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Nanopore-Based DNA Sequencing and DNA Motion Control

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Nanopores

Abstract

Compared to traditional Sanger’s DNA sequencing methods or currently commercialized next-generation-sequencing solutions (454, Roche, Basel; Solexa, Illumina, San Diego; SOLiD, Applied Biosystems, Foster City, CA, USA/Agencourt, Beverly, MA, USA; HelioScope, Helicos, Cambridge, MA, USA), nanopore-based DNA sequencing proposals have a number of advantages that fueled intense research efforts both in the industry and academia. If these efforts are successful, nanopore-based DNA sequencing will enable real-time single molecular DNA sequencing methods with little to no sample preparation. Nanopore sequencing has the potential to reduce the cost of sequencing of a whole human genome to less than $1,000. However, the road to conquer this technology is not without serious challenges. Two key issues in the field are to control the DNA translocation through the nanopore and to sense different DNA bases that compose the DNA molecule being sequenced. In this chapter, we present an overview of some commercial DNA sequencing technologies that will provide the context for our discussion of various nanopore DNA sequencing approaches. We will focus our discussion on the efforts to control the DNA translocation through the pore, as a step to realize the objective of nanopore-based DNA sequencing.

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Acknowledgments

The authors acknowledge useful discussions with members of the IBM DNA-transistor team: Ali Afzali, Arjang Hassibi, George Walker, Glenn Martyna, Philip Waggoner, Stanislav Polonsky, Stefan Harrer and Stephen Rossnagel. This work was supported in part by a grant from the National Institutes of Health (R01-HG05110-01).

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Authors and Affiliations

  1. IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA

    Hongbo Peng

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  1. Hongbo Peng
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  2. Binquan Luan
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  3. Gustavo Stolovitzky
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Corresponding author

Correspondence to Hongbo Peng .

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Editors and Affiliations

  1. Department of Electrical Engineering, Nanotechnology Research and Teaching Fac, University of Texas at Arlington, S. Cooper Street, Arlington, 76019-0119, Texas, USA

    Samir M. Iqbal

  2. Department of Electrical and Computer En, University of Illinois at Urbana-Champai, N. Wright Street 208, Urbana, 61820, Illinois, USA

    Rashid Bashir

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Peng, H., Luan, B., Stolovitzky, G. (2011). Nanopore-Based DNA Sequencing and DNA Motion Control. In: Iqbal, S., Bashir, R. (eds) Nanopores. Springer, Boston, MA. https://doi.org/10.1007/978-1-4419-8252-0_11

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  • DOI: https://doi.org/10.1007/978-1-4419-8252-0_11

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  • Online ISBN: 978-1-4419-8252-0

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