Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core

Many functional RNAs fold into a compact, roughly globularshapeby minimizing the electrostatic repulsion between their negativelycharged phosphodiester backbone. The fold of such close, compact RNAarchitecture is often so designed that its outer surface and complexcore both are predominately populated by phosphate groups looselysequestering bases in the intermediate layers. A number of helicaljunctions maintain the RNA core and its nano-water-pool. While thefolding of RNA is manifested by its counterion environment composedof mixed mono- and divalent salts, the concerted role of ion and waterin maintaining an RNA fold is yet to be explored. In this work, detailedatomistic simulations of SAM-I and Add Adenine riboswitch aptamers,and subgenomic flavivirus RNA (sfRNA) have been performed in a physiologicalmixed mono- and divalent salt environment. All three RNA systems havecompact folds with a core diameter of range 1-1.7 nm. The spatiotemporalheterogeneity of RNA hydration was probed in a layer-wise manner bydistinguishing the core, the intermediate, and the outer layers. Thelayer-wise decomposition of hydrogen bonds and collective single-particlereorientational dynamics reveal a nonmonotonic relaxation patternwith the slowest relaxation observed at the intermediate layers thatinvolves functionally important tertiary motifs. The slowness of thisintermediate layer is attributed to two types of long-resident watermolecules: (i) water from ion-hydration layers and (ii) structurallytrapped water (distant from ions). The relaxation kinetics of thecore and the surface water essentially exposed to the phosphate groupsshow well-separated time scales from the intermediate layers. In theslow intermediate layers, site-specific ions and water control thefunctional dynamics of important RNA motifs like kink-turn, observedin different structure-probing experiments. Most interestingly, wefind that as the size of the RNA core increases (SAM1 core < sfRNAcore< Add adenine core), its hydration tends to show faster relaxation.The hierarchical hydration and the layer-wise base-phosphatecomposition uniquely portray the globular RNA to act like a soft vesiclewith a quasi-dynamic nano-water-pool at its core.