Confined environment facilitates stacked conformations in Holliday Junction

Abstract

Holliday Junction (HJ) is an important intermediate in homologous recombination and is involved in DNA break repair. It is a highly dynamic structure and transitions between two stacked isomers through an intermediate open conformer. However, the insight into the effect of environmental confinement on HJ conformation population is incomplete. The understanding would be an important bridge between studies generally carried out in aqueous buffers and confined environments, as found in vivo. By employing fluorescence-based techniques we investigated the effect of confinement on HJ conformation using reverse micelle encapsulation as a model for confined space. We observed that inside the confinement of reverse micelle, HJ prefers to adopt stacked conformation. Most strikingly, even at lower divalent cation concentrations, the preference for stacked conformation is prevalent over an open conformation. The conformational heterogeneity also reduces with increasing degree of confinement. Our finding suggests that such confinement-induced changes in the conformer population might influence the interaction and activity of the HJ-recognizing proteins in the cellular environment.