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ISSN (electronic): 1472-2739
ISSN (print): 1472-2747
Rational tangle surgery and Xer recombination on catenanes

Isabel K Darcy, Kai Ishihara, Ram K Medikonduri and Koya Shimokawa

Algebraic & Geometric Topology 12 (2012) 1183–1210
Abstract

The protein recombinase can change the knot type of circular DNA. The action of a recombinase converting one knot into another knot is normally mathematically modeled by band surgery. Band surgeries on a 2–bridge knot N4mn1 2m yielding a (2,2k)–torus link are characterized. We apply this and other rational tangle surgery results to analyze Xer recombination on DNA catenanes using the tangle model for protein-bound DNA.

Keywords
tangle, DNA topology, recombination, surgery
Mathematical Subject Classification 2000
Primary: 57M25, 92C40
References
Publication
Received: 29 September 2011
Revised: 2 February 2012
Accepted: 3 February 2012
Published: 28 May 2012
Authors
Isabel K Darcy
Department of Mathematics and Applied Mathematical and Computational Sciences
University of Iowa
14 MLH
Iowa City IA 52242
USA
http://www.math.uiowa.edu/~idarcy/
Kai Ishihara
Department of Mathematics
Imperial College London
London SW7 2AZ
UK
http://www2.imperial.ac.uk/~kishihar/
Ram K Medikonduri
Pyxis Solutions
New York NY 10004
USA
Koya Shimokawa
Department of Mathematics
Saitama University
Saitama 338-8570
Japan
http://www.rimath.saitama-u.ac.jp/lab.en/kshimoka/index-e.html