Dynamics of DNA translocation through an attractive nanopore
Loading...
Access rights
© 2008 American Physical Society (APS). http://www.aps.org
URL
Journal Title
Journal ISSN
Volume Title
School of Science |
A1 Alkuperäisartikkeli tieteellisessä aikakauslehdessä
Unless otherwise stated, all rights belong to the author. You may download, display and print this publication for Your own personal use. Commercial use is prohibited.
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.