Title: Molecular Dynamics Simulation on DNA Duplex stretching
Abstract: Single-molecule DNA stretching experiments is a useful method to probe mechanical properties of DNA and the binding of small molecules and proteins to DNA. In these experiments, double-stranded DNA molecules are stretched by a force applied to opposite ends of the DNA, e.g., in an atomic force microscope or an optical tweezers instrument. Here we study the stretching behavior of the DNA duplex d(CGCAAAAAAGCG) 2 by molecular dynamics simulations. In particular, we calculate the change in free energy ∆F = ∆U − T ∆S as the DNA duplex is stretched. We seek to show that employing both the statistical mechanics, and also modeling of molecular systems(here, double stranded DNA molecule in water) aids us to better comprehend how the DNA molecule behaves under stretching conditions. In particular, we show how thermal fluctuations, and therefore, configurational entropies play role in the mechanical response and behaviour of the DNA molecule at the molecular level to fill in as much as possible the difference in the timescale of the experiment and of the simulation.