PMID: 11308680Apr 20, 2001Paper

Kinetic proofreading can explain the supression of supercoiling of circular DNA molecules by type-II topoisomerases

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
J YanJ F Marko

Abstract

The enzymes that pass DNA through DNA so as to remove entanglements, adenosine-triphosphate-hydrolyzing type-II topoisomerases, are able to suppress the probability of self-entanglements (knots) and mutual entanglements (links) between approximately 10 kb plasmids, well below the levels expected, given the assumption that the topoisomerases pass DNA segments at random by thermal motion. This implies that a 10-nm type-II topoisomerase can somehow sense the topology of a large DNA. We previously introduced a "kinetic proofreading" model which supposes the enzyme to require two successive collisions in order to allow exchange of DNA segments, and we showed how it could quantitatively explain the reduction in knotting and linking complexity. Here we show how the same model quantitatively explains the reduced variance of the double-helix linking number (supercoiling) distribution observed experimentally.

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Citations

Dec 23, 2003·Journal of Molecular Biology·Sonia TriguerosJoaquim Roca
Jun 25, 2002·Journal of Molecular Biology·Konstantin KleninAlexander Vologodskii
Jun 25, 2002·Journal of Molecular Biology·Spencer Campbell, Anthony Maxwell
Jul 23, 2004·Omics : a Journal of Integrative Biology·Chaitanya A AthaleChristian Mielke
Feb 26, 2009·Nucleic Acids Research·Zhirong LiuLynn Zechiedrich
Oct 1, 2008·Biological Reviews of the Cambridge Philosophical Society·Annick Lesne
Nov 5, 2013·Nucleic Acids Research·Belén Martínez-GarcíaJoaquim Roca
Jul 9, 2004·Journal of Molecular Biology·Gregory R Buck, E Lynn Zechiedrich
May 14, 2016·Physics of Life Reviews·Alexander Vologodskii
Apr 12, 2006·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Graham L RandallE Lynn Zechiedrich
Aug 30, 2008·Quarterly Reviews of Biophysics·Allyn J Schoeffler, James M Berger
Nov 27, 2018·Nucleic Acids Research·Riccardo ZiraldoStephen D Levene
Aug 21, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Zhirong Liu, Hue Sun Chan
Apr 7, 2010·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Zhirong LiuHue Sun Chan
Jun 22, 2007·Biochemistry·Andrew D Bates, Anthony Maxwell
Jul 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Andreas HankeStephen D Levene
Nov 30, 2019·The Journal of Physical Chemistry. B·Vahe Galstyan, Rob Phillips
Feb 11, 2015·Physics of Life Reviews·Warren Colomb, Susanta K Sarkar

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