Confined environment facilitates stacked conformations in Holliday Junction

Abstract

Holliday Junction (HJ) is an important intermediate for 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. In a constrained cellular environment, HJ is expected to behave differently than in vitro. This can affect target recognition by junction-binding proteins and their subsequent functions. However, the studies on the effect of the confined environment on HJ is extremely scanty. In this work, 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 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. Our finding suggests that such confinement-induced changes in the conformer population might affect the interaction and activity of the HJ-recognizing proteins in the cellular environment.