Salt Dependent Folding Energy Landscape of RNA Three-Way Junction

Abstract

RNAs are highly negatively charged molecules. Salt ions are crucial for RNA folding stability and conformational changes. In the present work, we employ the recently developed tightly bound ion (TBI) model, which accounts for the inter-ion correlations and the fluctuation of ion distributions, to investigate the ion-dependent free energy landscape for the three-way RNA junction in a 16S rRNA domain. The predicted electrostatic free energy landscape suggests that (a) ion-mediated electrostatic interactions cause an ensemble of unfolded conformations narrowly populated around the maximally extended structure and (b) Mg2+ ion-induced correlation effect may help bring the helices to the folded state. Non-electrostatic interactions, such as non-canonical interactions within the junctions and between junctions and helix stems, might further limit the conformational diversity of the unfolded state, resulting in a more ordered unfolded state than the one predicted from the electrostatic effect. Moreover, the folded state is predominantly stabilized by the coaxial stacking force. The TBI-predicted folding stability agrees well with the experimental measurements for the different Na+ and Mg2+ ion concentrations. For Mg2+ solutions, the TBI model, which accounts for the ion correlation effect, gives more accurate predictions than the Poisson-Boltzmann theory, which tends to underestimate the role of Mg2+ in stabilizing the folded structure. Detailed control tests in-dicate that the dominant ion correlation effect comes from the charge-charge Coulombic correlation rather than the excluded volume (size) correlation between the ions. Furthermore, the model gives quantitative predictions for the ion size effect in the folding stability.