Dynamics of DNA translocation through an attractive nanopore
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 A(m)C(n), we find that the translocation time decreases exponentially as a function of the volume fraction f(C) of the base C. For longer A sequences with f(C)<= 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 A(m)C(n), 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.
Physical Review E
"Dynamics of DNA translocation through an attractive nanopore" (2008). Faculty Bibliography 2000s. 659.