BPS2026 – RNA collapse and condensate formation tuned by temperature and counterions

Liquid-liquid phase separation (LLPS) is increasingly recognized as a central organizing principle for membraneless organelles in eukaryotic cells. The assembly and dissolution of RNA-rich condensates are governed by both intrinsic sequence properties and extrinsic factors such as temperature and ion concentration. Here, we developed a coarse-grained computational model to investigate the coupled effects of magnesium ions and temperature on RNA conformational ensembles and condensate formation. At the monomeric level, we observe a nonmonotonic size response: single-stranded RNA expands and then collapses in the presence of Mg 2+ as temperature increases. Preferential interaction coefficients show that Mg 2+ binding is enhanced at elevated temperature, indicating an entropically driven process. Partitioning of ion binding modes further reveals that diffusive ions rush in to form inner-sphere contacts with increasing temperature, whereas outer-sphere interactions remain largely unaffected. At the condensate level, simulations demonstrate that polyadenine (rA 30 ) undergoes lower critical solution temperature (LCST)-type phase separation. Within condensates, RNA chains display spatial heterogeneity: chains in the core of the condensate adopt extended conformations, whereas surface chains are more compact. Ion partition analysis reveals a corresponding shift from outer-sphere to inner-sphere Mg 2+ binding upon condensation. Together, these findings illustrate how RNA sequence, temperature, and divalent ion interactions synergistically regulate molecular conformations and mesoscale phase behavior. Our results provide mechanistic insight into the thermodynamics of RNA LLPS and suggest how Mg 2+ and temperature may tune condensate material properties relevant to cellular function.