Type II topoisomerase substrate geometry revealed through combined experiment and computation.

Type II topoisomerases, or topo II enzymes, play a crucial role in regulating DNA topology using a strand-passage mechanism. This process involves a transfer-segment DNA being passed through a gate-segment that has been temporarily cleaved. While researchers have gained significant insights into the binding and cleavage of the gate-segment DNA, capturing the transfer-segment DNA has been a more challenging task due to its transient nature.

However, a study has proposed a new method to resolve this issue by combining experimental single-molecule measurements with Brownian dynamics simulations.

The researchers correlated the unlinking rate of DNA passing through topo II with its geometric features, ultimately determining the complete three-dimensional preferred crossing geometry for strand passage. Surprisingly, the preferred crossing geometries for two different types of topo II enzymes, Escherichia coli topoisomerase IV and Methanosarcina mazei topoisomerase VI, were found to be distinct.

These unique geometries provide structural models of the DNA synapse that is selected for strand passage, as well as a mechanistic basis for the differing activities and biological functions of these two enzymes. This groundbreaking approach not only generalizes the study of topo II enzymes but also offers unique insights into the kinetic selection of DNA synapse structure.