BPS2026 – Mechanism of HCV 3'X RNA dimerization

The 3'X region of the hepatitis C virus genome is a highly conserved, 98-nucleotide noncoding sequence positioned at the 3' terminus. This critical riboregulatory element includes a 16-nucleotide dimer linkage sequence (DLS) that promotes in vitro dimerization of the first 55 nucleotides (3'X55). In this study, we apply a combined strategy using quantitative single-molecule FRET and analytical size-exclusion HPLC to investigate the structure, energetics, and dynamics of 3'X55 dimer formation. At elevated RNA concentrations, 3'X55 assembles into multiple dimeric conformations with distinct structural features. Transitions among these dimers occur slowly, requiring hours to reach equilibrium. Moreover, the observed concentration- and time-dependence of dimerization align well with a four-state kinetic framework, providing insight into how this RNA element regulates essential steps in the viral replication cycle.