Site-specific recombination is an important cellular process that yields a variety of knotted and catenated DNA products on supercoiled circular DNA  . Twist knots are some of the most common conformations of these products  . 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 like site-specific recombination is very limited. Here we present a topological model of site-specific recombination characterising all possible products of site-specific recombination on twist knot substrates, extending previous work of Buck and Flapan. We illustrate how to use our model to examine previously uncharacterized experimental data. We  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 recombination. Companion paper (arXiv:1007.2115v1 math.GT) provides topological proofs for the model presented here .
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 like site-specific recombination is very limited. Here we present a topological model of site-specific recombination characterising all possible products of this reaction on twist knot substrates, extending previous work of Buck and Flapan. We illustrate how to use our model to examine previously uncharacterised 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 recombination. 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 .
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is an important cellular process that yields a variety of knotted and catenated DNA products
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molecules can yield a variety of knots and catenanes
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and they can act as substrates for further rounds of site-specific recombination
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site-specific recombination
this reaction
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uncharacterized
uncharacterised
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also
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Companion paper (arXiv:1007.2115v1 math.GT) provides topological proofs for the model presented here
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