ArticleNature communications2016
Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Folding and unfolding dynamics of a DNA aptamer studied by heteronuclearJournal of magnetic resonance (San Diego, Calif. : 1997) · 2026Article
- Rho (bioRxiv : the preprint server for biology · 2026Article
- PlanarFold: a coarse-grained molecular dynamics model of RNA in two-dimensional space.Nature communications · 2026Article
- Viral RNAs as Dual Graphs: Extending the Motif Universe of RNAs.bioRxiv : the preprint server for biology · 2026Article
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- Quantifying MgbioRxiv : the preprint server for biology · 2026Article
- Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing.bioRxiv : the preprint server for biology · 2026Article
- Revealing hidden protonated conformational states in RNA dynamic ensembles.Nucleic acids research · 2025Article
- NMR methods for investigating functionally relevant biomolecular dynamics.Magnetic resonance letters · 2025Review
- Transformers in RNA structure prediction: A review.Computational and structural biotechnology journal · 2025Review
- 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
- Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field.Nucleic acids research · 2022Article
- Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs.Chemical reviews · 2022Review
- Assembly factors chaperone ribosomal RNA folding by isolating helical junctions that are prone to misfolding.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Chemical shift prediction of RNA imino groups: application toward characterizing RNA excited states.Nature communications · 2021Article
- 2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.Nucleic acids research · 2020Article
- Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.International journal of molecular sciences · 2020Review
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5 authors.
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Abstract
Intermediates play important roles in RNA folding but can be difficult to characterize when short-lived or not significantly populated. By combining (15)N relaxation dispersion NMR with chemical probing, we visualized a fast (kex=k1+k-1≈423 s(-1)) secondary structural switch directed towards a low-populated (∼3%) partially folded intermediate in tertiary folding of the P5abc subdomain of the 'Tetrahymena' group I intron ribozyme. The secondary structure switch changes the base-pairing register across the P5c hairpin, creating a native-like structure, and occurs at rates of more than two orders of magnitude faster than tertiary folding. The switch occurs robustly in the absence of tertiary interactions, Mg(2+) or even when the hairpin is excised from the three-way junction. Fast, highly modular secondary structural switches may be quite common during RNA tertiary folding where they may help smoothen the folding landscape by allowing folding to proceed efficiently via additional pathways.
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