Rupture of DNA Aptamer: new insights from simulations

TL;DR

This study uses simulations to explore how base-pockets and binding-pockets affect DNA aptamer stability, revealing differences in separation behavior under temperature and force that warrant further experimental validation.

Contribution

It provides new insights into the molecular mechanisms by which base-pockets and binding-pockets influence DNA aptamer stability through combined coarse-grained and atomistic simulations.

Findings

Differences in separation behavior under thermal fluctuations and force.

Binding-pockets enhance aptamer stability.

Simulation results suggest new experimental directions.

Abstract

Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules e.g. adenosinemonophosphate(AMP), adenosinetriphosphate(ATP) etc, form additional hydrogen bonds with base-pockets termed as "binding-pockets", which enhance the stability. Using the Langevin Dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single molecule experiments.