Third Generation DNA Sequencing with a Nanopore - Nanopores: Sensing and Fundamental Biological Interactions - page 287

Chapter 12
Third Generation DNA Sequencing
with a Nanopore

Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim,
Deqiang Wang, Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin,
Jeffrey Comer, Anthony H. Ho, Xueqing Zou, Aleksei Aksimentiev,
and Klaus Schulten

Abstract With the advent of Next-Generation-Sequencing (NGS) technologies, an
enormous volume of DNA sequencing data can be generated at low cost, placing
genomic science within the grasp of everyday medicine. However, mired in this
voluminous data, a new problem has emerged: the assembly of the genome from the
short reads. In this chapter we examine the prospects for sequencing DNA using a
synthetic nanopore. Nanopore sequencing has the potential for very long reads,
reducing the computational burden posed by alignment and genome assembly,
while at the same time eliminating logistically challenging and error-prone ampli-
fication and library formation due to its exquisite single molecule sensitivity. On the
other hand, long high fidelity reads demand stringent control over both the DNA
configuration in the pore and the translocation kinetics. We examine the prospects
for satisfying these specifications with a synthetic nanopore.

Keywords Sequencing DNA • Trapping DNA • Comparison between biological
and synthetic nanopores • Molecular dynamics simulations • Hydrodynamic
focusing •

-DNA

λ

12.1 Introduction

The Sanger method of DNA sequencing has transformed biology - it has given us the
first draft of the human genome at a price tag of about $2.7 billion [ 1 , 2 ]. The basis for
Sanger sequencing is the polymerase chain reaction (PCR), which is used in combi-
nation with dideoxy-terminated nucleotides to prematurely terminate the elongation
reaction. By mixing fluorescently labeled dideoxynucleotides with deoxynucleotides,
PCR is prematurely terminated, leading to fragmentary single-stranded copies of the