Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes   Unlinking Preference of Type-2 Topoisomerases

doi:10.1016/j.jmb.2010.05.007

CORC > 北京大学 > 化学与分子工程学院

	Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases
	Liu, Zhirong ; Zechiedrich, Lynn ; Chan, Hue Sun
刊名	分子生物学杂志
	2010
关键词	DNA supercoils writhe torsional energy self-avoiding lattice polygons Madras-Orlitsky-Shepp algorithm INTERTWINED CATENATED DIMERS SELF-AVOIDING WALKS LATTICE MONTE-CARLO ESCHERICHIA-COLI II TOPOISOMERASES THERMODYNAMIC PROPERTIES TOPOLOGY SIMPLIFICATION STATISTICAL-THEORY SUPERCOILED DNA WRITHING NUMBER
DOI	10.1016/j.jmb.2010.05.007
英文摘要	The mathematical basis of the hypothesis that type-2 topoisomerases recognize and act at specific DNA juxtapositions has been investigated by coarse-grained lattice polymer models, showing that selective segment passages at hooked juxtapositions can result in dramatic reductions in catenane and knot populations. The lattice modeling approach is here extended to account for the narrowing of variance of linking number (Lk) of DNA circles by type-2 topoisomerases. In general, the steady-state variance of Lk resulting from selective segment passages at a specific juxtaposition geometry j is inversely proportional to the average linking number, < Lk >(J), of circles with the given juxtaposition. Based on this formulation, we demonstrate that selective segment passages at hooked juxtapositions reduce the variance of Lk. The dependence of this effect on model DNA circle size is remarkably similar to that observed experimentally for type-2 topoisomerases, which appear to be less capable in narrowing Lk variance for small DNA circles than for larger DNA circles. This behavior is rationalized by a substantial cancellation of writhe in small circles with hook-like juxtapositions. During our simulations, we uncovered a twisted variation of the hooked juxtaposition that has an even more dramatic effect on Lk variance narrowing than the hooked juxtaposition. For an extended set of juxtapositions, we detected a significant correlation between the Lk narrowing potential and the logarithmic decatenating and unknotting potentials for a given juxtaposition, a trend reminiscent of scaling relations observed with experimental measurements on type-2 topoisomerases from a variety of organisms. The consistent agreement between theory and experiment argues for type-2 topoisomerase action at hooked or twisted-hooked DNA juxtapositions. (C) 2010 Elsevier Ltd. All rights reserved.; Biochemistry & Molecular Biology; SCI(E); PubMed; 12; ARTICLE; 5; 963-982; 400
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/150070]
专题	化学与分子工程学院
推荐引用方式 GB/T 7714	Liu, Zhirong,Zechiedrich, Lynn,Chan, Hue Sun. Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases[J]. 分子生物学杂志,2010.
APA	Liu, Zhirong,Zechiedrich, Lynn,&Chan, Hue Sun.(2010).Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases.分子生物学杂志.
MLA	Liu, Zhirong,et al."Action at Hooked or Twisted-Hooked DNA Juxtapositions Rationalizes Unlinking Preference of Type-2 Topoisomerases".分子生物学杂志 (2010).