Overall, our results reveal that ion-RNA interactions are governed by a delicate interplay between ion properties and RNA architecture, which itself is stabilized by those same ions.

The ion exchange kinetics remain virtually unchanged, demonstrating a surprising decoupling between spatial distribution and dynamical turnover. Our observation that the dwell time is independent of the RNA fold is likely due to the simple nature of RNAs studied here.

Importantly, the ion atmosphere of unstructured rU30 extends further into the solution compared to folded RNAs, despite having fewer bound ions. Interestingly, the bound ions around rU30 are distributed uniformly while specific binding emerges in A(CAG)9A and BWYV at low [X2+].

Unstructured rU30 favors diffuse Mg2+ retained through two or more hydration shells, whereas the CAG repeats and BWYV prefer more localized outer sphere Mg2+ binding. In contrast, Ca2+ tends to form inner-sphere contacts with all three RNAs, regardless of their folds.

Despite carrying nearly identical net charges by the RNAs, their ion atmospheres diverge strikingly based on RNA structural complexity, counterion concentration, and cation type.

We modeled an unstructured poly-uridylic tract (rU30), a semiflexible cytosine-adenine-guanine (CAG) repeats, and the tightly folded Beet Western Yellow Virus (BWYV) pseudoknot in a mixture of implicit monovalent salt and explicit divalent cations, X2+ (X = Mg or Ca).

We investigated how ion atmospheres of RNAs are modulated by their structural complexity using coarse-grain molecular dynamics simulations of three RNAs of similar net charge with differing structural complexity.

We are happy to share our recent work entitled "RNA structural complexity dictates its ion atmosphere" on bioRxiv (doi: . Thanks to @tienhung_91.