Language
English
Publication Date
1-30-2026
Journal
bioRxiv
DOI
10.64898/2026.01.28.702231
PMID
41659569
PMCID
PMC12873924
PubMedCentral® Posted Date
1-30-2026
PubMedCentral® Full Text Version
Pre-Print
Abstract
RNA function is governed by RNA folding, but strategies for measuring RNA folding thermodynamics are limited, and fundamental questions such as the energy of base pair opening remain debated. Here we introduce Probing-Resolved Inference of Molecular Energetics (PRIME) to extract nucleotide-resolution RNA structural energetics from scalable chemical probing experiments. Applying PRIME to diverse RNAs, we find that RNA base pairs and tertiary interactions dynamically open with free energies of 0.5-3 kcal/mol, revealing that RNA nucleotides ubiquitously sample open conformations at biologically accessible energies. PRIME further resolves energetic coupling across RNAs, providing an energetic understanding of RNA structural dynamics and long-range coordination in RNA folding. PRIME represents a widely accessible strategy for interrogating RNA thermodynamics, enabling mechanistic understanding and engineering of RNA biology.
Published Open-Access
yes
Recommended Citation
Choi, Edric K; Bose, Ritwika; Mathews, David H; et al., "Ubiquitous Low-Energy RNA Fluctuations and Energetic Coupling Measured by Chemical Probing" (2026). Faculty, Staff and Students Publications. 8190.
https://digitalcommons.library.tmc.edu/baylor_docs/8190