Chain deformation helps translocation

TL;DR

This paper investigates how chain deformation of single-stranded DNA influences its translocation through a nanopore, combining analytical solutions and hybrid simulations to reveal deformation effects and hydrodynamic interactions.

Contribution

It introduces a multi-scale hybrid simulation approach and analytical modeling to understand the role of deformation and hydrodynamics in DNA translocation.

Findings

Deformation occurs before reaching the pore, aiding translocation.

Electric field gradients induce chain extension near the pore.

Hydrodynamic interactions significantly affect translocation dynamics.

Abstract

Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the electric field inside and outside of a narrow pore is obtained. With an analysis based on "electrohydrodynamic equivalence" we determine the possibility of extension of a charged polymer due to the presence of an electric field gradient in the vicinity of the pore entrance. With a multi-scale hybrid simulation (LB-MD), it is shown that an effective deformation before reaching the pore occurs which facilitates the process of finding the entrance for the end monomers. We also highlight the role of long range hydrodynamic interactions via comparison of the LB-MD results with those obtained using a Langevin thermostat instead of the LB solver.