Molecular dynamics simulation of multivalent ion mediated DNA attraction

TL;DR

This study uses molecular dynamics simulations to analyze how multivalent ions mediate attraction between DNA molecules, revealing ion bridge formation as a key mechanism.

Contribution

It provides detailed atomistic insights into DNA attraction mediated by various multivalent ions, highlighting the role of ion bridges and their dynamics.

Findings

Ion bridges form between DNA molecules in the presence of multivalent ions.

Attractive forces are mediated by transient ion bridges.

Ion bridge lifetimes are on the order of a few nanoseconds.

Abstract

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e. multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.