Mathematical Methods in Dna Topology: Applications to Chromosome Organization and Site-Specific Recombination

Abstract

In recent years, knot theory and low-dimensional topology have been effectively used to study the topology and geometry of DNA under different spatial constraints, and to solve the topological mechanisms of enzymes such as site-specific recombinases and topoisomerases. Through continuous collaboration and close inter- action with experimental biologists, many problems approached and the solutions pro- posed remain relevant to the biological community, while being mathematically and computationally interesting. In this paper, we illustrate the use of mathematical and computational methods in a variety of DNA topology problems. This is by no means an exhaustive description of techniques and applications, but is rather intended to in- troduce the reader to the exciting applications of topology to the study of DNA. Many more examples will be found throughout this book