# Ion Condensation onto Ribozyme is Site-Specific and Fold-Dependent

## TL;DR

This study reveals that ion condensation onto the Azoarcus ribozyme is highly specific, site-dependent, and fold-dependent, contrasting with traditional theories of uniform ion binding, and is influenced by the ribozyme's architecture and shape fluctuations.

## Contribution

The paper demonstrates through simulations that ion binding to RNA is specific and depends on nucleotide position and folding state, challenging the notion of non-specific ion interactions.

## Key findings

- Ion condensation is highly site-specific and fold-dependent.
- Regions with high ion coordination are present even without tertiary interactions.
- Ion binding patterns differ markedly from those on rigid charged rods.

## Abstract

The highly charged RNA molecules, with each phosphate carrying a single negative charge, cannot fold into well-defined architectures with tertiary interactions, in the absence of ions. For ribozymes, divalent cations are known to be more efficient than monovalent ions in driving them to a compact state although Mg$^{2+}$ ions are needed for catalytic activities. Therefore, how ions interact with RNA is relevant in understanding RNA folding. It is often thought that most of the ions are territorially and non-specifically bound to the RNA, as predicted by the counterion condensation (CIC) theory. Here, we show using simulations of ${\it Azoarcus}$ ribozyme, based on an accurate coarse-grained Three Site Interaction (TIS) model, with explicit divalent and monovalent cations, that ion condensation is highly specific and depends on the nucleotide position. The regions with high coordination between the phosphate groups and the divalent cations are discernible even at very low Mg$^{2+}$ concentrations when the ribozyme does not form tertiary interactions. Surprisingly, these regions also contain the secondary structural elements that nucleate subsequently in the self-assembly of RNA, implying that ion condensation is determined by the architecture of the folded state. These results are in sharp contrast to interactions of ions (monovalent and divalent) with rigid charged rods in which ion condensation is uniform and position independent. The differences are explained in terms of the dramatic non-monotonic shape fluctuations in the ribozyme as it folds with increasing Mg$^{2+}$ or Ca$^{2+}$ concentration.