ArticleJournal of the American Chemical Society2008
Slow conformational dynamics at C2'-endo nucleotides in RNA.
Article in Journal of the American Chemical Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed, 52 citations in OpenAlex.
- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- In Vitro Methods to Decipher the Structure of Viral RNA Genomes.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Review
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Article
- Unveiling the druggable RNA targets and small molecule therapeutics.Bioorganic & medicinal chemistry · 2019Review
- 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
- Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility.The journal of physical chemistry letters · 2018Article
- SHAPE analysis of theRNA (New York, N.Y.) · 2017Article
- Fingerprinting the junctions of RNA structure by an open-paddlewheel diruthenium compound.RNA (New York, N.Y.) · 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
- RNA secondary structure modeling at consistent high accuracy using differential SHAPE.RNA (New York, N.Y.) · 2014Article
- Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions.RNA (New York, N.Y.) · 2014Article
- The cellular environment stabilizes adenine riboswitch RNA structure.Biochemistry · 2013Article
- Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7).RNA (New York, N.Y.) · 2013Article
- Structure-function analysis of ribonucleotide bypass by B family DNA replicases.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing.RNA (New York, N.Y.) · 2013Article
- Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.Biochemistry · 2013Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
RNA molecules undergo local conformational dynamics on timescales spanning picoseconds to minutes. Slower local motions have the greater potential to govern RNA folding, ligand recognition, and ribonucleoprotein assembly reactions but are difficult to detect in large RNAs with complex structures. RNA SHAPE chemistry employs acylation of the ribose 2'-hydroxyl position to measure local nucleotide flexibility in RNA and is well-characterized by a mechanism in which each nucleotide samples unreactive (closed) and reactive (open) states. We monitor RNA conformational dynamics over distinct time domains by varying the electrophilicity of the acylating reagent. Select C2'-endo nucleotides are nonreactive toward fast reagents but reactive toward slower SHAPE reagents in both model RNAs and in a large RNA with a tertiary fold. We conclude, first, that the C2'-endo conformation by itself does not govern SHAPE reactivity. However, some C2'-endo nucleotides undergo extraordinarily slow conformational changes, on the order of 10(-4) s(-1). Due to their distinctive local dynamics, C2'-endo nucleotides have the potential to function as rate-determining molecular switches and are likely to play central, currently unexplored, roles in RNA folding and function.
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What OpenQuestion holds
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.