Designing abiotic single nanotube membranes for bioanalytical and biomedical applications

2004·3.8 MB·English

by  Harrell, Christopher Chad

DESIGNING ABIOTIC SINGLE NANOTUBE MEMBRANES FOR
BIOANALYTICAL AND BIOMEDICAL APPLICATIONS
By
CHRISTOPHER CHAD HARRELL
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
2004
This document is dedicated to Tracy, Jodi, Otis, and Linda Harrell.
11
ACKNOWLEDGMENTS
I would like to thank Dr. Charles Martin and the entire Martin group members for
the opportunityto work with them over the course ofmytenure. Dr. Martin was
continuously supportive in guidance throughout my scientific development at the
University ofFlorida. Also, I would like to thank Dr. Martin for teaching me the ability
to become an effective scientific communicator. The Martin group members have been
very supportive and terrific examples ofingenuity and perseverance. Drs. Punit Kohli,
Zuzanne Siwy, Marc Wirtz, and Sang Bok Lee showed great patience in offering many
hours ofguidance and helpful ideas. Elizabeth Heins, Robbie Sides, Damian Odoms,
Dave Mitchell, and Buck Batson gave insightful advice on experimental ideas and design.
I would hke thank Buck Batson, Chris Baker and Robbie Sides for helping me
enjoy my time during my stay at University ofFlorida. I would like to thank my loving
wife, Tracy Harrell, for all ofher endless hours oflove and support throughout my
graduate studies. Also, I want to thank my parents Otis, and Linda Harrell, and my sister,
Jodi Harrell, for their love and support. Finally, I want to thank my family and loved
ones for instilling in me the ambition to continuously grow and succeed in life.
HI
TABLE OF CONTENTS
page
ACKNOWLEDGMENTS
iii
LIST OF FIGURES vii
INTRODUCTION AND BACKGROUND
1 1
Introduction 1
Background 2
Ion Track-Etch Process 2
Formation ofLatent Ion Tracks 3
Selective Etching ofIon Tracks 3
Template Synthesis 7
Synthetic Strategies in Template Synthesis 8
Electroless Deposition 8
Biological Ion Channels 12
Potassium Voltage-Gated Ion Channel 13
Resistive-Pulse Sensing (Stochastic Sensing) 17
Dissertation Overview 22
2 SYNTHETIC SINGLE NANOPORE AND NANOTUBE MEMBRANES 25
Introduction 25
Background 26
Experimental 28
Materials 28
Pore Etching 28
Isolating a Single Nanopore 28
Field-Emission Scanning Electron Microscopy (FESEM) 29
Electrochemical Measurements 31
Gold Nanotube Membranes 31
Results and Discussion 32
Microscopy 32
Electrochemical Measurements 34
A Single Au Nanotube Membrane 39
Conclusions 41
IV
FABRICATION OF ASYMMETRIC NANOTUBES WITHIN AN ABIOTIC
3
PLATFORM 45
Introduction 45
Experimental 46
Materials 46
Conical Pore Etching 47
Single Nanopore Membranes 47
Field-Emission Scanning Electron Microscopy (FESEM) 49
Results and Discussion- 49
Membrane Characterization 49
Nanopore Geometry 51
Conclusion 54
4 DNA-NANOTUBE ARTIFICIAL VOLTAGE-GATED ION CHANNELS 56
Introduction 56
Experimental 58
Materials 58
Pore Etching 59
Single Conical Nanopore Membranes 59
Field-Emission Scanning Electron Microscopy (FESEM) 60
Conical Au Nanotube Membranes 61
DNA
Modification 61
Polylysine Modification 62
Electrochemical Measurements 62
Results and Discussion 63
Membrane Characterization 63
DNA Modified Single Nanotube Membrane 64
Polylysine Modified Au Nanotubes 71
Determination ofNanotube Permselecfivity 72
Conclusion 79
5 ABIOTIC NANOPORES FOR SINGLE MOLECULE DETECTION 81
Introduction- 81
Experimental- 82
Materials 82
Conical Pore Etching 83
Single Nanopore Membranes 84
Electrochemical Measurements and Data Acquisition 85
Results and Discussion 85
Membrane Characterization 85
DNA
Single Stranded Translocation Kinetics 88
DNA DNA
Discriminafion ofSingle Stranded and Plasmid 94
Conclusion 97
CONCLUSION 99
5
LIST OF REFERENCES 102
BIOGRAPHICAL SKETCH 114
VI
LIST OF FIGURES
Figure page
1-1. (a) Principle of ion track-etching technique, (b) Swift heavy ions forming latent
ion tracks in dielectric solid, (c) Selective etching, resulting in an array of etch
troughs, pores, or channels 4
1-2. Definition ofcone half-angle a, bulk etch rate Vb and track etch-rate vj 5
1-3. Chemical structure ofpolycarbonate (PC) 6
1-4. Scanning electron images of different nanostructured materials developed by the
ion-track-etchingprocess, (a) PC (b) PET (c) Glass and (d) Mica 7
1-5. Scanning electron micrographs oftemplate membranes, (a) Polycarbonate track-
etched membrane and (b) AI2O3 membrane 9
1-6. Schematic diagram ofAu electroless plating procedure 10
1-7. Schematic illustration of Au nanotubes obtained fi^om the use of the electroless
gold deposition method 11
1-8. Schematic representation ofthe functional units ofa potassium voltage-gated ion
channel 14
1-9. Electromechanical gating mechanism of the biological potassium voltage-gated
ion channel 15
1-10. Current-voltage curve ofion current rectification within potassium voltage-gated
ion channel 16
1-11. Schematic illustration ofresistive-pulse sensing 18
1-12. Essential features of the staphylococcal x-hemolysin pore shown in a cross
section based on the crystal structure 20
A
2-1 schematic diagram ofthe isolation process using fluorescence microscopy. .30
. .
2-2. A fluorescent and Scanning electron micrograph of single 30 nm nanopore using
the isolation process 33
Vll
2-3. A fluorescent and scanning electron micrograph ofsingle 55 nm nanopore 34
A
2-4. plot of observed pore diameter versus etching time in 12-micron thick
polycarbonate films 35
2-5. FESEM image of a complete (12-|jm long) Au nanowire. Insets show magnified
views ofthe nanowire ends 36
A
2-6. plot ofmeasured and calculated values ofionic current versus number ofpores
in the membrane with apore diameter of55 nm 37
A
2-7. plot of ionic current versus applied potential across a single pore membrane
with a diameter of55 nm 38
2-8. A plot ofionic current versus Pore diameter^ ofsingle pore membranes 39
2-9. A plot of ionic current versus applied potential across a single Au nanotube
membrane 40
3-1. Eletrochemical etching cell 48
3-2. Scanning Electron micrographs ofthe large diameter ofa single conical nanopore
V
fabricated under the conditions of (a) 0.0 V, (b) 15.0 V, and (c) 30.0 applied
during the etching process 50
3-3. The change in pore diameter on the side exposed to the etching solution with
applied potential during the etching process 50
3-4. SEM ofAu conical nanowires ofpore geometry at (a) 0.0 V, (b) 15.0 V, and (c)
V
30.0 appHed during the pore etching process 51
3-5. RJR for three conical pores with the same J,=20 nm and di, equal 5 |am (upper), 3
|j,m (middle) and 1 \ira (lower), respectively 53
4-1. Scanning electron micrographs ofa conical nanopore. (a) neutralizing side before
electroless gold plating, (b) etch side before electroless gold plating, (c) the shape
ofsingle conical nanopore through the entire length ofthe membrane 64
4-2. (a) The current-voltage characteristics of a single conical gold nanotube. (b)
Tailoring the rectification properties of the single conical gold nanotube
membrane by ssDNA modification, (c) Extent of rectification of ( ) 30-mer
hairpin DNA, (•) 30-mer HS-ssDNA and (-) unmodified single gold nanotube
membrane 66
4-3. The effect ofrectificafion by changing the pore diameter (•) 27 nm, (A) 39 nm,
( ) 59 nm, and (+) 98 nm single gold nanotube membrane. The diameter ofthe
large opening was ~5 \im 69
viu
4-4. I-V curve for apolylysine modified Au nanotube 72
4-5. Current-voltage curve calculated from Eq. 4-2 74
4-6. Current-voltage curve calculated for an ideally CI permselective membrane 75
4-7. Current-voltage curve calculated for a non-permselective membrane 76
4-8. Current time traces of(a) no ssDNA present (b) 5 nM ssDNA non-complementary
to the ssDNA modified nanotube membrane and (c) 5 nM ssDNA that is
complementary to the ssDNA modified nanotube membrane 78
4-9. A single blockade event of (a) 5 nM ssDNA non-complementary to the ssDNA
modified nanotube membrane and (b) 5 nM ssDNA that is complementary to the
ssDNA modified nanotube membrane 78
5-1. FESEM image of the single nanopore membrane, (a) Surface image of the
nanopore that was exposed to the neutralizing solution, (b) Surface image ofthe
side of the membrane exposed to the etchant solution, (c) Au nanowire
representing the shape ofthe nanopore throughout the length ofthe membrane. .86
5-2. Current-time analysis of single nanopore membrane.(a) Ionic current
mV
measurement ofat 900 in the absence ofssDNA. (b) Blockade events of 10
nm ssDNA at an applied potential of 900 mV. (c) Single blockade event due to
the translocation ofa single ssDNA molecule 88
5-3. (a) Event diagram showing blockade level vs. translocation duration for 10 nM
ssDNA at 900 mV. (b) Current histogram for the above event diagram, (c) The
translocation duration histogram 89
5-4. Concentration dependence of ssDNA translocation events. The ssDNA was
added to the small pore side with an applied potential to the large pore side of900
mV
90
5-5. Voltage characteristics of ssDNA translocation events, (a) Plot of event duration
vs. the inverse of the applied potential, (b) The characteristic shape of the
translocafion event changes with the applied potential 91
5-6. (a) Blockade events of 10 nm Plasmid DNA at an applied potential of 900 mV.
(b) Single blockade event due to the Bumping ofa single Plasmid DNA molecule
at the mouth ofthe nanopore 92
5-7. (a) Event diagram showing blockade level vs. event duration for 10 nM Plasmid
DNA at 900 mV. (b) Current blockade histogram for the plasmid DNA bumping
events, (c) The event duration histogram for the plasmid DNA bumping 93
5-8. Blockade events of a mixture of Plasmid DNA and ssDNA at 10 nM with an
mV
applied potenfial of900 95
IX
5-9. (a) Event diagram showing current blockade vs. event duration for the solution
DNA
mixture of Plasmid and ssDNA. (b) The event duration histogram for the
plasmid DNA and ssDNA mixture at 10 nM with 900 mV applied potential, (c)
Current blockade histogram for the plasmid DNA and ssDNA mixture 96