Computational simulation demonstrates spontaneous helix formation during DNA renaturation via soft ellipsoid contact potential, indicating excluded volume effects drive coarse-grained assembly.
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 modelled 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 parameterisation 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.
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Das et al. (2026) studied this question.
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