Effect of salt concentration on the stability of heterogeneous DNA

TL;DR

This study investigates how salt concentration influences the stability of heterogeneous double-stranded DNA by modeling the effects of cations on DNA dissociation and stacking energies, comparing theoretical phase diagrams with experimental data.

Contribution

It introduces modifications to the Peyrard-Bishop-Dauxois model to analyze cation effects on heterogeneous DNA stability, linking salt concentration to molecular interactions.

Findings

Cation concentration affects DNA melting temperature.

Modified model aligns with experimental force-extension data.

Salt shields negative charges, stabilizing DNA structure.

Abstract

We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution, act as shielding agents thereby reducing the repulsion between these strands. We study several heterogeneous DNA molecules. We calculate the phase diagrams for DNA molecules in thermal as well as in force ensembles using Peyrard-Bishop-Dauxois (PBD) model. The dissociation and the stacking energies are the two most important factors that play an important role in the DNA stability. With suitable modifications in the model parameters we investigate the role of cation concentration on the stability of different heterogeneous DNA molecules. The objective of this work is to understand how these cations modify the strength of different pairs or bases along the strand. The phase diagram for the force ensemble case (a dsDNA is pulled from an end) is compared with the experimental results.