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Simulation of DNA Supercoil Relaxation.

ABSTRACT: Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead. The bead, which also serves to manipulate DNA, experiences significant drag and thereby obscures supercoil dynamics. Here we employ our discrete wormlike chain model to bypass experimental limitations and simulate the dynamic response of supercoiled DNA to a single strand nick. From our simulations, we make three major observations. First, extension is a poor dynamic measure of supercoil relaxation; in fact, the linking number relaxes so fast that it cannot have much impact on extension. Second, the rate of linking number relaxation depends upon its initial partitioning into twist and writhe as determined by tension. Third, the extensional response strongly depends upon the initial position of plectonemes.

SUBMITTER: Ivenso ID

PROVIDER: S-EPMC4880802 | biostudies-other | 2016 May

REPOSITORIES: biostudies-other

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Simulation of DNA Supercoil Relaxation.

Ivenso Ikenna D ID Lillian Todd D TD

Biophysical journal 20160501 10

Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead. The bead, which also serves to manipulate DNA, experiences significant drag and thereby obscures supercoil dynamics. Here we employ our discrete wormlike chain model to bypass experimental limitations and simulate the dynamic r ...[more]

PMID: 27224483

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Dataset Information

Simulation of DNA Supercoil Relaxation.

Publications

Simulation of DNA Supercoil Relaxation.

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