Direct observation of topoisomerase conformational dynamics

Synopsis

Type IA DNA topoisomerases (topo IA) are conserved among all domains of life due to their critical roles in regulating DNA supercoiling, DNA unlinking, and RNA processing. Topo IA share a unique ATP-independent strand-passage mechanism in which the enzyme binds and cleaves a single-stranded DNA segment, forming a protein-DNA gate through which a second strand of DNA is passed followed by religation of the cleaved DNA. Although this strand-passage model is widely accepted, opening of the topo IA protein-DNA gate has never been directly observed.  We developed a single-molecule assay to directly measure gate opening by type IA topos.  We found that the protein-DNA gate opens by 6 nm and can close against relatively large forces.  More recently, we discovered that the gate dynamics of bacterial type IA topos depend on the Mg²⁺ concentration. Experiments and molecular dynamics simulations reveal an Mg²⁺-dependent molecular switch that drives gate opening and closing. More generally, these results indicate an unexpected role for divalent cations in modulating protein conformational dynamics.  Direct observation of type IA topoisomerase conformational dynamics has contributed to the resolution of mechanistic questions while revealing unanticipated behavior of this important class of topoisomerases.