot of surface coverage (theta) versus concentration of Hoechst 33342. -2-1012-20-15-10-50 Current (nA)Transmembrane Potential (V) Figure 3-4. I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21 m) in the presense of the following concentrations of Amitriptyline: 0 nM (black square), 90 M (red circle), 390 M (green triangle), 11.2 mM (blue triangle). 61

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0200040006000800010000120000.00.20.40.60.81.0 Surface CoverageConcentration(M) Figure 3-5. Plot of surface coverage (theta) versus concentration of Amitriptyline. -2-1012-25-20-15-10-50 Current (nA)Transmembrane Potential (V) Figure 3-6. I-V curves for a conical nanopore sensor (tip diameter =57 nm, base diameter 1.21 m) in the presense of the following concentrations of Bupivacaine: 0 nM (black square), 0.67 mM (red circle), 2 mM (green triangle), 11.6 mM (blue triangle). 62

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0200040006000800010000120000.00.20.40.60.81.0 Surface CoverageConcentration (M) Figure 3-7. Plot of surface coverage (theta) versus concentration of Bupivacaine. 63

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Table 3-1. Rectification ratio in various concentration of Hoechst 33342 at transmembrane potential difference of 2 V. Concentration (M) 0 5.3 15 2.3 mM Rectification ratio 33.2 10.9 0.94 0.07 64

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Table 3-2. Rectification ratio in various concentration of Amitriptyline at transmembrane potential difference of 2 V. Concentration (M) 0 90 390 11.2 mM Rectification ratio 33.4 22.03 15.7 1.03 65

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Table 3-3. Rectification ratio in various concentration of Bupivacaine at transmembrane potential difference of 2 V. Concentration (mM) 0 0.67 2 11.6 Rectification ratio 34 26.4 17.8 6.3 66

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CHAPTER 4 INVESTIGATION OF SELF-ASSEMBLED PROTEIN DIMERS THROUGH AN ARTIFICAL ION CHANNEL FOR DNA SENSING Introduction Resistive-pulse 105 sensors, which when applied to molecular and macromolecular analytes 14, 17, 19, 24, 27, 29, 79, 81, 82, 94, 105, 114, 121, 122, 142-145 are sometimes referred to as stochastic sensors, 105, 145 use a nanopore in a synthetic or biological membrane as the sensor element. In resistive pulse sensing, the membrane containing the nanopore is mounted between two electrolyte solutions, and analytes are driven through the nanopore by applying a transmembrane potential difference across the pore. The resulting ionic current flowing through the nanopore is measured and as the analytes translocate through the nanopore downward current pulses are produced by the transient blocking of ion current. The frequency of such current pulses is proportional to the concentration of the analyte, and the magnitude and duration of the current pulse encodes the identity of the analyte. The majority of ideal resistive pulse sensing work has utilized the biological protein nanopore, -hemolysin(-HL), embedded in a supported lipid-bilayer membrane as the sensing element. The -HL nanopore can be made selective by biological or chemical engineering, and has been used to detect numerous different analytes including metal ions, 121 DNA, 122,143 proteins, 81 and small molecules. 144 However, there is a key impediment to developing practical sensors based on this biological technology. This problem concerns the fragility of the supported lipid-bilayer membrane that houses the nanopore, which leads to extremely short lifetimes. 145 In order to replace the biological nanopore, artificial nanopores embedded in a mechanically and chemically robust synthetic membrane have been prepared. One of the techniques used to create these artificial nanopores is a microlithographic method, which uses a focused ion or electronbeam to bear the nanopore into a silicon or SiN membrane. In 30, 89 14 17 3 3 order 67

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to achieve specific counting and detection of analytes, such as DNA, DNA probe functionalized single nanopores have been used. 147 We and others have been exploring an alternative technology, named the track-etching method, 34, 37, 148, 149, 150 for preparing nanopores for resistive-pulse sensors. 130 In the current study, we describe selectively resistive-pulse sensing of short stranded DNA (40 bases) through a conically-shaped nanopores embedded in track-etched PET membrane. Numerous studies have been done before to understand the behavior of translocation of ssDNA and double stranded DNA through a nanopores. 14, 117-118 In order to improve the selective translocation of DNA through a nanopore, functionalized solid-state nanopore 147 has been used to selectively detect DNA. However the lifetimes of these selective nanopores will decrease after the conformation of immobilized probe DNA change due to translocation of the target DNA. Another issue concerning the functionalized nanopores is that one pore can be justly used to detect one certain target DNA. Here we explore another strategy of using a bare conically-shaped nanopore embedded in a PET polymer. The tip diameter of the nanopore is 9 nm with a 520 nm base diameter. The two Streptavidin conjugated DNA probes (20 base each) selectively hybridize a distinct part of the target DNA. As the size of Streptavidin conjugated DNA probes (4.5 nm x 4.5 nm) 151 is much smaller than the tip diameter of the conical nanopore, so the Streptavidin conjugated DNA probes can not be detected and be filtered on purpose. The size of the finally self-assembled complex was double than that of each Streptavidin conjugated DNA probe. Unspecific DNA will not induce the assembly of the two Streptavidin conjugated DNA probes. So we can easily distinguish the target DNA from unspecific DNA, using the conical-shaped nanopore in the polymer membrane. 68

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The analyte was driven electrophoretically through the conical nanopore (from base to tip), and these translocation events were observed as transient blocks in the ion current. Without the interference of free Streptavidin conjugated DNA probes, the current-pulse signatures can be associated with the final assembled complex induced by the target DNA. One of the advantages of this technique is that it has provided a simple approach without further purification processes 161 and functionalization procedures. 147 Experimental Materials and Methods 12 m thick poly(ethylene terephthalate) membranes (3 cm in diameter) irradiated with a single swift heavy ion of 2.2 GeV kinetic energy to create a single damaged track through the film were obtained from GSI Darmstadt, Germany. Biotin labelled Oligonucleotide probes, specific and unspecific DNA were purchased from Alpha DNA, Inc. Streptavidin and bis-tris propane was obtained from Sigma Aldrich. The oligonucleotide sequence for the Biotin labelled oligonucleotide probe 1 is Biotin-ACACACACACTCATCTGTGA-3, and the oligonucleotide sequence for probe 2 is 5-AGAGAACCTGGGATATATAT-Biotin. The sequence for target DNA is 5-ATATATATCCCAGGTTCTCTTCACAGATGAGTGTGTGTGT-3. The sequence for unspecific DNA is 5-ACACAAAACCTATGTACACATGACAGATGAGTGTGTGTGT-3. Preparation of the Conical Nanopores From Figure 4-1, it demonstrates a typical cell for fabricating the conical pore on the ion tracked PET membrane. One piece of ion-tracked PET membrane was mounted between the cells; the etching solution (9.0 M NaOH) was placed in one half of the cell and the stopping solution (1.0 M formic acid plus 1.0 M KCl) in the other half of the cell. Two platinum wire electrodes were immersed in two cells containing solution and a Keithley 6487 picometer voltage source (Keithley Instruments, Cleveland, OH) was used to apply a transmembrane 69

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potential difference of 1 V during etching, with polarity such that the anode was in the etch solution. Etching was terminated after two hours by replacing the solution in the etch half-cell with stop-etch solution. The membrane was then rinsed with purified water (Barnstead D4641, E-pure filters). The tip diameter obtained after the first etch was normally in the range of 1 to 7 nm 135 after 2 hours of the first step-etch, a second step-etch was applied to modulate the tip diameter of the conical nanopore. The etching solution (1 M NaOH) was placed on both sides of the conductivity cell. A platinum electrode was immersed into each half-cell solution, and the Keithley 6487 picometer voltage source was used to apply a transmembrane potential difference of 1 V and to measure the nanopore ion current. Etching was terminated at desired current values by replacing the etching solution in both half cells with the stopping solution. The membrane remained in the stop etch for at least 30 min and was then rinsed with purified water before measuring the current-voltage curve. Assembly of DNA-Protein Complex 100 l of Streptavidin solution (33 M in buffer 20 mM bis-tris propane, pH 9, 1 M KCl), was mixed with 10.7 l probe 1 (28 M in buffer 20 mM bis-tris propane, pH 9, 1M KCl) and 25 l probe 2 (12 M in buffer 20 mM bis-tris propane, pH 9, 1 M KCl), this mixture was diluted into 3 ml, and the final concentration for each molecule was 1.1 M for Streptavidin, 100 nM for Biotin labelled probe 1 and 100 nM for Biotin labelled probe 2. After 30 minutes reaction carried out between probes and Streptavidin, the abundance of Streptavidin was monovalent when the ratio exceeds up to 2.5. In previous paper, 153 It was confirmed that if the ratio of Streptavidin to Biotin-labelled DNA is above 2.5, the majority is monovalent conjugate. Here the ratio (5.5) we used is far beyond the ratio they used in order to make sure that the main product is monovalent. For the control experiment in the present study, the unspecific DNA was added into the Streptavidin conjugated probes solution with a final concentration of 100 nM in 3 ml. For the 70

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present study of target DNA sensing, the target DNA was added into the Streptavidin conjugated probes solution with the final concentration 100 nM in 3 ml. after the assembly lasts for 5 hours. The solution was added into the half cell facing the base opening. At pH 9, Streptavidin (pI ~7.0) 154 and DNA were highly negatively charged, therefore when applying negative potential on the electrode in the half cell facing base opening, the assembled complex would be driven from base to tip. Current-Pulse Measurements To measure the currents-pulse, the single pore embedded membrane was mounted in the cell. Both half cells were filled with ~3 ml of 20 mM bis-tris propane buffer solution (pH =9) that was also 1 M in KCl. An Ag/AgCl electrode ((BAS, West Lafayette, IN) was placed into each half-cell solution and connected to an axopatch 200B (Molecular Devices Corporation, Union City, CA) patch-clamp amplifier. The Axopatch was used to apply the desired transmembrane potential and to measure the resulting ion current flow through the electrolyte-filled nanotube. The current was recorded in the voltage-clamp mode with a low-pass Bessel filter at 2 kHz bandwidth. The signal was digitized using a Digidata 1233A analog-to-digital converter (Molecular Devices Corporation), at a sampling frequency of 10 kHz. Data were recorded and analyzed using pClamp 9.0 software (Molecular Devices Corporation). Results and Discussion Calculation of the Tip Diameter of the Single Conical Nanopore Three critical parameters including tip diameter and length and base diameter are used to define the conical-shaped nanopore. The area close to the tip opening is the sensing zone where the majority of nanopore resistance is located. Electrochemical technique is used to measure the tip diameters. 29 In a typical procedure, the membrane was mounted between two halves of a conductivity cell, and the half cells were filled with phosphate-buffered saline (100 mM 71

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NaH 2 PO 4 1M KCl). Keithley 6487 picometer voltage source and Ag/AgCl electrodes immersed in each solution were utilized to obtain a current-voltage curve for the nanopore. The experimental slope of this linear I-V curve between -0.2 V and 0.2 V is the ionic conductance, G, (in siemens S) of the nanopore which is given by 157 LddGtbkcl4)( (4-1) where kcl is the experimentally measured conductivity of the KCl-based electrolyte (Scm -1 ), L is the length of the nanopore (membrane thickness), is the experimentally measured diameter of the base opening, and is the diameter of the tip opening. bd td It is challenging to locate a single nanopore embedded in PET membrane using SEM. Second, a repeatable and accurate data are required to identify accurately both tip and base pore diameters. We have developed a series of techniques to control the etch rate and a model to calculate accurately the pore size. From our previous work, the etching rate calculated from multipore membranes was (2.17.19 nm/min) 135 and it was used to obtain the diameter of the base opening after the first step etching. The average base diameter is 520 45 nm after 2 hrs of etching. 135 The tip diameter obtained after the first etch was always in the range of 1 to 7 nm 135 after 2 hours of the first etching. In the present study, we assume the increase of both base diameter and tip diameter in second step-etch is equal. The final diameter of the base opening is equal to the summary of the diameter of the tip opening and 520 45 nm. The base diameter for this experiment is 530 nm. The conductivity of the buffer used for measurement is 117 (S.cm -1 ), the ionic conductance of the nanopore, G, calculated from the slope of the linear I-V curves, is 3.59186E-9(S). The calculated tip diameter from equation 4-1 for membrane 1 was 9 nm (Figure 4-2). 72

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Current-Pulses of the Self-Assembled Complex With buffer solution (20 mM bis-tris propane, 1 M KCl and 3 mM MgCl 2 ) in both half cells, a steady-state ion current of -3.7 nA (Figure 4-4A ) was observed for the bare conically shaped nanopore with tip diameter of 9 nm under transmembrane potential -1 V. The current was slight decreased to -3.5 nA after adding solution which contains 1.1 M Streptavidin, 100 nM probe 1, 100 nM probe 2, and 100 nM unspecific DNA into the half cell facing the base opening of the nanopore. The current was decreased, which is possibly due to the unspecific absorption of protein and DNA. No current-pulses were observed. Since the size of the single Streptavidin conjugated probe (4.5 nm) is much smaller than the tip diameter (9 nm) of conical nanopore and no link occurs between the two Streptavidin conjugated probes with the presence of unspecific DNA, no current-pulse was observed in such a condition. The currentpulse was observed after 100 nM target DNA has been added to the solution that contained 1.1 M Streptavidin, 100 nM probe 1 and 100 nM probe 2 in the half cell facing the base opening of the nanopore. Figure 4-4c depicts a typical currents-pulse that was generated from target DNA linked Streptavidin dimers. The continuous current-pulses indicate that the translocation of the target DNA-linked protein dimer. The histogram of current-pulse amplitude for solution that was 1.1 M Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA shows the average current amplitude (400 pA) (Figure 4-5). The statistics of the current-pulse duration predicts the distribution of the sizes of the mass transfer through the pore. A typical histogram currents-pulse duration of solution containing 1.1 M Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA is depicted in Figure 4-6, where a broadly distributed current-pulse duration was observed. The majority of these counts of the current-pulse durations are below 100 ms. It is concluded that the current-pulse 73

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below 100 ms is generated from the dimer, and the current-pulse above 100 ms is generated from multimer. These data are in accordance with previous data. 153 The above phenomenon can be explained through the structure of Streptavidin. Streptavidin has four binding sites available for binding Biotins through which four possible complexes can be formed: mono-, di-, triand tetracomplex. By increasing the ratio of Streptavidin to Biotin-labelled DNA up to 2.5, the majority of conjugates will be bi-valent complex with less tri-valent complex. In this project, we use the ratio up to 5.5 to ensure that the majority of the conjugates are dimers and to minimize trimers. Scatter plots of current-pulse amplitude, i, vs. current-pulse duration, t, are often used to summarize resistive-pulse data. 14, 27, 83, 130 The scatter plot for a solution that was 1.1 M Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA shows that the majority of pulses was located below 100 ms and other current-pulses were broadly distributed (Figure 4-7). These data also confirm the above conclusions that a current-pulse signature can be obtained for the protein dimer induced by target DNA. In addition, no current pulses were observed for a control solution containing unspecific DNA. These data proved that unspecific DNA does not bind protein conjugated probes. In order to reproduce the results, we etched another conicalshaped nanotube with a tip diameter of 10 nm. From the scatter plot (Figure 4-8) of a solution that contained 1.1 M Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA, data showed the same trend that we had concluded earlier. Under the transmembrane potential difference -1 V, very long current pulses of duration lasting for more than 12 s exist. The very long current-pulse duration event can be stopped by an increase of the voltage to -3 V. The protein mutimers (or multimers) causing these long current-pulse durations was forced to translocate through the 74

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sensing zone by increasing the trans-membrane potential difference. In order to get the current-pulses continually without interruption, we increased the voltage to -2 V. The scatter plot (Figure 4-9) of a solution that was 1.1 M Streptavidin, 100 nM probe 1, 100 nM probe 2 and 100 nM target DNA reinforce our point that this current pulse was caused by protein dimer or multimer. Conclusion We have presented here a new approach to sensing DNA through a conical-shaped nanopore embedded in PET polymer. The translocation of each protein conjugated probe is undetectable due to the size much smaller than the tip opening of the bare conical nanopore. On the contrary, the translocation of target DNA linked complex is detectable because the size of target DNA linked two components is double the size of each component and also comparable to the diameter of the tip opening of the nanopore. The sensing of target DNA can be accomplished by analyzing current-pulses due to translocation of the complex linked by target DNA. The concept of target analyte inducing self-assembling at the molecular level can be extended to detect small molecules and proteins based on a nanopore technique. 75

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Figure 4-1. Scheme of the experimental setup with the conductivity cell. The left compartment is filled with a stopping solution (1.0 M KCl and 1.0 M Formic acid), and the right compartment is filled with a etching solution (9.0 M NaOH). -0.2-0.10.00.10.2-0.8-0.6-0.4-0.20.00.20.40.60.8 Current(nA)Voltage(V) Figure 4-2. The current-voltage curve of conical pore in 1M KCl with applied -1.0 V voltage. The tip opening of the nanopore is 9 nm and the base opening is 530 nm. 76

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Figure 4-3. Analytical sensor based on conical nanopore embedded in PET membrane. In the absence of target DNA or in the existence of unspecific DNA, the translocation of Streptavidin conjugated DNA probes was not detectable from base to tip. The size of target DNA induced self-assembled DNA-protein complex is double that of Streptavidin conjugated DNA probes; the translocation of the complex will cause current-pulses. Figure 4-4. Current-time transients for a bare conical nanotube sensor with tip diameter =9 nm. (A) buffer only. (B) Buffer plus 100nM unspecific DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. (C) Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential for A, B and C was -1000 mV. 77

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20030040050060005101520253035404550 CountsPeak amplitude(pA) Figure 4-5. Histograms of DNA-protein complex current-pulse-peak amplitude data for nanotube with tip diameter =9 nm. Buffer plus 100nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV. 020004000100001200002468160180200 CountsDuration(ms) Figure 4-6. Histograms of DNA-protein complex current-pulse-duration data for nanotube with tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV. 78

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020004000600080001000012000160240320400480560640 Peak Amplitude (pA)Duration (ms) Figure 4-7. Scatter plot of current-pulse magnitude (i) vs. current-pulse duration (t) for DNA-protein complex Tip diameter =9 nm. Buffer plus 100 nM target DNA, 1.1 MStreptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV. 020040060080010001200140050100150200250300350400450 Peak amplitude(pA)Duration(ms) Figure 4-8. Scatter plot of current-pulse magnitude (i) vs. current-pulse duration (t) for DNA-protein complex Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -1000 mV. 79

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0200040006000800010000120001400002004006008001000 CountsDuration(ms) Figure 4-9. Scatter plot of current-pulse magnitude (i) vs. current-pulse duration(t) for DNA-protein complex Tip diameter =10 nm. Buffer plus 100 nM target DNA, 1.1 M Streptavidin and 100 nM probe 1 and 100 nM probe 2. Applied transmembrane potential was -2000 mV. 80

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CHAPTER 5 FUNCTIONALIZATION AND DIAMETER CONTROL OF SINGLE CONICAL NANOPORE IN ION-TRACK PET MEMBRANE VIA LAYER-BY-LAYER METHOD Introduction Resistive-pulse 105 sensors, which when applied to molecular and macromolecular analytes 14, 17, 19, 24, 27, 29, 79, 81, 82, 94, 105, 114, 121, 122, 142-145 are sometimes referred to as stochastic sensors, 105, 145 use a nanopore in a synthetic or biological membrane as the sensor element. In resistive pulse sensing, the membrane containing the nanopore is mounted between two electrolyte solutions, and analytes are driven through the nanopore by applying a transmembrane potential difference across the pore. The resulting ionic current flowing through the nanopore is measured and as the analytes translocate the nanopore downward current pulses are produced by the transient blocking of ion current. The frequency of such current pulses is proportional to the concentration of the analyte, and the magnitude and duration of the current pulse encodes the identity of the analyte. The majority of resistive pulse sensing work has utilized the biological protein nanopore, -hemolysin(-HL), embedded in a supporting lipid-bilayer membrane as the sensing element. The -HL nanopore can be made selective by biological or chemical engineering and has been used to detect numerous different analytes including metal ion, 121 DNA, 122, 143 proteins, 81 and small molecules. 144 However, there is a key impediment to developing practical sensors based on this biological technology. This problem concerns the fragility of the supporting lipid bilayer membrane that houses the nanopore, which leads to extremely short lifetimes. 145 In order to replace the biological nanopore, artificial nanopores embedded in a mechanically and chemically robust synthetic membrane 30, 89 have been prepared. The common technique used to create these artificial nanopores is a microlithographic method, using a focused ion 14 or electron 17 beam to bear the nanopore into a silicon or Si 3 N 3 membrane. In order to 81

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achieve specific counting and detection of analytes, Nilsson and co-workers 148 have locally functionalized single nanopores by combining controlled silicon oxide growth at the nanopore entrance with a silicon nitride layer and sliane chemistry. We and others have been exploring an alternative technology, called the track-etching method, 34, 37, 148-150 for preparing nanopores for resistive-pulse sensors. 19, 24, 27, 29, 30, 89 Biomolecules such as small molecules, 24 DNA, 19, 27 proteins 29 and nanoparticles 30 can be tested with this device. Furthermore,Virus sensors are developed based on track-etched nanopores. 89 Recent work from our lab has shown that highly selective sensors can be prepared by biofunctionalization of the conical gold nanotube embedded within a mechanically and chemically robust polymeric membrane. 29 In the present study, the layer-by-layer film-forming method, 155 based on the highly specific binding constant (10 15 M -1 ) between Biotin and Streptavidin, was used to modulate the tip diameter of the conical nanopore and to biofunctionalize the single conical nanopores. In our lab, the layer-by-layer film-forming method, 155 alternating ,-diorganophosphonate/Zr chemistry, has been utilized to prepare cylindrical nanotubes with accurately controlled inside diameter. 156, 157 The inner surface of these nanotubes can be further functionalized through the attachment of DNA. 148 Protein-functionalized nanotubes have also been prepared with the similar alternating strategy 158 : the alumina template membrane was alternately exposed to a solution of desired protein and then to a solution of glutaraldehyde. With this method the inside surface of the alumina membranes is functionalized with the desired protein. Unlike deposition of proteins inside the whole cylindrical nanotubes in alumina nanopores, 158 the deposition of proteins onto the sensing zone area of conical-shaped nanopore is the critical part of this work. Stability of the multilayers in the sensing zone is the prerequisite for further developing these nanopores into practical sensors. Single conical nanopores are fabricated in ion-tracked PET 82

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membrane by using a two-step etching procedure. 135 Multi-Biotin labelled bovine serum albumin, driven by applying a transmembrane potential difference from the large-diameter (base) opening to the small-diameter (tip) pore opening, was non-specifically adsorbed onto the inner surface of the nanopore as a first layer. Streptavidin specifically interacting with multi-Biotin labelled protein is then deposited as a second layer. Multilayers can be deposited by repeating the same procedure as that for depositing the second layer. In this way, the diameter of the tip opening can be adjusted by controlling the number of protein layers; the final layer can be any Biotin labelled biomolecule, for example, Biotin-labelled antibody, Biotin-labelled aptamer etc. Experimental Materials Poly(ethylene terephthalate) membranes (3 cm in diameter, 12 m in thickness) irradiated with a single swift heavy ion of 2.2 GeV kinetic energy to create a single damaged track through the film were obtained from GSI Darmstadt, Germany. Multi-Biotin labelled bovine serum albumin (BSA) and EZ-Link sulfo-NHS-LC-Biotin(sulfosuccinimidyl-6-(Biotinamido)Hexanoate) were purchased from Pierce. Streptavidin, Biotin labelled IgA and polylysine(MW70 kDa-150 kDa) were obtained from Sigma Aldrich. Preparation of the Conical Nanopores Figure 5-1 demonstrates a typical cell used for fabricating a conical pore on an ion-tracked PET membrane. One piece of ion-tracked PET membrane was mounted between the cells; the etching solution (9.0 M NaOH) was placed in one half cell and the stopping solution (1.0 M formic acid plus 1.0 M KCl) in the other half cell. Two platinum wire electrodes were placed in the two side solutions and a Keithley 6487 picometer voltage source (Keithley Instruments, Cleveland, OH) was used to apply a transmembrane potential difference of 1V during etching, with polarity such that the anode was in the etch solution. Etching was terminated after two 83

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hours by replacing the solution in the etch half-cell with stop-etch solution. The membrane was then rinsed with purified water (Barnstead D4641, E-pure filters). The tip diameter measurement obtained after the first etch was normally in the range of 1 to 7 nm 135 after 2 hours of the first step-etch, and the second step etch was applied to modulate the tip diameter of the conical nanopore. Etching solution (1 M NaOH) was placed in both sides of the conductivity cell. A platinum electrode was immersed into each half-cell solution, and the Keithley 6487 picometer voltage source was used to apply a transmembrane potential difference of 1 V and measure the nanopore ion current. Etching was terminated at desired current values by replacing the etching solution in both half cells with the stopping solution. The membrane remained in the stop etch for at least 30 min and was then rinsed with purified water before measuring the current-voltage curve. Determination of the Diameter of Nanopore It has been challenging to locate a single nanopore embedded in a PET membrane using SEM and we have developed a series techniques to control and determine the etch rate. From our previous work, the etching rate calculated from multipore membranes was (2.17.19 nm/min) 135 and was used to obtain the diameter of the base opening after the first step etching. The average base diameter was 520 45 nm after 2 hrs etching. 135 The tip diameter obtained after the first etch has always been in the range of 1 to 7 nm 135 after 2 hours of the first etching. In the present study, the final diameter of the base opening was equal to the sum of the tip diameter plus 520 45 nm. Layer-by-Layer Protein Assembly Proteins were dissolved in a phosphate buffer (50 mM, pH 7). The layer-by-layer deposition is illustrated in Figure 5-2. Multi-Biotin labelled BSA (3 M) was driven by applying a transmembrane potential difference (1.0 V) from the large-diameter (base) opening to the 84

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small-diameter (tip) pore opening for 1 hour, and the membrane was left in the same BSA solution overnight. Multi-Biotin labelled BSA was non-specifically adsorbed on the surface of the nanopore as the first layer. Streptavidin (0.5 M) filled in both half-cells was driven into the nanopore by alternately applying voltages of 200 mV and -200 mV for 2 hours. If more than three layers were deposited, the experimental conditions were the same as those for the second layer. In experiments where Biotin labelled IgA was used as a final layer, the concentration used was 200 nM. The conductivity cells were rinsed 3 times with DI water between each step. When Biotin labelled polylysine has been used for first layer, this step was slightly different. A 0.01(w/v)% polylysine solution filled in both half-cells was driven by applying a voltage (1 V) from the base opening to tip opening for 1 hour and left in the same solution overnight. After the conductivity cells were rinsed several times using DI water, NaHCO 3 (pH 8.5, 50 mM) buffer solution containing 50 mM Biotin linker was filled into cells and left to react for 1 hour. The experimental conditions for additional layers were the same as those described above. Results and Discussion Calculation of the Tip Diameter of the Single Conical Nanopore The tip diameter is measured electrochemically as previously reported. 29 Briefly, the membrane was mounted between two halves of a conductivity cell, and the half cells were filled with phosphate-buffered saline (100 mM NaH 2 PO 4 1 M KCl). Keithley 6487 picometer voltage source and Ag/AgCl electrodes immersed in each solution were utilized to obtain a current-voltage curve for the nanopore. The experimental slope of this linear I-V curve between -0.2 V and 0.2 V is the ionic conductance, G, (in siemens S) of the nanopore which is established by 37 LddGtbkcl4)( (5-1) 85

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where kcl is the experimentally measured conductivity of the KCl-based electrolyte (S.cm -1 ), L is the length of the nanopore (membrane thickness), is the experimentally measured diameter of the base opening, and is the diameter of the tip opening. bd td Controlling Tip Diameter of Single Conical Nanopore Our lab has developed two methods to control precisely the tip diameter of the conical nanopore: one method 135 is using the two-step etching to control the tip diameter; the second method 13 is using an electroless gold plating in the conical nanopore to adjust the tip diameter. In the paper 29 it has been demonstrateed that agents used for the molecular recognition containing gold concial nanotube can selectively detect proteins, Biotin labelled antibody was immobilized on the gold nanotube through protein-multilayers construction. Here we demonstrate that the tip diameter can be modulated by manipulating the layers of proteins that are based on the strong interaction between Biotin and Streptavidin on the bare conical nanopore embedded in PET. Mult-Biotin labelled BSA (3 M) was driven through the base opening by maintaining a transmembrane potential difference 1 V, It is easier to deposit the BSA onto the inner wall of the nanopore when driven from the base opening rather than from the tip opening due to the conical shape of the nanopore. After the membrane had been kept in protein solution overnight, the I-V curves were measured. The slope of the I-V curves for nanopore A (starting tip diameter of 33 nm) after non-specific deposition of muti-Biotin labelled BSA as the first layer had a different slope from that for the bare nanopore (Figure 5-3). The slope of the I-V curves is equivalent to the conductivity of the nanopore and will be used to determine the tip diameter (Table 3-1). After first layer deposition, the tip diameter decreased by 7 nm. Comparing the dimensions of BSA 159 with the decrease of tip diameter, it is found that the that deposition of one layer of BSA proteins on the tip area contributes to the decrease of tip 86

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opening. Therefore another different Streptavidin layer will be deposited on the first layer. Then the tip diameter decreases (6nm) after deposition of Streptavidin (4.5 nm 4.5 nm) 151 as the second layer, which is suggested to be the cause of drop of tip diameter. By controlling the number of layers of proteins, the tip diameter can be well adjusted to 9nm after deposition of 4 layers of proteins. If the final layer is Streptavidin, we can attach another Biotin-labelled biochemical molecular-recognition agents and use this single pore for sensing the target analytes. Multi-Biotin labelled polylysine (or other multi-Biotin labelled molecules) can also be absorbed on the nanopore wall and employed as the first layer. This was demonstrated by using bare PET nanopore B with a starting tip diameter of 71nm (Figure 5-4 and Table 5-2). From Figure 5-4 and Table 5-2, the tip diameter decreased by 1 nm after polylysine, which is constistent with the thickness between 0.7 nm and 1.3 nm of polylysine deposited on the glass substrate. 160-162 The diameter of the tip opening was successfully decreased to 45 nm after deposition of 5 layers of protein on the nanopore wall by alternative deposition of multi-Biotin labelled BSA and Streptavidin. The deposition of the first layer is very critical. In order to successfully deposit multi-Biotin labelled protein, a transmembrane voltage difference (1V) was applied to drive the protein from base to tip in order to increase the physical interaction between multi-Biotin labelled protein and the conical nanopore wall. The deposition of protein on the pore wall could be monitored by the change of current. The strong binding affinity between Biotin and Streptavidin (Kd = 10 -15 M) 155 was used to deposit the next layers for which voltage (200mV) was used to drive the protein into the tip area. In previous work, it was established that 29 even without applying voltage, Streptavidin could easily react with the Biotin attached on the nanopore wall. 87

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The corresponding current drop through the nanopore could be observed after each layer has been successfully deposited. Shown in Figure 5-5 and Table 5-3, shows a final layer of Biotin labelled IgA which was successfully attached to the second Streptavidin layer in nanopore C. The procedure for the deposition of the first layer and the second layer remained the same as that used for the deposition of protein in the nanopore A. From table 5-3, we can see the decrease of tip diameter after attaching protein IgA up to 5 nm from Table 5-3. Any other Biotin labelled molecular recognition agent may be attached to the protein nanopore in the same way. Stability of Protein Nanopore To investigate the stability of three types of membranes, The tests were conducted lasting for over a week long. The stability of nanopore A and C was great as illustrated in Figure 5-6. For nanopore C, the tip diameters in the first day and seventh day showed the same value 8.7 nm. Nanopore B also has a high stability during the test days. In the paper 157 It has been shown the multilayer proteins deposition in a cylindrical nanopore, crosslinker(glutaaldehyde) was however, not necessary in the present situation and rather resulted in a slight decrease of tip diameter after the application of crosslinker overnight for nanopore B. Nanopore B was immersed into a glutaradehyde solution (1% in 50mM phosphate buffer, PH 7.4) before storage. A 5nm decrease of the tip diameter was observed after cross linking. From Figure 5-6 it can be seen that nanopore B was stable during the test days. Conclusion We have presented here a new approach to control the conical pore diameter by applying layer-by-layer technique to fabricate multilayers of proteins within the conical pore inner surface. Multilayer constructions were based on the strong interaction between Streptavidin and Biotin-modified proteins. In addition, we can modify the nanopore with any biochemical 88

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molecular-recognition agents labelled with Biotin. These controllable single nanopores enabled us to investigate the sensing properties of species biomolecules, such as various sizes and biofunctional proteins. We believe the stability of this protein nanopore offers great potential for further practical applications as a biosensor. 89

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Figure 5-1. Scheme of the experimental setup with the conductivity cell. During etching the left compartment is filled with stopping solution (1.0 M KCl and 1.0 M formic acid), the right compartment is filled with etching solution (9.0 M NaOH). Figure 5-2. Schematic diagram for Layer-by-layer assembly of proteins on single conical PET membrane: (1) Bare single conical nanopore embedded in PET membrane, (2) non-specific deposition of multi-Biotin labelled protein as the first layer, (3) specific deposition of Streptavidin as the second layer, (4) specific deposition of multi-Biotin labelled protein as the third layer. 90

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-0.2-0.10.00.10.2-3-2-10123 nAV Figure 5-3. I-V curves after each assembly step with nanopore A: Black line(square) represents data for nanopore after second step etch, red line (circle) for nanopore after multi-Biotin labelled BSA nonspecific absorption, green line (triangle) for nanopore after Streptavidin adsorption, blue line (triangle) for nanopore after Biotin BSA adsorption, turquoise (square) for nanopore after Streptavidin adsorption. 91

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01234545505560657075 Diameter of tip opening(nm)Number of protein layers Figure 5-4. Diameter of tip opening as a function of the number of protein layers within nanopore B. The first layer is multi-Biotin labelled polylysine, second layer is Streptavidin, third layer is multi-Biotin labelled BSA, fourth layer is Streptavidin, and fifth layer is multi-Biotin labelled BSA. 123412141618202224262830 Diameter of tip opening(nm)Number of protein layers Figure 5-5. Diameter of tip opening as a function of different protein layer within nanopore C. The first layer is multi-Biotin labelled BSA, second layer is Streptavidin, and third layer is Biotin labelled IgA. 92

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123456710152025303540 Nanopore diameter(nm)Days Figure 5-6. Diameters of tip opening versus 7 days for three single nanopores. Black circle represents the tip diameter of nanopore A, green triangle represents that of nanopore B, blue square represents that of nanopore C. 93

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Table 5-1. Diameter of tip opening and base opening after each protein layer assembly within nanopore A. D0 represents initial pore size, D1, D2, D3 and D4 represent the pore size after deposition of Biotin labelled BSA, deposition of Streptavidin, deposition of Biotin labelled BSA and deposition of Streptavidin respectively. Diameter of tip opening (nm) after each layer deposition Diameter of base opening (nm) after each layer deposition D0 33 553 D1 26 546 D2 20 540 D3 15 535 D4 9 529 94

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Table 5-2. Diameter of tip opening and base opening after each protein layer assembly within nanopore B. D0 represents initial pore size, D1,,D2, D3, D4, D5 represent the pore size after deposition of multi-Biotin labelled polylysine, deposition of Streptavidin, deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of mulit-Biotin labelled BSA respectively. Diameter of tip opening (nm) after each layer deposition Diameter of base opening (nm) after each layer deposition D0 71 591 D1 70 590 D2 61 581 D3 53 573 D4 49 569 D5 45 565 95

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Table 5-3. Diameter of tip opening and base opening after each protein layer assembly within nanopore C. D0 represents initial pore size, D1, D2, D3 represent the pore size after deposition of multi-Biotin labelled BSA, deposition of Streptavidin and deposition of Biotin labelled IgA. Diameter of tip opening (nm) after each layer deposition Diameter of base opening (nm) after each layer deposition D0 29 549 D1 20 540 D2 18 538 D3 13 533 96

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CHAPTER 6 CONCLUSIONS There is increasing interest in using nanopores in synthetic or biological membranes as biosensors. In this dissertation, we have demonstrated that track-etched artificial conically shaped nanopore can be functionalized and tuned by layer-by-layer method and can be used to selectively sensing drug molecules based on ion-current rectification and DNA linked protein dimer without probes interference In chapter 2, a new paradigm making use of the well-known ion-current rectification phenomenon displayed by conically shaped nanopores is demonstrated. The sensor element in this case is a single conically shaped nanopore in a polyimide(Kapton) membrane. The sensing paradigm entails placing electrolyte solutions on either side of the membrane and using electrodes in each solution to scan the applied transmembrane potential and measure the resulting ion current flowing through the nanopore. As has been discussed in detail by us and others, conically shaped nanopores with excess surface charge on the pore walls, and sufficiently small tip openings, show non-linear current voltage curves; i.e., such pores are ion-current rectifiers. Because the polyimide nanopores used here have excess anionic surface charge, rectification is observed at positive applied tranmembrane potential. We have found that when the nanopore is exposed to a very hydrophobic yet cationic, drug molecule (Hoechst 33258), adsorption of this molecule on the pore walls neutralizes the excess negative surface charge. As a result the nanopore does not rectify as strongly, and the magnitude of the decrease in rectification scales with the concentration of the drug molecule. Ultimately at high concentrations of the drug, the sign of the excess surface charge switches from net negative to net positive, and the nanopore rectified at negative applied transmembrane potential. We describe this new nanopore-based sensing paradigm here. 97

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In chapter 3, we demonstrate the ability of conical nanopore embedded in polymer membrane to selectively sensing drug molecules based on ion current rectification phenomenon. As has been pointed out in chapter 2, hydrophobicity is the dominant force which contributes the absorption of positive drugs to the hydrophobic pore wall of Kapton membrane. This conclusion paves the foundation for exploration of selectivity based on hydrophobicity. We choose three positive drugs which have different hydrophobicity. In this chapter, we demonstrate the three hydrophobic drugs can be be totally discriminated due to the different binding constant. We believe this powerful sensing ability based ion current rectification can be extended to sense other interesting biomolecules, for example, DNA and protein. In chapter 4, we demonstrate promising tool for sensing DNA-linked protein dimmer which is relevant to biological process, for example, gene expression, DNA degradation and virus detection. The promising tool is a bare conically shaped nanopore embedded in track-etched PET membrane. Biotin-labeled DNA probe react with excess Streptavidin to from Streptavidin conjugated DNA probe. Two Streptavidin conjugated monovalent DNA probes can bind two distinct segments of target DNA. The size of target DNA linked complex is double that of each Streptavidin conjugated monovalent DNA probe. By precisely controlling the tip diameter of conical nanopore embedded in PET polymer, the events due to translocation of the streptravidin conjugated monovalent DNA probes through the nanopore can be filtered and undetected on purpose; the current-pulses due to translocation of the target DNA linked complex can be detected. In order to confirm that two Streptavidin conjuaged DNA probes are linked by target DNA ,we test if two protein conjugated DNA probes can be linked by multi-mismatched DNA. The multi-mismatched DNA will not induce the complex formation. The current-pulse signatures for the self-assembled complex can be used to confirm the existence of target DNA 98

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and DNA linked protein dimer. The concept of size dependent detection of self-assembled complex on molecule level shows strong promise for detection of biomolecules without interference of probes. In chapter 5, we demonstrate a new way to tailor the single conical nanopores embedded in PET (polyethylene terephthalate) membranes via a layer-by-layer assembly technique, which is based on strong interaction between Biotin and Streptavidin. Single conical nanopores are fabricated in ion-tracked PET membranes by using a two-step etch procedure. Multi-Biotin labeled BSA (or multi-Biotin labeled polylysine) was driven into the tip of the single conical nanopore from the base of the pore opening by applying a transmembrane potential difference (1V), and nonspecifically adsorbed onto the inner wall of the nanopore as a first layer. Streptavidin was then placed on both sides of the nanopore, and specifically interacted with the multi-Biotin labeled protein and was thus deposited as a second layer by alternately applying a transmembrane potential difference of 200mV and -200mV. Multilayers were formed by repeating the same procedure as for depositing the second layer. Most importantly, the diameter of tip opening can be adjusted by controlling the number of protein layers. The conical nanopore can also be made selective with this method by depositing any Biotin labeled ligand on the final layer, which can be used for specifically sensing target analytes. The layer-by-layer assembled conical protein nanopores have shown great stability and may allow for fabricating practical biosensors based on these conical nanopores. 99

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BIOGRAPHICAL SKETCH JiaHai Wang was born in a beautiful place in China. He spent 4-year undergraduate study in University of Hui Bei in Hui Bei province and obtained a B.S. in chemical engineering in June 2000. After that, he pursued masters degree in Dalian Institute of Chemical Physics, Chinese Academy of Science under the guidance of Dr. GuoZhong He and Dr. KeLi Han. In August 2003, after he obtained M.S. in physical chemistry, JiaHai Wang joined Dr. Charles R. Martins group in the Department of Chemistry at the University of Florida and continue his Ph.D. study in the fields of bio-nano. He completed his research in March 2008, obtaining a Doctor of Philosophy degree. 108