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Updated: Aug 17, 2026

Practical Aspects of Sample Preparation and Setup of 1H R1ρ Relaxation Dispersion Experiments of RNA
Published on: July 9, 2021
NMR spectroscopy of RNA duplexes containing pseudouridine in supercooled water
Kersten T Schroeder1, Jack J Skalicky, Nancy L Greenbaum
1Department of Chemistry and Biochemistry, Dittmer Laboratory of Chemistry, Florida State University, Tallahassee, FL 32306-4390, USA.
Abstract:
We have performed NMR experiments in supercooled water in order to decrease the temperature-dependent exchange of protons in RNA duplexes. NMR spectra of aqueous samples of RNA in bundles of narrow capillaries that were acquired at temperatures as low as -18 degrees C reveal resonances of exchangeable protons not seen at higher temperatures. In particular, we detected the imino protons of terminal base pairs and the imino proton of a non-base-paired pseudouridine in a duplex representing the eukaryotic pre-mRNA branch site helix. Analysis of the temperature dependence of chemical shift changes (thermal coefficients) for imino protons corroborated hydrogen bonding patterns observed in the NMR-derived structural model of the branch site helix. The ability to observe non-base-paired imino protons of RNA is of significant value in structure determination of RNA motifs containing loop and bulge regions.
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