Untwisting and untangling DNA: Symmetry breaking by topoisomerases

Abstract

Replication wreaks topological havoc on the genome. Ahead of replication forks DNA is over‐wound, while nascent DNA molecules are intertwined behind them, leading to linked chromosomes. Replication and chromosome segregation depend on the resolution of these topological tangles. Topoisomerases solve these problems by relaxing positive supercoils ahead of replication forks and decatenating replicated chromosomes. Consistent with these roles, members of the type II family of topoisomerases asymmetrically relax positive and negative supercoils. Topoisomerase IV (Topo IV), a bacterial type II topoisomerase, removes positive supercoils ~20 fold faster than negative supercoils. Current models explaining this asymmetry suggest that Topo IV binds DNA segments juxtaposed at an acute crossing angle. Single‐molecule experiments permitted us to directly test this hypothesis by measuring unlinking rates of single left‐ and right‐handed DNA crossings. Combining these measurements with Monte Carlo simulations of the DNA crossings provides a measure of the preferred crossing angle for Topo IV. Surprisingly, the preferred crossing angle is larger than previous estimates and can not account for the asymmetric supercoil relaxation rates. Single‐molecule relaxation measurements reveal that the asymmetry results from processivity differences of Topo IV in relaxing positively and negatively supercoiled DNA.