DNA topology regulation by essential type II topoisomerases (Topo II) involves the formation of transient enzyme-induced double-stranded breaks on DNA called cleavage complexes. Although Topo II does not read the DNA sequence directly, the location and frequency of these cleavage complexes on DNA exhibit marked sequence preferences. Recent advances in high-sensitivity mapping techniques have identified 20–50-fold more cleavage sites than previously identified, revealing that Topo II cleaves DNA at tens of thousands of sites on genomic DNA with frequencies varying by three orders of magnitude. We hypothesize that Topo IIs employs an indirect readout mechanism for G-segment selection and cleavage that involves sensing the physical properties and conformations of the DNA rather than the sequence directly. This study integrates high-resolution in vitro cleavage site profiling with all-atom molecular dynamics simulations of Topo II bound to G-segment sequences with different cleavage frequencies. By quantifying sixteen distinct DNA shape parameters, we explore the conformational variability and characteristics that influence G-segment capture and cleavage-relegation equilibrium by Topo II. This work highlights how Topo II enzymes rely on an indirect readout mechanism through which local DNA shape parameters guide sequence-selective cleavage.
Prajapati et al. (Sun,) studied this question.