Choi: Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing

Abstract: RNA structures undergo dynamic fluctuations that are intimately linked to RNA biological function. However, our knowledge of the energetics governing these fluctuations has been limited by resolution versus throughput tradeoffs of existing biophysical methods. Here, we introduce Probing-Resolved Inference of Molecular Energetics (PRIME), a kinetic framework that extracts RNA structural energetics at nucleotide-resolution from widely accessible chemical probing experiments readout by high-throughput sequencing. Applying PRIME to diverse RNAs, we find that RNA base pairs dynamically open with free energies of 0.5-3 kcal/mol, approximately half of commonly inferred values. In complex multi-state RNAs, we find that both secondary and tertiary interactions are energetically coupled across long distances, with global folding often entailing local destabilization of individual nucleotides that is compensated by net energetic stabilization throughout an RNA molecule. Together, our data reveal that RNA nucleotides ubiquitously sample open states at energies that are far more accessible to biological processes than appreciated and provide a link between these local nucleotide fluctuations and collective RNA behavior, creating a new foundation for understanding myriad RNA functions that are driven by dynamic RNA interactions. PRIME establishes a new scalable platform for RNA biophysics, opening new avenues for understanding and engineering RNA function. Speaker: Edric Choi is a PhD researcher in the Lucks Lab at Northwestern University, part of the Center for Synthetic Biology (CSB) and the National Institute for Theory and Mathematics in Biology (NITMB), where he studies RNA structure and dynamics using high-throughput chemical probing. He received his undergraduate training in Biochemistry and Computer Science at Denison University, where he was first introduced to chemical probing through studies of RNA thermometers, and later worked on RNase P and disease-linked tRNAs with Venkat Gopalan at The Ohio State University. His research focuses on developing quantitative frameworks to interpret probing data and connect RNA structure, energetics, and function.