Solid-State Nanopore Sensors for Nucleic Acid Analysis - Nanopores: Sensing and Fundamental Biological Interactions - page 2

Keywords -hemolysin • phi29 • Nanopores in Al 2 O 3 Membranes • Surface

Charges in Nanopores • Surface Enhanced DNA Transport

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1.1 Introduction

Our quest to better understand the origins of inheritance, individuality, disease and
evolution has led to some of the greatest scientific and technological discoveries in
history. This journey has taken us from the macro-scale world that we live in, to the
micro-scale environments in which cells and bacteria operate, down to the nano-
scale in which single molecules of DNA, RNA and proteins exist. The discovery of
microorganisms in the late 1600s by Anton Van Leeuwenhoek laid the foundation
for modern microbiology and bacteriology, making possible the discovery of
processes such as cell division and cell differentiation. Gregor Mendel's discovery
of the laws of inheritance through observations involving the physical traits passed
on between generations of pea plants, laid the foundation for modern day genetics.
Latter work by Oswald Avery confirmed that this genetic information is carried by
deoxyribonucleic acid or DNA.
The discovery of DNA as the blue prints of life in all living organisms is of
fundamental importance in medicine and biology. DNA contains the instruction set
that is used to encode RNA and proteins, the machinery that drives all cellular
activity. Chemically, DNA consists of two long polymers composed of simple sub-
units called nucleotides arranged in a double helix structure. Each nucleotide contains
a sugar-phosphate backbone attached to one of four types of molecules called bases,
specifically Adenine, Thymine, Cytosine and Guanine. It is the sequence of these four
bases along the DNA backbone that encodes the genetic information that defines
the various characteristics of an organism. Due to the vast information content of
DNA and its importance in regulating cellular behavior, widespread research is
focused on the development of technologies applicable to DNA analysis.
Gel electrophoresis is the most commonly used tool in DNA analysis and is the
work-horse of conventional DNA Sanger sequencing platforms [ 73 ]. In gel electro-
phoresis, charged biopolymers are electrically driven through a 'gel', consisting of
a heterogeneous, three-dimensional matrix of pores ranging in diameter from a few
nanometers up to hundreds of nanometers. The gel is composed of either polyacryl-
amide or agarose depending on the specific weight and composition of the analyte
of interest. Electrophoresis of DNA is made possible by the charged nature of this
polymer in solution. The isoelectric point of the phosphate group on the DNA
backbone is ~1 resulting in a single negative charge per nucleotide under most
experimental conditions, including physiological pH. In solution, this charge
is partially shielded due to counterion condensation according to Manning
theory [ 57 ]. During gel electrophoresis, strong interactions between DNA and the
pore network result in the fine separation of even relatively similar molecular