Predicting Knot and Catenane Type of Products of Site-specific Recombination on Twist Knot Substrates

TL;DR

This paper introduces a topological model to predict and analyze the variety of DNA knot and catenane products resulting from site-specific recombination on twist knot substrates, aiding understanding of cellular processes.

Contribution

The paper extends previous models to systematically characterize all possible recombination products on twist knots, including multiple rounds and distinguishing processive from distributive recombination.

Findings

Model characterizes all products of site-specific recombination on twist knots.

Enables analysis of experimental data and product sequence determination.

Provides a systematic approach applicable to various recombination systems.

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 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.