title: Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion.
abstract: Catenation is the process by which cyclic strands are combined like the links of a chain, whereas knotting changes the linking properties of a single strand. In the cell, topoisomerases catalyzing strand passage operations enable the knotting and catenation of DNA so that single- or double-stranded segments can be passed through each other. Here, we use a system of closed DNA structures involving a paranemic motif, called PX-DNA, to bind double strands of DNA together. These PX-cohesive closed molecules contain complementary loops whose linking by Escherichia coli topoisomerase 1 (Topo 1) leads to various types of catenated and knotted structures. We were able to obtain specific DNA topological constructs by varying the lengths of the complementary tracts between the complementary loops. The formation of the structures was analyzed by denaturing gel electrophoresis, and the various topologies of the constructs were characterized using the program Knotilus.
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Yoel P
authors.initials: YP
authors.lastname: Ohayon
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Ruojie
authors.initials: R
authors.lastname: Sha
authors.affiliation: Department of Mathematics, University of Western Ontario , London, ON N6A 3K7, Canada.
authors.forename: Ortho
authors.initials: O
authors.lastname: Flint
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Arun Richard
authors.initials: AR
authors.lastname: Chandrasekaran
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Hatem O
authors.initials: HO
authors.lastname: Abdallah
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Tong
authors.initials: T
authors.lastname: Wang
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Xing
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Chemistry, New York University , New York, New York 10003, United States.
authors.forename: Nadrian C
authors.initials: NC
authors.lastname: Seeman
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004264:DNA Topoisomerases, Type I / Q000378:metabolism; D043864:DNA, Catenated / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation
chemical_list: D043864:DNA, Catenated; D004247:DNA; D004264:DNA Topoisomerases, Type I
keywords: 3′,3′ and 5′,5′ linkages; DNA catenane; DNA knot; linking number; paranemic cohesion; topoisomers; topological linkage