Dynamics of DNA translocation through an attractive nanopore

Abstract

We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) 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, {\textit 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 $C$. %(${\epsilon }_{pC}<{\epsilon }_{pA}$). For longer $A$ sequences with $f_C\le 0.5$, 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 technic.

7 pages, 7 figures

References in corpus (14)

• Influence of polymer-pore interactions on translocation
• Sequence dependence of DNA translocation through a nanopore
• Langevin Dynamics Simulations of Polymer Translocation through Nanopores
• Polymer translocation through a nanopore - a showcase of anomalous diffusion
• Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion
• Anomalous Dynamics of Unbiased Polymer Translocation through a Narrow Pore
• Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''
• Dynamical Scaling Exponents for Polymer Translocation through a Nanopore
• Pore-blockade Times for Field-Driven Polymer Translocation
• Hydrodynamic correlations in the translocation of biopolymer through a nanopore: theory and multiscale simulations
• Heteropolymer translocation through nanopores
• Passage Times for Polymer Translocation Pulled through a Narrow Pore
• Polymer Translocation out of Planar Confinements
• Probability distributions for polymer translocation

Cited by in corpus (2)

• Translocation Dynamics with Attractive Nanopore-Polymer Interactions
• Polymer translocation out of confined environments