The internal 'slithering' dynamics of supercoiled DNA

John F. Marko

doi:10.1016/S0378-4371(97)00295-1

The internal 'slithering' dynamics of supercoiled DNA

John F. Marko^*

^*Corresponding author for this work

Molecular Biosciences

Research output: Contribution to journal › Article › peer-review

23 Scopus citations

Abstract

DNAs in bacteria are usually circular and supercoiled in the manner of a twisted telephone cord. Supercoil dynamics, in addition to usual Zimm relaxation, include a long relaxation time corresponding to the 'slithering' of DNA sequence around inside the supercoil; this is believed to be important in bringing distant DNA sequences together in bacterial cells. Simple 'repton' models of slithering are proposed and numerically investigated for unbranched and branched supercoils. The first passage time by slithering for two distant sites on a N-monomer molecule with no branches is found to be ∼N³, as for conventional reptation. Allowing supercoil branching and branch motion, effects expected for large DNAs, reduces this time to ∼N².

Original language	English (US)
Pages (from-to)	263-277
Number of pages	15
Journal	Physica A: Statistical Mechanics and its Applications
Volume	244
Issue number	1-4
DOIs	https://doi.org/10.1016/S0378-4371(97)00295-1
State	Published - Oct 1 1997

ASJC Scopus subject areas

Statistics and Probability
Condensed Matter Physics

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abstract = "DNAs in bacteria are usually circular and supercoiled in the manner of a twisted telephone cord. Supercoil dynamics, in addition to usual Zimm relaxation, include a long relaxation time corresponding to the 'slithering' of DNA sequence around inside the supercoil; this is believed to be important in bringing distant DNA sequences together in bacterial cells. Simple 'repton' models of slithering are proposed and numerically investigated for unbranched and branched supercoils. The first passage time by slithering for two distant sites on a N-monomer molecule with no branches is found to be ∼N3, as for conventional reptation. Allowing supercoil branching and branch motion, effects expected for large DNAs, reduces this time to ∼N2.",

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N2 - DNAs in bacteria are usually circular and supercoiled in the manner of a twisted telephone cord. Supercoil dynamics, in addition to usual Zimm relaxation, include a long relaxation time corresponding to the 'slithering' of DNA sequence around inside the supercoil; this is believed to be important in bringing distant DNA sequences together in bacterial cells. Simple 'repton' models of slithering are proposed and numerically investigated for unbranched and branched supercoils. The first passage time by slithering for two distant sites on a N-monomer molecule with no branches is found to be ∼N3, as for conventional reptation. Allowing supercoil branching and branch motion, effects expected for large DNAs, reduces this time to ∼N2.

AB - DNAs in bacteria are usually circular and supercoiled in the manner of a twisted telephone cord. Supercoil dynamics, in addition to usual Zimm relaxation, include a long relaxation time corresponding to the 'slithering' of DNA sequence around inside the supercoil; this is believed to be important in bringing distant DNA sequences together in bacterial cells. Simple 'repton' models of slithering are proposed and numerically investigated for unbranched and branched supercoils. The first passage time by slithering for two distant sites on a N-monomer molecule with no branches is found to be ∼N3, as for conventional reptation. Allowing supercoil branching and branch motion, effects expected for large DNAs, reduces this time to ∼N2.

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The internal 'slithering' dynamics of supercoiled DNA

Abstract

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