Abstract
RNAs are major drivers of phase separation in the formation of biomolecular condensates. Recent studies suggest that RNAs can also undergo protein-free phase separation in the presence of divalent ions or crowding agents. Much remains to be understood regarding how the complex interplay of base stacking, base pairing, electrostatics, ion interactions, and structural propensities governs the phase behaviour of RNAs. Here we develop an intermediate resolution model for condensates of RNAs (iConRNA) that can capture key local and long-range structure features of dynamic RNAs and simulate their spontaneous phase transitions in the presence of . Representing each nucleotide using 6 or 7 beads, iConRNA considers specific RNA base stacking and pairing interactions and includes explicit ions to study -induced phase separation. Parametrized using theoretical and experimental data, the model can correctly reproduce the chain properties of A-form helical poly(rA) and coil poly(rU), and essential structures of several RNA hairpins. With an effective ion model, iConRNA simulations successfully recapitulate the experimentally observed lower critical solution temperature (LCST)-type phase separation of poly(rA) and the dissolution of poly(rU). Furthermore, the phase diagrams of CAG/CUG/CUU-repeat RNAs correctly reproduce the experimentally observed sequence- and length-dependence of phase separation propensity. These results suggest that iConRNA can be a viable tool for studying homotypic RNA and potentially heterotypic RNA-protein phase separations.
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