RNA2PS: A sequence-specific coarse-grained RNA model linking structure, thermodynamics and phase separation

RNA plays a central role in the formation and regulation of biomolecular condensates, yet a quantitative understanding of how RNA sequence, structure, and thermodynamics jointly determine phase behaviour, particularly in repeat expansion RNAs, remains incomplete. Here, we introduce RNA2PS, a sequence-specific RNA coarse-grained model for phase-separation that predicts RNA structure from sequence, achieving quantitative agreement for both single-stranded conformations and duplex helical geometry relative to crystallographic PDB structures. RNA2PS represents each nucleotide by two beads that separate the phosphate–ribose backbone from the base. This representation decouples electrostatic interactions from directional base pairing, while explicitly incorporating strand polarity (5′ → 3′) and local sequence context at the trimer level. Canonical and wobble base pairing are modelled through a multi-body potential with sequence-dependent coordination. Importantly, RNA2PS captures sequence-dependent duplex stability at the nearest-neighbour level and reproduces experimental melting temperatures across a diverse set of sequences. RNA2PS shows that phase separation of trinucleotide repeat RNAs is governed by transient inter-strand duplexes that form reversible cross-links. Competition between intra- and intermolecular base pairing regulates the density of labile RNA–RNA interactions, giving rise to strong sequence- and length-dependent differences in condensation that reproduce cellular RNA foci formation. Overall, RNA2PS provides a near-quantitative predictive framework that links sequence-encoded hybridization thermodynamics to mesoscale condensation of pure RNA sequences.