Topological Linkage of DNA Tiles Bonded by Paranemic Cohesion

Yoel P. Ohayon, Ruojie Sha, Ortho Flint, Arun Richard Chandrasekaran, Hatem O. Abdallah, Tong Wang, Xing Wang, Xiaoping Zhang, Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Pages (from-to)10296-10303
Number of pages8
JournalACS nano
Issue number10
StatePublished - Sep 13 2015


  • 3′,3′ and 5′,5′ linkages
  • DNA catenane
  • DNA knot
  • linking number
  • paranemic cohesion
  • topoisomers
  • topological linkage

ASJC Scopus subject areas

  • General Materials Science
  • General Engineering
  • General Physics and Astronomy


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