Phase Separation Modulates the Thermodynamics and Kinetics of RNA Hybridization

Biomolecular condensates can influence cellular function in a number of ways, including by changing the structural dynamics and conformational equilibria of the molecules partitioned within them. Here we use methyl transverse relaxation optimized spectroscopy (methyl-TROSY) NMR in conjunction with 2 '-O-methyl labeling of RNA to characterize the thermodynamics and kinetics of RNA-RNA base pairing in condensates formed by the C-terminal intrinsically disordered region of CAPRIN1, an RNA-binding protein involved in RNA transport, translation, and stability. CAPRIN1 condensates destabilize RNA-RNA base pairing, resulting from a similar to 270-fold decrease and a concomitant similar to 15-fold increase in the on- and off-rates for duplex formation, respectively. The similar to 30-fold slower diffusion of RNA single strands within the condensed phase partially accounts for the reduced on-rate, but the further similar to 9-fold reduction likely reflects shedding of CAPRIN1 chains that are interacting with the RNA prior to hybridization. Our study emphasizes the important role of protein solvation in modulating nucleic acid recognition processes inside condensates.