Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing
This study uses time-resolved DMS-MaP chemical probing to measure RNA structural dynamics at nucleotide resolution across three model RNAs: the Salmonella agsA fourU RNA thermometer, the HIV-1 TAR hairpin, and the P4-P6 domain of the Tetrahymena group I intron ribozyme. The goal of this work is to characterize individual nucleotides fluctuation towards quantitative inference of local RNA folding energetics. These datasets support the development of PRIME (Probing-Resolved Inference of Molecular Energetics), a framework that extracts free-energy estimates for canonical, non-canonical, and tertiary structural elements directly from chemical probing time courses. The resulting data provide a resource for studying RNA folding thermodynamics, benchmarking computational models, and understanding how dynamic structural features contribute to RNA function.