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Dynamics of DNA translocation through an attractive nanopore
Kaifu Luo1, Tapio Ala-Nissila, See-Chen Ying
1Department of Applied Physics, Helsinki University of Technology, P.O. Box 1100, FIN-02015 TKK, Espoo, Finland. luokaifu@gmail.com
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
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