Unraveling the Tangled Complexity of DNA: Combining Mathematical Modeling and Experimental Biology to Understand Replication, Recombination and Repair

¹ Department of Biology, Agnes Scott College, Decatur, GA 30030, USA
² Department of Biology, Beloit College, Beloit, WI 53511, USA

^⋆ Corresponding author. E-mail: srobic@agnesscott.edu

Abstract

How does DNA, the molecule containing genetic information, change its three-dimensional shape during the complex cellular processes of replication, recombination and repair? This is one of the core questions in molecular biology which cannot be answered without help from mathematical modeling. Basic concepts of topology and geometry can be introduced in undergraduate teaching to help students understand counterintuitive complex structural transformations that occur in every living cell. Topoisomerases, a fascinating class of enzymes involved in replication, recombination and repair, catalyze a change in DNA topology through a series of highly coordinated mechanistic steps. Undergraduate biology and mathematics students can visualize and explore the principles of topoisomerase action by using easily available materials such as Velcro, ribbons, telephone cords, zippers and tubing. These simple toys can be used as powerful teaching tools to engage students in hands-on exploration with the goal of learning about both the mathematics and the biology of DNA structure.