The hepatitis C virus (HCV) genome is a positive-sense, single-stranded RNA that is highly structured with multiple conserved regions critical to viral propagation. This work focuses on a cis-regulatory element, 5BSL3.2, which has been shown to interact with the 3′X RNA of HCV. Recent work has detailed the structural dynamics of 3′X, illustrating interconversion between two distinct conformations may impact viral propagation. In this presentation, we detail the effects of 5BSL3.2 on the 3′X conformational equilibrium via single-molecule FRET and by applying a novel four-state equilibrium model. These methods reveal the equilibrium constants of conformational interconversion and the binding affinities of the respective 3′X conformations. Our results demonstrate that 5BSL3.2 can not only bind to both 3′X conformations but can also modulate the conformational equilibrium, promoting one of the intrinsic structures of 3′X. This work supports an emerging hypothesis that suggests the 3′X-5BSL3.2 interaction is central to a riboregulatory network that controls viral replication and translation.
Rogers et al. (Sun,) studied this question.