ArticleJournal of the American Chemical Society2012
The mechanisms of RNA SHAPE chemistry.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 126 papers.
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Who cites it
126 citing papers in PubMed.
- Markov models of SHAPE data improve secondary structure prediction.bioRxiv : the preprint server for biology · 2026Article
- Nucleobase Coordination With MgChemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Structure and sequence characteristics of 5'-stem-loop 1 modulate the escape from nsp1-mediated repression in SARS-CoV-2 variants.Nucleic acids research · 2026Article
- SHAPE-MaP-Based Assessment of the Structure of Citrus Tristeza Virus Long Non-Coding RNA.Viruses · 2026Article
- Evolutionary refinement of the ZIKV 5' UTR dictates a trade-off between RNA stability and promoter accessibility.NAR molecular medicine · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- DeepRMSF: a deep learning-based automated approach for predicting atomic-level flexibility in RNA structure.Briefings in bioinformatics · 2026Article
- Mapping the RNA Chaperone Activity of the Trypanosoma brucei Editosome Using SHAPE-Chemical Probing.Methods in molecular biology (Clifton, N.J.) · 2026Article
- In Vivo RNA Chemical Footprinting Analysis in Archaea.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Fluorogenic Covalent Probes for RNA.Journal of the American Chemical Society · 2025Article
- Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.Nucleic acids research · 2025Article
- Consistent features observed in structural probing data of eukaryotic RNAs.NAR genomics and bioinformatics · 2025Article
- IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling.NAR genomics and bioinformatics · 2025Article
- Site-Selective Modification and Labeling of Native RNA.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Review
- RNA infrastructure profiling illuminates transcriptome structure in crowded spaces.Cell chemical biology · 2024Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- On the aqueous origins of the condensation polymers of life.Nature reviews. Chemistry · 2024Review
- Functional Validation of SAM Riboswitch Element A fromBiochemistry · 2024Article
- Selective Arylation of RNA 2'-OH Groups via SAngewandte Chemie (International ed. in English) · 2024Article
- Second-Generation Chiral Amino Acid Derivatives Afford High Stereoselectivity and Stability in Aqueous RNA Acylation.The Journal of organic chemistry · 2024Article
66 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
The biological functions of RNA are ultimately governed by the local environment at each nucleotide. Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approach for measuring nucleotide structure and dynamics in diverse biological environments. SHAPE reagents acylate the 2'-hydroxyl group at flexible nucleotides because unconstrained nucleotides preferentially sample rare conformations that enhance the nucleophilicity of the 2'-hydroxyl. The critical corollary is that some constrained nucleotides must be poised for efficient reaction at the 2'-hydroxyl group. To identify such nucleotides, we performed SHAPE on intact crystals of the Escherichia coli ribosome, monitored the reactivity of 1490 nucleotides in 16S rRNA, and examined those nucleotides that were hyper-reactive toward SHAPE and had well-defined crystallographic conformations. Analysis of these conformations revealed that 2'-hydroxyl reactivity is broadly facilitated by general base catalysis involving multiple RNA functional groups and by two specific orientations of the bridging 3'-phosphate group. Nucleotide analog studies confirmed the contributions of these mechanisms to SHAPE reactivity. These results provide a strong mechanistic explanation for the relationship between SHAPE reactivity and local RNA dynamics and will facilitate interpretation of SHAPE information in the many technologies that make use of this chemistry.
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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.