Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Biology

Background:

• Repeat RNA sequences, such as those in trinucleotide repeat disorders, can self-associate into condensates.
• The structural dynamics and aggregation propensity of these RNA molecules are critical for understanding their biological roles and associated pathologies.

Purpose of the Study:

• To investigate the relationship between the free energy landscape of repeat RNA monomers and their self-assembly kinetics.
• To determine the primary factors governing the rates and yield of RNA condensate formation.

Main Methods:

• Utilized coarse-grained molecular simulations of (CAG)n RNA monomers (n=30 and 31).
• Analyzed the salt-dependent free energy gap (ΔG) between ground and excited monomer states.
• Modeled both perfect and slipped hairpin structures, including those with overhangs.

Main Results:

• For even repeat lengths, the free energy gap (ΔG) between perfect and slipped hairpin states is the key determinant of self-assembly rates and yield.
• For odd repeat lengths, the free energy (G) of the ground state (slipped hairpin) predicts self-association kinetics.
• Increased monovalent salt concentration (C) elevates ΔG and G, thereby reducing dimer formation rates.
• Shuffled sequences exhibit larger ΔG, significantly suppressing their aggregation propensity.

Conclusions:

• The free energy landscape, specifically the energy gap between conformational states, is a critical regulator of repeat RNA self-assembly.
• An inverse correlation exists between the free energy gap and RNA aggregation, a principle applicable beyond (CAG)n repeats.