A dynamic model of DNA Supercoiling

The dynamics of DNA supercoiling is important for many biological functions of DNA, such as gene expression regulation. In this investigation we first studied DNA supercoiling generation through a Brownian dynamics simulation of DNA, which is modeled as a discrete worm-like chain. Two well-separated time scales are observed: mechanical balance along the DNA can be regarded as instantaneous (10^-3∼10^-2ms) when compared to the global configuration change of the DNA supercoil structure (>10⁰ms). Based on this time separation, we developed a new model where the fast mechanical balancing dynamics are coarse grained. While the numerical simulation of DNA supercoil dynamics based on this model can be shown to fully reproduce DNA dynamical behavior above millisecond time scale, the computational efficiency is great improved. In our example of a DNA segment of 6000 base pairs, simulation based on the new model is times faster than the original Brownian dynamics simulations, making numerical study of DNA dynamics at biologically relevant time scales (e.g.1∼10 sec ) possible.