Intragenomic riboregulatory interaction modulates the conformation of the hepatitis C virus 3′X RNA

The 3′X RNA of the hepatitis C virus (HCV) is a highly conserved noncoding element required for viral replication. This RNA is known to make intragenomic interactions with another highly conserved element, 5BSL3.2, located in the open reading frame of the HCV genome. This RNA-RNA interaction is part of a riboregulatory network that is hypothesized to control various aspects of viral replication. Here, we used single-molecule FRET to characterize the binding mechanism of this riboregulatory interaction. Binding affinities and equilibrium constants were determined under a wide range of experimental conditions. Our results suggest that 5BSL3.2 differentially associates with the two conformations populated by the first 55 nucleotides of 3′X (3′X55), modestly favoring one bound conformation over the other. These findings shed new light on the structural nature of this interaction and appear to support an emerging hypothesis wherein the presence or absence of this intragenomic interaction influences viral translation and replication.