High temperature unfolding simulations of a single stranded DNA i-motif

TL;DR

This study uses high-temperature molecular dynamics and biased metadynamics simulations to analyze the unfolding pathways of a DNA i-motif, revealing consistent unfolding mechanisms across different temperatures.

Contribution

It provides a comparative analysis of DNA i-motif unfolding at different temperatures using advanced simulation techniques, highlighting consistent pathways and dynamics.

Findings

Unfolding pathways are similar at 300 K and 500 K.

Unfolding involves a few dominant eigenvectors.

Two main unfolding mechanisms identified.

Abstract

We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement of the concerted motion at both temperatures. The transition can be described by a few number of eigenvectors indicating a simple unfolding process. Two main mechanisms for the unfolding pathway at 500 K can be detected which are in good agreement to the results of the biased simulation at 300 K.