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

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.