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Nanopores pp 287-311 | Cite as

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
  • Klaus Schulten
Chapter

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 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.

Keywords

Sequencing DNA Trapping DNA Comparison between biological and synthetic nanopores Molecular dynamics simulations Hydrodynamic focusing λ-DNA 

Notes

Acknowledgments

We gratefully acknowledge numerous contributions and our close collaboration with Jiunn Heng, Chuen Ho and Greg Sigalov. This work was funded by grants from National Institutes of Health [R01 HG003713A, PHS 5 P41-RR05969], the Large Resource Allocation Committee [MCA05S028], the Petroleum Research Fund (48352-G6), and the National Science Foundation [TH 2008–01040 ANTC, PHY-0822613 and DMR-0955959].

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Gregory Timp
    • 1
  • Utkur Mirsaidov
  • Winston Timp
  • Jiwook Shim
  • Deqiang Wang
  • Valentin Dimitrov
  • Jan Scrimgeour
  • Chunchen Lin
  • Jeffrey Comer
  • Anthony H. Ho
  • Xueqing Zou
  • Aleksei Aksimentiev
  • Klaus Schulten
  1. 1.Stinson-Remick HallUniversity of Notre DameNotre DameUSA

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