Perspectives on Viral RNA Genomes and the RNA Folding Problem

Area of Science:

• Virology
• Structural Biology
• Biophysics

Background:

• Viral RNA genomes are structurally dynamic, adopting multiple conformations essential for various stages of the viral life cycle, including replication and assembly.
• Understanding these dynamic RNA structures is crucial for deciphering viral mechanisms and developing antiviral strategies.
• The inherent flexibility and potential for disorder in viral RNA pose significant challenges for structural analysis.

Purpose of the Study:

• To investigate the dynamic structural changes of viral RNA genomes.
• To characterize the multiple conformations adopted by viral RNA in equilibrium.
• To explore the role of RNA structure and dynamics in viral assembly and host interaction.

Main Methods:

• Utilizing high-resolution asymmetric cryo-electron microscopy to visualize viral RNA structures.
• Employing chemical probing techniques to assess RNA structural accessibility and disorder.
• Applying the Detection of RNA Folding Ensembles using Expectation Maximization (DREEM) algorithm to analyze probing data and identify RNA conformational ensembles.

Main Results:

• Identified multiple, distinct RNA conformations existing in dynamic equilibrium within viral particles.
• Quantified the degree of structure and disorder across different regions of the viral RNA genome.
• Demonstrated the applicability of chemical probing and DREEM for studying dynamic RNA structures in vitro, in virio, and in vivo.

Conclusions:

• Viral RNA is not static but exists as a dynamic ensemble of structures.
• These dynamic structural changes are fundamental to viral processes like assembly and host evasion.
• Advanced techniques like chemical probing coupled with DREEM provide powerful tools for studying complex viral RNA folding.