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

In this paper, we employ the soft ellipsoid contact type potential (ECP) in a generic coarse grained model of DNA and study the renaturation process. The interactions between the bases are modeled using our ECP type potential, along with other interactions to capture bending, dihedral and solvent effects implicitly. Structure and helix formation is primarily driven by non-spherical geometry of the bases and excluded volume effects. Simulation results demonstrate that two isolated strands in a random initial configuration undergo spontaneous helix formation during annealing. The model captures the qualitative features of the coil-helix transition as well as the morphology of the helical structure. However, the present parameterization of our model does not yet capture the proper right chirality and detailed helical geometry associated with DNA. Thus, its capability for making any quantitative predictions remains limited. Statistical and physical properties of our model are discussed in detail.