Numerical simulation on the mechanical characteristics of double-stranded DNA under axial stretching and lateral unzipping

Abstract

The mechanical characteristics of the long-chain double-stranded DNA (dsDNA) molecule under the axial stretching and lateral unzipping are studied by the clustered atomistic-continuum method (CACM). The CACM consisted of the clustered atom method (CAM) and the atomistic-continuum method (ACM). The CAM treats the specific atomic group as the superatom, and the ACM describes the chemical binding energies between (super)atoms by virtual elements. The Newtonian based model of the dsDNA includes the superatoms of the backbones?base pairs and the virtual elements of the stacking energies?hydrogen bonds. The effective properties of the superatoms are numerically extracted from the single-stranded DNA experiments. Good agreements were achieved between the dsDNA numerical results and the single molecular experimental results. Via the simulation of stretching dsDNA, the mechanical responses, including the twisting of the backbone and variation of the elastic deformation energy and stacking energy, can be elucidated. Moreover, the predictive capability of the dsDNA CACM model is then examined. Furthermore, the dsDNA model with sequential information is subjected to the unzipping loading, and the in silico results reveal that the sliding of the backbones and the sequential dependent mechanical responses.