Mechanistic basis for relaxation of DNA supercoils by human topoisomerase IIIα–RMI1–RMI2

Topoisomerase enzymes are essential for the regulation of DNA topology. Human topoisomerase IIIα is a Type 1A topoisomerase that exists as a complex with RMI1 and RMI2, known as TRR. The TRR complex can unlink entwined DNA strands and is known to be important for resolving DNA replication and recombination intermediates. It has recently been proposed that TRR can also relax transient negatively supercoiled loops of DNA generated by the translocase PICH and that this activity may help to facilitate the resolution of ultrafine anaphase bridges (UFBs) between segregating sister chromatids. However, the mechanism by which TRR interacts with, and processes, negatively supercoiled DNA is not well understood. Here, we establish a single-molecule strategy to simultaneously measure real-time changes in supercoiling density and visualize the interactions of TRR with underwound DNA using a combination of optical tweezers and fluorescence imaging. We demonstrate that TRR relaxes highly negatively supercoiled DNA in a processive manner and that the timescale for relaxation is less than the expected lifetime of the negatively supercoiled loops generated by PICH. We also show that in the absence of free protein in solution, TRR remains bound to the DNA for long time periods after the torsional stress has been released. Our findings provide a mechanistic basis for how TRR can relax negative supercoils, consistent with its proposed role in UFB resolution. Moreover, our assay could also be widely applied to study the interactions of other families of topoisomerases with negatively supercoiled DNA.