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bioRxiv · 10.1101/2025.10.20.683600

Temperature-Dependent Ion Migration Underlies Sequence-Specific RNA Collapse

Zhang, H.·MAITY, H.·Nguyen, H.
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Abstract

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 SAXS profiles across a broad range of ionic conditions and reveal a non-monotonic 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. Statement of SignificanceIons and temperature strongly influence RNA structure and dynamics, yet the molecular mechanisms by which these factors jointly regulate RNA behavior remain poorly understood. Using coarse-grained simulations with temperature-dependent Mg2+-phosphate interactions, we report how ion binding reorganizes around single-stranded RNAs as temperature increases. We found that unstructured RNAs undergo a non-monotonic structural transition: thermal disruption of base stacking first expands the chain, followed by the collapse driven by enhanced Mg2+ binding. This collapse arises from a temperature-induced migration of Mg2+ from diffusive ion atmosphere to direct inner-sphere binding, linking RNA compaction to ion dehydration and entropy-driven binding. These results reveal that the RNA ion atmosphere is a dynamic, structure-coupled component of RNA organization and provide a mechanistic basis for thermoresponsive RNA condensation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/683600v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fe79beorg.highwire.dtl.DTLVardef@eaac88org.highwire.dtl.DTLVardef@e52bc1org.highwire.dtl.DTLVardef@19bbea0_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Zhang, H., MAITY, H., Nguyen, H.. 2025-10-21. Temperature-Dependent Ion Migration Underlies Sequence-Specific RNA Collapse. https://doi.org/10.1101/2025.10.20.683600

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