Temperature-dependent ion migration underlies sequence-specific collapse of unstructured RNA

Ions and temperature jointly regulate RNA structure, dynamics, and phase behavior, yet their coupled effects remain poorly understood at the molecular level. Single-stranded RNA (ssRNA), a ubiquitous and functionally versatile class of RNA, presents a particularly challenging target due to its intrinsic flexibility and pronounced sensitivity to ionic and thermal perturbations. Here, we extend our previously validated coarse-grained RNA model by introducing temperature-dependent divalent ion-phosphate potentials along with revised stacking interactions to elucidate how electrostatics, stacking, and hydration collectively determine ssRNA behavior. Our simulations quantitatively reproduce experimental small-angle X-ray scattering profiles across a broad range of ionic conditions and reveal a nonmonotonic temperature dependence of RNA compaction: ssRNAs expand upon heating, reach a sequence-specific maximum size, and then collapse as enhanced counterion condensation dominates. Rising temperature strengthens ion-RNA interactions, leading to a reorganization from diffusive to inner-sphere coordination, directly linking RNA collapse to ion dehydration. Our results establish that the ion atmosphere is a dynamic, sequence-encoded extension of RNA structure. This framework provides molecular insight into how temperature and ions govern RNA conformational transitions, offering a microscopic basis for RNA thermoadaptation, cold-induced misfolding, and RNA phase transitions.