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Nucleic Acids Research Advance Access published online on April 24, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn192
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Computational Biology

3D visualization software to analyze topological outcomes of topoisomerase reactions

I. K. Darcy1,*, R. G. Scharein2 and A. Stasiak3

1Department of Mathematics, University of Iowa, Iowa City, IA 52245, USA, 2Hypnagogic Software, Vancouver, BC, Canada and 3Centre for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne-Dorigny, Switzerland

*To whom correspondence should be addressed. Tel: +1 319 335 0714; Fax: +1 319 335 0627; Email: idarcy{at}math.uiowa.edu

Received January 16, 2008. Revised March 31, 2008. Accepted April 3, 2008.

The action of various DNA topoisomerases frequently results in characteristic changes in DNA topology. Important information for understanding mechanistic details of action of these topoisomerases can be provided by investigating the knot types resulting from topoisomerase action on circular DNA forming a particular knot type. Depending on the topological bias of a given topoisomerase reaction, one observes different subsets of knotted products. To establish the character of topological bias, one needs to be aware of all possible topological outcomes of intersegmental passages occurring within a given knot type. However, it is not trivial to systematically enumerate topological outcomes of strand passage from a given knot type. We present here a 3D visualization software (TopoICE-X in KnotPlot) that incorporates topological analysis methods in order to visualize, for example, knots that can be obtained from a given knot by one intersegmental passage. The software has several other options for the topological analysis of mechanisms of action of various topoisomerases.


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