ArticleProceedings of the National Academy of Sciences of the United States of America2009
C2'-endo nucleotides as molecular timers suggested by the folding of an RNA domain.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
31 citing papers in PubMed, 40 citations in OpenAlex.
- Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition.bioRxiv : the preprint server for biology · 2026Article
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures.Nucleic acids research · 2021Article
- Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA.Journal of the American Chemical Society · 2020Article
- Deconstructing internal ribosome entry site elements: an update of structural motifs and functional divergences.Open biology · 2018Review
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Ribosome-dependent conformational flexibility changes and RNA dynamics of IRES domains revealed by differential SHAPE.Scientific reports · 2018Article
- SHAPE analysis of theRNA (New York, N.Y.) · 2017Article
- Genetic variation and RNA structure regulate microRNA biogenesis.Nature communications · 2017Article
- 'Z-DNA like' fragments in RNA: a recurring structural motif with implications for folding, RNA/protein recognition and immune response.Nucleic acids research · 2016Article
- Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound.RNA (New York, N.Y.) · 2016Article
- Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches.RNA biology · 2016Article
- Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis.Nature protocols · 2015Article
- Review toward all RNA structures, concisely.Biopolymers · 2015Review
- The role of RNA conformation in RNA-protein recognition.RNA biology · 2015Article
- Magnesium-dependent folding of a picornavirus IRES element modulates RNA conformation and eIF4G interaction.The FEBS journal · 2014Article
- RNA secondary structure modeling at consistent high accuracy using differential SHAPE.RNA (New York, N.Y.) · 2014Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
- The cellular environment stabilizes adenine riboswitch RNA structure.Biochemistry · 2013Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
A striking and widespread observation is that higher-order folding for many RNAs is very slow, often requiring minutes. In some cases, slow folding reflects the need to disrupt stable, but incorrect, interactions. However, a molecular explanation for slow folding in most RNAs is unknown. The specificity domain of the Bacillus subtilis RNase P ribozyme undergoes a rate-limiting folding step on the minute time-scale. This RNA also contains a C2'-endo nucleotide at A130 that exhibits extremely slow local conformational dynamics. This nucleotide is evolutionarily conserved and essential for tRNA recognition by RNase P. Here we show that deleting this single nucleotide accelerates folding by an order of magnitude even though this mutation does not change the global fold of the RNA. These results demonstrate that formation of a single stacking interaction at a C2'-endo nucleotide comprises the rate-determining step for folding an entire 154 nucleotide RNA. C2'-endo nucleotides exhibit slow local dynamics in structures spanning isolated helices to complex tertiary interactions. Because the motif is both simple and ubiquitous, C2'-endo nucleotides may function as molecular timers in many RNA folding and ligand recognition reactions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.