Using Knot Theory to Model and Analyze DNA Replication and Recombination

Abstract

Due to DNA supercoiling inside the nucleus of a cell, DNA can be modeled as a mathematical knot. We will analyze and examine the knots and links that arise after single or multiple rounds of DNA recombi- nation using the tangle model. We will also examine how the topology of a DNA strand is modified during DNA replication and which enzymes directly alter the topology of the strand. The goal is to better understand the mechanism of site-specific recombination and knotted DNA replication through mathematical models.