Gregory Timp, Utkur Mirsaidov, Winston Timp, Jiwook Shim, Deqiang Wang,
Valentin Dimitrov, Jan Scrimgeour, Chunchen Lin, Jeffrey Comer, Anthony Ho,
Xueqing Zou, Aleksei Aksimentiev, and Klaus Schulten.
3rd generation DNA sequencing with a nanopore.
In Samir M. Iqbal and Rashid Bashir, editors, Nanopores: Sensing
and Fundamental Biological Interactions, chapter 12, pp. 287-312. Springer,
Berlin, 2011.
TIMP2011
With the advent of Next-Generation-Sequencing (NGS) technologies, an enormous volume
of DNA sequencing data can be generated at low cost, plac-ing 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 amplification 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.
