Unraveling Ribonucleic Acid Unfolding: A Quantitative Comparison of Solution and Gas-Phase Unfolding

Abstract

Ribonucleic acids (RNAs) are challenging structural biology targets, as numerous barriers exist to determining their high-resolution structures and specific biological functions. Previous results have highlighted the utility of collision-induced unfolding (CIU) to relatively rapidly assess noncoding (nc)RNA higher-order structure (HOS) information. Yet, there remain many gaps in our understanding of how these data can be related to the structures adopted by RNAs in solution as current correlations are largely qualitative. In this study, we describe significant advancements in RNA CIU. Previous RNA CIU reports reveal minimal-to-no RNA unfolding events (or features) upon being subjected to standard CIU conditions. Here, we increase the RNA CIU information through supercharging and quantitatively evaluate the improved RNA CIU data obtained to solution-phase unfolding data collected across a range of Mg²⁺ concentrations. Finally, we apply our supercharged CIU experiment to mitochondrial encephalopathy, lactic acidosis, and stroke-like episode (MELAS)-associated mt-tRNA leucine (Leu, UUR) (mt-tRNA^Leu(UUR)) species. Our data demonstrate strong quantitative correlations between gas-phase and solution-phase RNA unfolding events as a function of Mg²⁺ and MELAS-associated mutations. Taken together, these results indicate strong, solution-relevant relationships for CIU data collected for these RNAs. We conclude our work by discussing future work targeting RNA CIU annotation, broader biophysical characterization of disease-associated RNAs using CIU, and CIU-enabled transcriptomic analysis.