Implementing Sequence-Dependent Mechanical Properties in a DNA Mesoscale Model

DNA sequence is believed to play an important role in the efficiency of many biologically relevant processes such as nucleosome packing, loop formation and viral encapsidation by influencing the conformational and mechanical properties of DNA. Here we present a DNA model that can reproduce experimentally and computationally observed sequence-dependent mechanical properties. The model accounts for both sequence-dependent base-pair step deformability and base-pairing. The model can capture the de/re-hybridization of DNA and reproduce its melting behavior as a function of CG content, chain length and salt concentration. In addition, the model has also been parameterized to reproduce the atomistic level distributions of bond distances, bend and torsion angles, and in doing so, the model has proved to qualitatively reproduce the sequence-dependent base-pair step deformability. Finally, we look at the effects of this parameterization on the persistence length of short DNA segments.