Dynamics of DNA translocation through an attractive nanopore

TL;DR

This study uses 2D Langevin dynamics simulations to explore how DNA sequence composition and orientation affect translocation times through an attractive nanopore, revealing potential for rapid DNA sequencing.

Contribution

It introduces a coarse-grained DNA model with variable base-pore interactions to analyze sequence-dependent translocation dynamics and pattern recognition.

Findings

Translocation time decreases exponentially with the volume fraction of base C.

Orientation of DNA affects translocation time for longer sequences with certain compositions.

Waiting time patterns can determine DNA sequence parameters such as repeat units and length.

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 $A_mC_n$, 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 $A_mC_n$, 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.