Abstract

We present the results of high temperature 500 K Molecular Dynamics simulations of a single-stranded DNA i-motif. The unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a remarkable agreement between the trajectories. We found that the unfolding process can be described by two main mechanisms with a small number of eigenvectors.

Keywords: DNA i-motif, Molecular Dynamics, Metadynamics, High temperature unfolding, trajectories, eigenvectors, square deviation, applied methods, Nose-Hoover, equilibrium