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



Joseph E. Reiner, Joseph W. Robertson, Arvind Balijepalli, Daniel L. Burden, Bryon S. Drown, John J. Kasianowicz


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.
Journal of Chemical Physics


DNA sequencing, Nanopore


Reiner, J. , Robertson, J. , Balijepalli, A. , Burden, D. , Drown, B. and Kasianowicz, J. (2012), The Effects of Diffusion on an Exonuclease/Nanopore-Based DNA Sequencing Engine, Journal of Chemical Physics, [online],, (Accessed June 23, 2024)


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Created December 6, 2012, Updated October 12, 2021