DNA Torque and Topology during Replication

During DNA replication, the mechanical unwinding and separation of DNA by the replisome generates torsional stress that can lead to the over-winding (+supercoiling) of DNA in front of the replisome and intertwining (precatenanes) of the daughter strands behind the replisome. Topoisomerases play a crucial role in regulating this torsional stress but, if not resolved in a timely manner, the perturbations of the DNA topological landscape can create a physical barrier to the progression of the replisome and the synthesis of new DNA. In addition to the actions of the replisome and topoisomerases, the intrinsic mechanical properties of DNA play an important role in the accumulation, suppression, and resolution of torsional stress.

Using both single and braided chromatin fibers, we directly measured torque within chromatin as replication forks advance. We showed that a single chromatin substrate is torsionally softer than a braided substrate, indicating that DNA supercoiling should preferentially partition in front of the replisome. We also demonstrated that yeast topoisomerase II displays a strong preference for a single chromatin fiber over a braided fiber. These results suggest a synergistic coordination as the mechanical properties of chromatin driving DNA supercoiling ahead of the fork, where supercoiling is more efficiently removed by topoisomerase II. (Le et al., Cell, 2019).