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Tangle analysis of
difference topology experiments: Applications to a Mu
protein-DNA complex
Isabel K Darcy, John Luecke and Mariel Vazquez |
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Algebraic & Geometric Topology 9 (2009) 2247–2309
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Abstract |
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We develop topological methods for analyzing difference topology experiments involving –string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes. We analyze such experiments for the Mu protein-DNA complex. We characterize the solutions to the corresponding tangle equations by certain knotted graphs. By investigating planarity conditions on these graphs we show that there is a unique biologically relevant solution. That is, we show there is a unique rational tangle solution, which is also the unique solution with small crossing number. |
Keywords
$3$–string tangle, DNA topology, tangle method, difference
topology, Mu transpososome, graph planarity, Dehn surgery,
handle addition lemma
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Mathematical Subject Classification 2000
Primary: 57M25, 92C40
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References |
Publication
Received: 31 October 2007
Revised: 14 July 2009
Accepted: 20 July 2009
Published: 30 October 2009
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Authors |
| Isabel K Darcy | |
| Department of Mathematics University of Iowa Iowa City, IA 52242 USA |
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| http://math.uiowa.edu/~idarcy | |
| John Luecke | |
| Department of Mathematics The University of Texas at Austin 1 University Station C1200 Austin, TX 78712-0257 USA |
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| Mariel Vazquez | |
| Department of Mathematics San Francisco State University 1600 Holloway Avenue San Francisco, CA 94132 USA |
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| http://math.sfsu.edu/mariel/ | |
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