Evaluation of Modeling the Influence by Monovalent Cations in DNA Structure on Very Cation Sensible Structures ‘G-Quadruplex DNA’ using Molecular Dynamics with Charmm Force Field

Abstract

The structure of bio-molecules such as DNA and RNA depends strongly on the cation binding sites. Epigenetic regulation mechanism may depend in part on the structure of DNA and its ability to interact with regulatory proteins. Understanding of the dynamic role of cations on DNA structure and how they get affected by several modifications involved in chromatin remodeling will give light on how exactly these mechanisms control such complicated scenarios. Nevertheless, even the location and effect of the cations on DNA or RNA structure on simple systems (protein free) is not clearly understood or predictable, or how well we can model such systems with the current available modeling methods. We choose a model system of G-quadruplex DNA, molecules well known to depend for its structures strongly on the cations present, to study the effect of the cation location and number in the modeling of these structures in order to evaluate how well molecular dynamics (CHARMM) performs.