Journal article
3D visualization software to analyze topological outcomes of topoisomerase reactions
Nucleic acids research, Vol.36(11), pp.3515-3521
06/2008
DOI: 10.1093/nar/gkn192
PMCID: PMC2441796
PMID: 18440983
Abstract
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.
Details
- Title: Subtitle
- 3D visualization software to analyze topological outcomes of topoisomerase reactions
- Creators
- I K Darcy - University of IowaR G Scharein - University of LausanneA Stasiak - University of Lausanne
- Resource Type
- Journal article
- Publication Details
- Nucleic acids research, Vol.36(11), pp.3515-3521
- DOI
- 10.1093/nar/gkn192
- PMID
- 18440983
- PMCID
- PMC2441796
- ISSN
- 0305-1048
- eISSN
- 1362-4962
- Grant note
- GM67242 / NIGMS NIH HHS R01 GM067242 / NIGMS NIH HHS
- Language
- English
- Date published
- 06/2008
- Academic Unit
- Mathematics
- Record Identifier
- 9984241058002771
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