Journal article
Coloring the Mu transpososome
BMC bioinformatics, Vol.7(1), pp.435-435
10/05/2006
DOI: 10.1186/1471-2105-7-435
PMCID: PMC1636074
PMID: 17022825
Abstract
Background: Tangle analysis has been applied successfully to study proteins which bind two segments of DNA and can knot and link circular DNA. We show how tangle analysis can be extended to model any stable protein-DNA complex. Results: We discuss a computational method for finding the topological conformation of DNA bound within a protein complex. We use an elementary invariant from knot theory called colorability to encode and search for possible DNA conformations. We apply this method to analyze the experimental results of Pathania, Jayaram, and Harshey (Cell 2002). We show that the only topological DNA conformation bound by Mu transposase which is biologically likely is the five crossing solution found by Pathania et al (although other possibilities are discussed). Conclusion: Our algorithm can be used to analyze the results of the experimental technique described in Pathania et al in order to determine the topological conformation of DNA bound within a stable protein-DNA complex. © 2006 Darcy et al; licensee BioMed Central Ltd.
Details
- Title: Subtitle
- Coloring the Mu transpososome
- Creators
- Isabel K Darcy - University of IowaJeff Chang - Mathematics Department, University of Iowa, Iowa City, IA 52242, USA Mathematics Department, University of Texas at Austin, Austin, TX 78712, USA Mathematics Department, Indiana University, Bloomington, IN 47405, USA Mathematics Department, Florida State University, Tallahassee, FL 32306, USA Mathematics Department, Texas Woman's University, Denton, TX 76204, USA Credit Suisse First, Boston, MA 02110, USANathan Druivenga - Indiana UniversityColin McKinney - University of IowaRam K Medikonduri - University of IowaStacy Mills - Florida State UniversityJunalyn Navarra-Madsen - Texas Woman's UniversityArun Ponnusamy - Credit SuisseJesse Sweet - The University of Texas at AustinTravis Thompson - University of Iowa
- Resource Type
- Journal article
- Publication Details
- BMC bioinformatics, Vol.7(1), pp.435-435
- Publisher
- BioMed Central
- DOI
- 10.1186/1471-2105-7-435
- PMID
- 17022825
- PMCID
- PMC1636074
- ISSN
- 1471-2105
- eISSN
- 1471-2105
- Language
- English
- Date published
- 10/05/2006
- Academic Unit
- Mathematics
- Record Identifier
- 9984240773302771
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