Predicting Knot or Catenane Type of Site-Specific Recombination Products

Abstract

Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. We develop a model of this process, and give extensive experimental evidence that the assumptions of our model are reasonable. We then characterize all possible knot or catenane products that arise from the most common substrates. We apply our model to tightly prescribe the knot or catenane type of previously uncharacterized data.

17 pages, 4 figures. Revised to include link to the companion paper, arXiv:0707.3896v1, that provides topological proofs underpinning the conclusions of the current paper. References updated