Coarse grained modeling of self assembled DNA 3D structure using pragmatic soft ellipsoid contact potential

Abstract

In this paper, we present a coarse-grained model of DNA based on the soft ellipsoid contact potential (ECP) to evaluate the base pairing interaction properly. We extend the ellipsoid contact like potential model (ECP), suitably modified and used previously by our group to model lipid bilayer phases with considerable success. This potential is used for base-base interactions, along with other potentials to capture bending, dihedral and solvent effects. The model shows a phase transition during hybridization and is able to reproduce the experimental melting curves with sufficient adequacy. Thermodynamical, along with conformational characteristics and structural properties of our model are studied in detail.