Force-induced unzipping of double-stranded DNA: An all-atom molecular simulation

We employed all-atom molecular dynamics simulations to investigate the unzipping of a double-stranded DNA (dsDNA) by applying various forces on the mass centers of the base pairs. To characterize the conformational evolution during the unzipping process, we monitored parameters such as the separation between the two strands and the shape factor. Our observations revealed distinct conformational transitions in the dsDNA unzipping, wherein the structure evolved from a rod-like to a disk-like configuration and subsequently reverted to a rod-like form under a stretching force. Furthermore, we analyzed the hydrogen bond (H-bond) breakage to elucidate the microscopic mechanism underlying dsDNA unzipping. The results demonstrated that H-bond breakage occurred sequentially, initiating from the point of force application, in which, prior to complete H-bond breakage, the H-bonds in base pairs entered a quasi-break state under the influence of stretching forces. Meanwhile, we systematically investigated the variations of conformational changes and H-bond breakage with different stretching forces. The results show that the H-bond breaking time has an exponential relationship with the magnitude of the stretching force.