Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences

Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)_n (n = 30 and 31) show that the salt-dependent free energy gap, ΔG_S, between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (G_S) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, C_S, increases, ΔG_S and G_S increase, which decreases the rates of dimer formation. In contrast, ΔG_S for shuffled sequences, with the same length and sequence composition as (CAG)₃₁, is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.