RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.

Area of Science:

• Molecular Biology
• Biophysics
• Genetics

Background:

• RNA G-quadruplexes (rG4s) are vital structural elements in gene regulation, translation, and genome stability.
• rG4s in untranslated regions of mRNAs influence translation efficiency and localization.
• rG4s in long noncoding RNAs and telomeric RNA are implicated in RNA processing and cellular aging.

Purpose of the Study:

• To elucidate the atomic-level folding mechanisms of parallel-stranded RNA G-quadruplexes.
• To investigate the folding pathways of specific RNA sequences, including TERRA.

Main Methods:

• All-atom enhanced-sampling molecular dynamics simulations.
• Well-tempered metadynamics coupled with solute tempering.

Main Results:

• RNA G-quadruplex folding initiates from a compacted coil ensemble with dynamic guanine stacking and pairing.
• The formation of three-quartet rG4s occurs through diverse pathways involving strand rearrangements.
• Two-quartet rG4 structures serve as common transitory ensembles, indicating a complex, multipathway folding process.

Conclusions:

• RNA G-quadruplex folding is more complex than previously predicted, without distinct G-hairpin or G-triplex intermediates.
• Enhanced sampling methodologies present challenges for multidimensional free-energy surfaces.
• Force-field limitations were identified as a factor in the simulations.