Ion assisted structural collapse of a single stranded DNA: a molecular dynamics approach

TL;DR

This study uses molecular dynamics simulations to show how divalent salt (MgCl2) causes single stranded DNA to initially collapse and then expand due to overcharging, highlighting differences from monovalent salt effects.

Contribution

It reveals the detailed effects of divalent salt on ssDNA structure and dynamics, emphasizing the role of overcharging and non-sequential base stacking, which was not well understood before.

Findings

Divalent salt causes ssDNA to collapse and then expand with increasing concentration.

Overcharging leads to chain swelling and structural changes in ssDNA.

Divalent salt effects differ significantly from monovalent salt interactions.

Abstract

The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of additional salt, a source of excess oppositely charged ions. Under such conditions single stranded DNA adopts a collapsed coil like conformation, typically characterized by stacking base pairs. Using atomistic molecular dynamics simulation, we demonstrate that in the presence of additional divalent salt (MgCl2) single stranded DNA (Dickerson Drew dodecamer) initially collapses and then expands with increasing salt concentration. This is due to the overcharging induced DNA chain swelling, a dominant factor at a higher divalent salt concentration. In a nutshell, our simulations show how in the presence of divalent salt, non-sequential base stacking and overcharging competes and affect single stranded DNA dynamics unlike a monovalent salt.