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Publication Citation: The Effects of Diffusion on an Exonuclease/Nanopore-Based DNA Sequencing Engine

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Author(s): Joseph E. Reiner; Joseph W. Robertson; Arvind K. Balijepalli; Daniel L. Burden; Bryon S. Drown; John J. Kasianowicz;
Title: The Effects of Diffusion on an Exonuclease/Nanopore-Based DNA Sequencing Engine
Published: December 07, 2012
Abstract: The ability to electronically detect and characterize individual polynucleotides as they are driven through a single protein ion channel may eventually prove useful for rapidly sequencing DNA (base-by-base) in a ticker tape-like fashion. More recently, a variation on this method was proposed to use the nanopore to instead detect single nucleotides cleaved sequentially by an exonuclease enzyme in close proximity to one entrance of the nanopore. We analyze the exonuclease/nanopore-based DNA sequencing engine using analytical theory and computer simulations that describe the transport of the nucleobases. The available data and analytical results suggest that the proposed method will be limited to reading < 70 bases, imposed in part by the short lifetime each nucleotide spends in the vicinity of the detection element within the pore and the ability to accurately discriminate between the four mononucleotides. Suggestions on how to improve the method are provided.
Citation: Journal of Chemical Physics
Volume: 137
Issue: 21
Pages: pp. 214903 - 214903-7
Keywords: DNA sequencing; Nanopore
Research Areas: Medical Devices, Single Molecule Biophysics, DNA, Bioscience & Health
DOI: http://dx.doi.org/10.1063/1.4766363  (Note: May link to a non-U.S. Government webpage)
PDF version: PDF Document Click here to retrieve PDF version of paper (3MB)