ArticleJournal of the American Chemical Society2008
Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) 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 72 papers.
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Who cites it
72 citing papers in PubMed, 89 citations in OpenAlex.
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- Cryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor.The Journal of biological chemistry · 2025Article
- Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.Nucleic acids research · 2025Article
- Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.RNA (New York, N.Y.) · 2024Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- In Vitro Methods to Decipher the Structure of Viral RNA Genomes.Pharmaceuticals (Basel, Switzerland) · 2021Review
- CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome ofInternational journal of molecular sciences · 2021Article
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias.The journal of physical chemistry. B · 2021Article
- SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction.Frontiers in molecular biosciences · 2021Article
- IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles.Nucleic acids research · 2020Article
- Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.Nucleic acids research · 2020Article
- Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy.Wiley interdisciplinary reviews. RNA · 2019Review
- RNA Structural Differentiation: Opportunities with Pattern Recognition.Biochemistry · 2019Review
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Coupling Green Fluorescent Protein Expression with Chemical Modification to Probe Functionally Relevant Riboswitch Conformations in Live Bacteria.Biochemistry · 2018Article
- In-cell RNA structure probing with SHAPE-MaP.Nature protocols · 2018Article
- Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.The journal of physical chemistry. B · 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
12 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The functions of most RNA molecules are critically dependent on the distinct local dynamics that characterize secondary structure and tertiary interactions and on structural changes that occur upon binding by proteins and small molecule ligands. Measurements of RNA dynamics at nucleotide resolution set the foundation for understanding the roles of individual residues in folding, catalysis, and ligand recognition. In favorable cases, local order in small RNAs can be quantitatively analyzed by NMR in terms of a generalized order parameter, S2. Alternatively, SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) chemistry measures local nucleotide flexibility in RNAs of any size using structure-sensitive reagents that acylate the 2'-hydroxyl position. In this work, we compare per-residue RNA dynamics, analyzed by both S2 and SHAPE, for three RNAs: the HIV-1 TAR element, the U1A protein binding site, and the Tetrahymena telomerase stem loop 4. We find a very strong correlation between the two measurements: nucleotides with high SHAPE reactivities consistently have low S2 values. We conclude that SHAPE chemistry quantitatively reports local nucleotide dynamics and can be used with confidence to analyze dynamics in large RNAs, RNA-protein complexes, and RNAs in vivo.
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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.