ArticleNucleic acids research2017
Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 47 citations in OpenAlex.
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
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- Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing.bioRxiv : the preprint server for biology · 2026Article
- Application of Fourier Transform Infrared Spectroscopy for Structural Analysis of RNAs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Revealing hidden protonated conformational states in RNA dynamic ensembles.Nucleic acids research · 2025Article
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- Elucidating microRNA-34a organisation within human Argonaute-2 by dynamic nuclear polarisation-enhanced magic angle spinning NMR.Nucleic acids research · 2024Article
- N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition.Nucleic acids research · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- An RNA excited conformational state at atomic resolution.Nature communications · 2023Article
- Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble.Journal of the American Chemical Society · 2023Article
- Structural Significance of Conformational Preferences and Ribose-Ring-Puckering of Hyper Modified Nucleotide 5'-Monophosphate 2-Methylthio Cyclic NCell biochemistry and biophysics · 2022Article
- Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs.Chemical reviews · 2022Review
- Mutate-and-chemical-shift-fingerprint (MCSF) to characterize excited states in RNA using NMR spectroscopy.Nature protocols · 2021Review
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.Nucleic acids research · 2020Article
- Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction.Nature communications · 2020Article
- Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon RJournal of biomolecular NMR · 2020Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies have shown that RNAs exist in dynamic equilibrium with short-lived low-abundance 'excited states' that form by reshuffling base pairs in and around non-canonical motifs. These conformational states are proposed to be rich in non-canonical motifs and to play roles in the folding and regulatory functions of non-coding RNAs but their structure proves difficult to characterize given their transient nature. Here, we describe an approach for determining sugar pucker conformation in RNA excited states through nuclear magnetic resonance measurements of C1΄ and C4΄ rotating frame spin relaxation (R1ρ) in uniformly 13C/15N labeled RNA samples. Application to HIV-1 TAR exposed slow modes of sugar repuckering dynamics at the μs and ms timescale accompanying transitions between non-helical (C2΄-endo) to helical (C3΄-endo) conformations during formation of two distinct excited states. In contrast, we did not obtain any evidence for slow sugar repuckering dynamics for nucleotides in a variety of structural contexts that do not undergo non-helical to helical transitions. Our results outline a route for significantly improving the conformational characterization of RNA excited states and suggest that slow modes of repuckering dynamics gated by transient changes in secondary structure are quite common in RNA.
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