DNA in nanopore-counterion condensation and coion depletion

TL;DR

This study uses molecular dynamics simulations to analyze how DNA affects ion distribution in nanopores, revealing counterion condensation and coion depletion, which are crucial for understanding DNA translocation.

Contribution

The paper provides detailed insights into ion behavior around DNA in nanopores, highlighting effects not previously characterized in such systems.

Findings

Counterions condense on DNA, neutralizing it

Coions are nearly completely depleted from the pore

Results have implications for DNA translocation experiments

Abstract

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through alpha-hemolysin nanopores are discussed.