Molecular dynamics simulations of a single stranded (ss) DNA

TL;DR

This study uses molecular dynamics simulations to analyze the conformational stability of a 12-base ssDNA model under different thermodynamic conditions, aiding biosensor development.

Contribution

It provides detailed atomistic insights into ssDNA behavior in various thermodynamic ensembles using MD simulations, which was previously less explored.

Findings

ssDNA stability varies with thermodynamic conditions

Conformational changes depend on temperature and pressure

MD simulations reveal detailed backbone dynamics

Abstract

The objective of the present study was to develop an understanding of short single-stranded DNA (ssDNA) to assist the development of new DNA-based biosensors. A ssDNA model containing twelve bases was constructed from the 130-145 codon sequence of the p53 gene. Various thermodynamic macroscopic observables such as temperature, energy distributions, as well as root mean square deviation (RMSD) of the nucleic acid backbone of the ssDNA were studied using molecular dynamics (MD) simulations. The AMBER program was used for building the structural model of the ssDNA, and atomistic MD simulations in three different ensembles were carried out using the NAMD program. The microcanonical (NVE), conical (NVT) and isobaric-isothermal (NPT) ensembles were employed to compare the equilibrium characteristics of ssDNA in aqueous solutions. Our results indicate that the conformational stability of the ssDNA is dependent on the thermodynamic conditions.