# Structural flexibility in the ordered domain of the dengue virus strain 2 capsid protein is critical for chaperoning viral RNA replication

## TL;DR

This study shows that the Dengue virus capsid protein uses structural flexibility to help RNA replication by performing both annealing and strand displacement.

## Contribution

The study reveals that flexibility in the ordered domain of Denv2C is essential for strand displacement, while the disordered region acts as a counterion for annealing.

## Key findings

- Denv2C's ordered region flexibility is critical for RNA strand displacement.
- A rigid mutation in the ordered region limits Denv2C to only RNA annealing.
- The disordered region of Denv2C functions as a macromolecular counterion during annealing.

## Abstract

Viral replication necessitates intricate nucleic acid rearrangements, including annealing and strand displacement to achieve the viral RNA functional structure. Often a single RNA chaperone performs these seemingly incompatible functions. This raises the question of what structural and dynamic features of such chaperones govern distinct RNA rearrangements. While cationic intrinsically disordered regions promote annealing by playing a charge-screening role, how the same chaperone mediates strand displacement remains elusive. Here, we investigate the annealing and strand displacement of the 5’ upstream AUG region (5UAR) as chaperoned by the Dengue virus strain 2 capsid protein (Denv2C) as a model RNA chaperone. Through single molecule analysis and molecular simulations, we demonstrate that Denv2C regulates nucleic acid melting, folding, annealing, and strand displacement via flexibility in its ordered region. A mutation that renders the Denv2C ordered region rigid, converts Denv2C into a mere annealer. Our findings underscore the role of Denv2C’s disordered region as a “macromolecular counterion” during RNA annealing, while a flexible ordered region is crucial for effective strand displacement.

The online version contains supplementary material available at 10.1007/s00018-025-05712-x.