Luo Kaifu, Ala-Nissila Tapio, Ying See-Chen, Bhattacharya Aniket
Department of Applied Physics, Helsinki University of Technology, P.O. Box 1100, FIN-02015 TKK, Espoo, Finland.
Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Dec;78(6 Pt 1):061911. doi: 10.1103/PhysRevE.78.061911. Epub 2008 Dec 9.
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<or=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.
