# Spontaneous dimerization of the hepatitis C virus 3′X RNA

## TL;DR

This study reveals how a specific RNA sequence from the hepatitis C virus can form multiple dimeric structures, which may influence viral replication.

## Contribution

A novel integrative approach combining single-molecule FRET and size-exclusion HPLC is used to study RNA dimerization dynamics.

## Key findings

- 3′X55 RNA can form multiple dimeric species with distinct structural properties.
- Interconversion between dimeric species is slow, taking hours to reach equilibrium.
- Dimerization behavior is explained by a four-state kinetic model.

## Abstract

The 3ʹX RNA of the hepatitis C virus is a highly conserved, 98-nucleotide, non-coding sequence located at the 3ʹ terminus of the viral genome. This essential riboregulatory element contains a 16-nucleotide sequence, known as the dimer linkage sequence (DLS), which has been shown in vitro to facilitate the dimerization of the first 55 nucleotides of 3ʹX (3ʹX55). Here, we employ a novel integrative approach based on quantitative single-molecule FRET and analytical size-exclusion HPLC to monitor the structural, energetic, and dynamic aspects of 3ʹX55 dimerization. At high RNA concentrations, we see that 3′X55 can adopt multiple dimeric species with different structural properties. The interconversion between these species is slow, requiring several hours to reach equilibrium. Finally, the concentration- and time dependence of dimerization are both well described by a simple four-state kinetic model, which may explain how this riboregulatory interaction governs critical RNA-dependent processes during viral replication.