Dynamics of DNA translocation through an attractive nanopore

Kaifu Luo, Tapio Ala-Nissilä, See-Chen Ying, Aniket Bhattacharya

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42 Citations (Scopus)
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Abstract

We investigate the dynamics of single-stranded DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases A and C, having different base-pore interactions, e.g., a strong (weak) attractive force between the pore and the base A (C) inside the pore. From a series of studies on hetero-DNAs with repeat units AmCn, we find that the translocation time decreases exponentially as a function of the volume fraction fC of the base C. For longer A sequences with fC⩽0.5, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length N with repeat units AmCn, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of m, n, and N, respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection.
Original languageEnglish
Article number061911
Pages (from-to)1-7
JournalPhysical Review E
Volume78
Issue number6
DOIs
Publication statusPublished - 2008
MoE publication typeA1 Journal article-refereed

Keywords

  • DNA
  • nanopore
  • translocation

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