Abstract
The stresses induced in DNA during cell processes such as replication and transcription lead to the formation of plectonemic supercoils. Supercoiling in turn affects these processes. As a result of this relationship between supercoiling and these processes, the degree of supercoiling in DNA needs to be controlled closely in order to optimize these cell processes. This control is facilitated by enzymes such as type 1b topoisomerases and nicking endonucleases which relax supercoiling in DNA.The dynamics of DNA supercoil relaxation have been studied in recent experiments by means of single-molecule magnetic and/or optical tweezer experiments. Novel as these experiments are, they do not permit a direct observation of the structural changes that occur in DNA during supercoil relaxation. They depend on components (e.g. a paramagnetic bead) attached to the DNA to indirectly obtain information about these dynamics.We studied the dynamics of supercoil relaxation by means of Brownian Dynamics simulations of a discrete wormlike-chain (dWLC) model of DNA. These simulations parallel the single-molecule experiments in which a single DNA molecule is held under constant tension so that its end-to-end extension increases as supercoils are relaxed by a nicking endonuclease. The dWLC model accounts for elasticity, electrostatics and entropic forces as well as for hydrodynamic interactions.From the simulation results, we more directly extract the rate at which supercoiling in DNA is relaxed by nicking endonucleases. We also determine the dependence of the relaxation timescales on the tension applied to the DNA molecule.
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