Nucleic Acids Research Advance Access published online on August 1, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm532
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Computational Biology |
Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
1Laboratoire d’Analyse Ultrastructurale, Faculté de Biologie et de Médecine, Université de Lausanne, 1015 Lausanne-Dorigny, Switzerland and 2School of Informatics, Indiana University, 901 E, 10th St., Bloomington, IN 47408, USA
*To whom correspondence should be addressed. Tel: 0041 216924282; Fax: 0041 216924105; Email: andrzej.stasiak{at}unil.ch
Received May 2, 2007. Revised June 26, 2007. Accepted June 26, 2007.
We performed numerical simulations of DNA chains to understand how local geometry of juxtaposed segments in knotted DNA molecules can guide type II DNA topoisomerases to perform very efficient relaxation of DNA knots. We investigated how the various parameters defining the geometry of inter-segmental juxtapositions at sites of inter-segmental passage reactions mediated by type II DNA topoisomerases can affect the topological consequences of these reactions. We confirmed the hypothesis that by recognizing specific geometry of juxtaposed DNA segments in knotted DNA molecules, type II DNA topoisomerases can maintain the steady-state knotting level below the topological equilibrium. In addition, we revealed that a preference for a particular geometry of juxtaposed segments as sites of strand-passage reaction enables type II DNA topoisomerases to select the most efficient pathway of relaxation of complex DNA knots. The analysis of the best selection criteria for efficient relaxation of complex knots revealed that local structures in random configurations of a given knot type statistically behave as analogous local structures in ideal geometric configurations of the corresponding knot type.
Present address: Yannis Burnier, Laboratoire de Physique des Particules et de Cosmologie, Ecole Polytechnique Fédérale de Lausanne, 1015-Lausanne, Switzerland.
Present Address: Cedric Weber, Institut Romand de Recherche Numérique en Physique des Matériaux, Ecole Polytechnique Fédérale de Lausanne, 1015-Lausanne, Switzerland. The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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