Dynamics of DNA translocation through an attractive nanopore

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© 2008 American Physical Society (APS). http://www.aps.org
Journal Title
Journal ISSN
Volume Title
School of Science | A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Date
2008
Major/Subject
Mcode
Degree programme
Language
en
Pages
061911/1-7
Series
Physical Review E, Volume 78, Issue 6
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.
Description
Keywords
DNA, translocation, nanopore
Other note
Citation
Luo, Kaifu & Ala-Nissilä, Tapio & Ying, See-Chen & Bhattacharya, Aniket. 2008. Dynamics of DNA translocation through an attractive nanopore. Physical Review E. Volume 78, Issue 6. P. 061911/1-7. ISSN 1539-3755 (printed). DOI: 10.1103/physreve.78.061911.