title: Local site preference rationalizes disentangling by DNA topoisomerases.
abstract: To rationalize the disentangling action of type II topoisomerases, an improved wormlike DNA model was used to delineate the degree of unknotting and decatenating achievable by selective segment passage at specific juxtaposition geometries and to determine how these activities were affected by DNA circle size and solution ionic strength. We found that segment passage at hooked geometries can reduce knot populations as dramatically as seen in experiments. Selective segment passage also provided theoretical underpinning for an intriguing empirical scaling relation between unknotting and decatenating potentials.
authors.affiliation: College of Chemistry and Molecular Engineering, Center for Theoretical Biology, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China.
authors.forename: Zhirong
authors.initials: Z
authors.lastname: Liu
authors.forename: Lynn
authors.initials: L
authors.lastname: Zechiedrich
authors.forename: Hue Sun
authors.initials: HS
authors.lastname: Chan
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000648:ultrastructure*; D004789:Enzyme Activation; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding
chemical_list: D004247:DNA; D004264:DNA Topoisomerases, Type I