Eur. Phys. J. Special Topics 165, 175-182 (2008)
https://doi.org/10.1140/epjst/e2008-00861-1

Cutting DNA: Mechanics of the topoisomerase

¹ School of Engineering, Aberdeen University, AB24 3, FX Aberdeen, UK
² Dept. of Applied Mathematics & Theoretical Physics, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, CB3 0WA, UK

Corresponding author: jmtt2@damtp.cam.ac.uk

Abstract

Taking the accurate theoretical solutions of Coleman and Swigon for a DNA plasmid in a plectonemic state under imposed link and responsive writhe, we examine in detail the working of the two types of cutting enzyme (topoisomerase Type 1 and topoisomerase Type 2). The mechanical processes involved can generate a plethora of outcomes, all assigning different levels of relaxation to the molecule. Alternative outcomes arise when there are co-existing (meta-) stable equilibrium states. Resolution of the outcome would then require a dynamic analysis of the relaxation process, though the Maxwell criterion can offer some guidance.