title: Tightening of DNA knots by supercoiling facilitates their unknotting by type II DNA topoisomerases.
abstract: Using numerical simulations, we compare properties of knotted DNA molecules that are either torsionally relaxed or supercoiled. We observe that DNA supercoiling tightens knotted portions of DNA molecules and accentuates the difference in curvature between knotted and unknotted regions. The increased curvature of knotted regions is expected to make them preferential substrates of type IIA topoisomerases because various earlier experiments have concluded that type IIA DNA topoisomerases preferentially interact with highly curved DNA regions. The supercoiling-induced tightening of DNA knots observed here shows that torsional tension in DNA may serve to expose DNA knots to the unknotting action of type IIA topoisomerases, and thus explains how these topoisomerases could maintain a low knotting equilibrium in vivo, even for long DNA molecules.
authors.affiliation: Laboratoire de Physique de la Matière Vivante, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Witz
authors.forename: Giovanni
authors.initials: G
authors.lastname: Dietler
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
mesh_terms: D020029:Base Pairing; D003198:Computer Simulation; D004250:DNA Topoisomerases, Type II / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism*; D004586:Electrophoresis; D008958:Models, Molecular; D009690:Nucleic Acid Conformation
chemical_list: D004278:DNA, Superhelical; D004250:DNA Topoisomerases, Type II