Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

Isabel K. Darcy; John Luecke; Mariel Vazquez

doi:10.2140/agt.2009.9.2247

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arXiv · 0710.4150

Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex

Isabel K. Darcy·John Luecke·Mariel Vazquez

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Abstract

We develop topological methods for analyzing difference topology experiments involving 3-string tangles. Difference topology is a novel technique used to unveil the structure of stable protein-DNA complexes involving two or more DNA segments. 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.

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Isabel K. Darcy, John Luecke, Mariel Vazquez. 2007-10-22. Tangle analysis of difference topology experiments: applications to a Mu protein-DNA complex. https://doi.org/10.2140/agt.2009.9.2247

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