Abstract
Essential cellular processes such as replication and transcription induce torsional stresses in DNA which lead to an accumulation of supercoils. Excessive, as well as insufficient, levels of supercoiling can impede the progress of these processes. Therefore, topoisomerases are necessary to maintain an optimal degree of DNA supercoiling. Recent experiments have considered the relaxation dynamics of DNA supercoils by both Topo1B and nicking endonucleases. In these experiments, nicking endonucleases or topoisomerases act on individual torsionally constrained DNA molecules which are held at constant tension. Unfortunately, supercoil relaxation dynamics occur faster than can be measured by observing merely the end-to-end extension of the DNA, as in magnetic or optical trap assays. Our objective is to simulate the relaxation of DNA supercoils to better understand the dynamics and quantify the relaxation timescales. We represent DNA with a coarse-grained Brownian dynamics model which accounts for DNA bending, torsion, electrostatics, and hydrodynamics. Our simulations are designed to parallel experiments and permit direct comparisons to the experiments.
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