Biophysical Society Thematic Meeting| Santa Cruz 2018

Genome Biophysics: Integrating Genomics and Biophysics to Understand Structural and Functional Aspects of Genomes

Poster Abstracts

17-POS Board 17 Modeling Dynamics of Supercoiling and Applications to RNA Polymerase Biao Wan , Xinliang Xu, Jin Yu. Beijing Computational Science Research Center, Beijing, China. The quantitative description of DNA structures and its dynamics is of importance in understanding many processes in cells. Double helical structure endows DNA with the twisting rigidity and elasticity that allow supercoiling an important means to mechanically communicate in essential genetic processes, such as transcription and replication. For the in-extensible DNA chain model, one of coarse-grained representations of DNA, namely the 'discrete worm-like chain' (DWLC) has offered numerous predictions about properties of supercoiled DNA. In the model, DNA is regarded as a series of elastic segments with potentials of stretching bonds, bending and twisting angles, accompanied by the electrostatic interactions. Its dynamics is realized through Brownian dynamics (BD). During transcription ， RNA polymerases (RNAPs) generate supercoiling along DNA by exerting torques on it. The increasing resisting torque from DNA in turn slows down the RNAP as the positive supercoiling is built up, which can even cease the transcription when the resisting torque reaches a threshold, called stalling torque (‘Ma J and Wang M D. Science, 2013, 340:1580.’). By performing the BD simulations of the DWLC, we studied the supercoiling relaxation under certain torques and tensions. We found that the relaxation depends on the torque and the tension imposed on the DNA, and also depends on the length of the DNA. Based on these results, we could investigate whether DNA supercoiling during transcription is built up in a quasi–static process. For equilibrium cases, detailed results including phase diagrams were shown. For the cases out of equilibrium, however, the non-equilibrium effects caused by the torque can also be demonstrated to be important in transcription. Since the theoretical description of the supercoiling relaxation and propagation are still lack of, we also tried to bring some insights from simulations of the supercoiling generation in the RNAP transcription.

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