Influence of pore dielectric boundaries on the translocation barrier of DNA

TL;DR

This study examines how dielectric boundary forces affect DNA translocation through nanopores, showing that polarization significantly increases the energy barrier and alters ion distributions, with implications for nanopore sensing.

Contribution

It introduces an efficient computational method to evaluate polarization effects on DNA translocation barriers in nanopores, considering salt and counterion distributions.

Findings

Polarization effects significantly increase the translocation free energy barrier.

Induced charges alter counterion distributions around DNA.

Adding salt influences the electrostatic interactions during translocation.

Abstract

We investigate the impact of dielectric boundary forces on the translocation process of charged rigid DNA segments through solid neutral nanopores. We assess the electrostatic contribution to the translocation free energy barrier of a model DNA segment by evaluating the potential of mean force in absence and presence of polarization effects by means of coarse-grained molecular dynamics simulations. The effect of induced polarization charges has been taken into account by employing ICC*, a recently developed algorithm that can efficiently compute induced polarization charges induced on suitably discretized dielectric boundaries. Since water has a higher dielectric constant than the pore walls, polarization effects repel charged objects in the vicinity of the interface, with the effect of significantly increasing the free energy barrier. Another investigated side effect is the change of the counterion distribution around the charged polymer in presence of the induced pore charges. Furthermore we investigate the influence of adding salt to the solution.