Sequence dependence of DNA translocation through a nanopore

TL;DR

This study uses simulations to explore how DNA sequence composition and orientation affect translocation dynamics through nanopores, revealing potential for structural analysis based on translocation behavior.

Contribution

It demonstrates that DNA sequence details influence translocation times and that sequence periodicity can be inferred from residence time patterns, advancing nanopore-based DNA analysis.

Findings

Translocation time depends on DNA block length and orientation.

Sequence periodicity affects nucleotide residence times.

Measurement can reveal DNA structural information.

Abstract

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {\em block length} $2n$ as well as on the {\em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.