Abstract
As is known, various important physiological functions and gene engineering processes, such as RNA transcription/DNA replication/DNA repair, involve specific bio-physical mechanics of DNA. Therefore, in this study, a novel single-stranded DNA (ssDNA) model based on the atomistic-continuum mechanics method (CAM) is conducted to simulate the mechanical behavior of ssDNA. It is often assumed that the elastic behavior of single-chain polymer can be modeled as the freely joint chain (FJC) of orientationally independent Kuhn segment. In this research, an atomistic-continuum mechanics model of ssDNA based on equivalent-spring method would be first conducted and the simulation result would be further validated by the experimental result. A spring element is chosen to represent the covalent bond between neighbor atoms of backbone in ssDNA. To describe the material properties of the spring in ssDNA backbone structure, the Cornell's second generation force field potential energy and Universal force field is utilized to simulate the bond stretching and bond angle energy terms. The method proposed here would be used to study the mechanical behavior in DNA packaging and release form viral capsids in the future.