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

Published

December 7, 2012

Author(s)

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

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

Pub Type

Journals

Download Paper

https://doi.org/10.1063/1.4766363

Local Download

Keywords

DNA sequencing, Nanopore

Citation

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], https://doi.org/10.1063/1.4766363, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=911429 (Accessed October 15, 2025)