Abstract
Site-specific recombination on supercoiled circular DNA molecules can yield a variety of knots and catenanes. Twist knots are some of the most common conformations of these products, and they can act as substrates for further rounds of site-specific recombination. They are also one of the simplest families of knots and catenanes. Yet, our systematic understanding of their implication in DNA and important cellular processes such as site-specific recombination is very limited. Here, we present a topological model of site-specific recombination characterizing all possible products of this reaction on twist knot substrates, extending the previous work of Buck and Flapan. We illustrate how to use our model to examine previously uncharacterized experimental data. We also show how our model can help determine the sequence of products in multiple rounds of processive recombination and distinguish between products of processive and distributive recombinations. This model studies generic site-specific recombination on arbitrary twist knot substrates, a subject for which there is limited global understanding. We also provide a systematic method of applying our model to a variety of different recombination systems.
Original language | English |
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Pages (from-to) | 350-67 |
Number of pages | 18 |
Journal | Journal of Molecular Biology |
Volume | 411 |
Issue number | 2 |
Early online date | 7 Jun 2011 |
DOIs | |
Publication status | Published - 12 Aug 2011 |
Keywords
- DNA, Superhelical
- Models, Biological
- Nucleic Acid Conformation
- Recombinases
- Recombination, Genetic
- Journal Article
- Research Support, Non-U.S. Gov't