Two-Phase Dynamics of DNA Supercoiling Based on DNA Polymer Physics Model

Abstract

DNA supercoils are generated in genome regulation processes, such as transcription, replication and also provide mechanical feedback to such processes. Under tension, DNA supercoil can present a coexistence state of plectonemic (P) and stretched (S) phases. Experiments have revealed the dynamic behaviors of plectoneme, e.g. diffusion, nucleation and hopping (M.T.van Loenhout et.al.Science 2012). In presenting the dynamics of supercoiling under tension based on the worm-like chain (WLC) model of DNA, we demonstrated fast dynamics on the DNA to reach torque equilibrium within the P and S phases, and then identified the two phase-boundaries as slow variables. According to the time-scale separation, we thus developed a two-phase dynamic model of DNA supercoiling. For calibration, we compared numerical results of the two-phase dynamic model with that from the discrete WLC model for DNA at thousands base pair (bp) length. Then the DNA supercoiling dynamics detected experimentally, including the nucleation, diffusion and hopping of plectoneme, have been successfully reproduced using our two-phase dynamic model at trivial computational cost. Our study therefore presents an efficient and physics-based method to describe the supercoiling dynamics of DNA and can be implemented to explore multi- scale physical mechanism of the DNA supercoiling-dependent processes.