Short talk 3
Dynamic RNA conformational ensembles as drug targets: an integrated NMR and chemical probing approach

Presenting Author: Rosalie Koros

Uppsala universitet, Department of Medical Biochemistry and Microbiology, IMBIM, Husargatan 3, 75237 Uppsala, SE, rosalie.koros@imbim.uu.se

Author(s)
Rosalie Koros¹, Dr. Christian Steinmetzger¹, Dr. Rubin Dasgupta¹, Dr. Joanna Sajkowska¹, Prof. Katja Petzold¹

¹ Uppsala universitet

RNA is an emerging therapeutic target, but rational drug discovery is constrained by incomplete knowledge of conformational dynamics. RNA exists as dynamic conformational ensembles, sampling transient states on μs–ms timescales that may define ligand-binding opportunities invisible to X-ray crystallography or cryo-EM. R1ρ relaxation dispersion NMR spectroscopy uniquely accesses these states at atomic resolution, detecting and quantifying conformational exchange directly.

This project investigates the conformational dynamics of the ribosomal A-site within helix 44 of the bacterial small ribosomal subunit, a clinically validated drug target bound by aminoglycoside antibiotics. NMR measurements on unlabelled A-site constructs have confirmed correct sample folding, establishing the foundation for relaxation dispersion experiments and antibiotic titrations. In parallel, in vivo chemical probing of bacterial rRNA in E. coli using SHAPE (2A3) and DMS reagents followed by targeted Oxford Nanopore sequencing has yielded reproducible nucleotide-resolution reactivity profiles. These data will be compared to NMR-informed ground and excited state information, to determine whether dynamic signatures detected by NMR are reflected in probing reactivities.

 

The broader goal is to develop a quantitative framework linking probing signatures to NMR-derived exchange parameters, enabling identification of druggable RNA motifs across biologically relevant systems.

 

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