Mechanical behavior of double-stranded DNA at atomistic scale

Besides its key role in many of the major processes of cell biology, including DNA replication, DNA repair, DNA recombination, etc., DNA molecule can serve as a promising material in nanostructures. enhance the understanding of different overstretched DNA structures.In silico tensile tests were performed using all atom molecular dynamics method to study nanomechanical behavior of DNA duplex. The DNA molecule is immersed in the Monte Carlo equilibrated periodic TIP3P water bath and is elongated with va rious pullingspeeds. The double-stranded DNA is stretched from opposite end of each strand under shear mode. Forceextension curves were obtained and atomistic structures of DNA dodecamer were investigated. The results of this study show that the rupture force of short DNA duplex is a nonlinear function of the pulling velocity. At larger extensions correspond to the first structural transitionphenomenon, the average number of H-bonds is observed to be almost constant. Presented results provide a fundamental molecular understanding of the DNA stretching mechanism