ArticleNucleic acids research2021
A novel SHAPE reagent enables the analysis of RNA structure in living cells with unprecedented accuracy.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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78 citing papers in PubMed, 100 citations in OpenAlex.
- A Workflow for Identifying Helicase-Dependent RNA Structural Changes in Transcriptional Termination: From DMS Sequencing Analysis to Reporter Assay-Based Validation.Methods in molecular biology (Clifton, N.J.) · 2027Article
- FAST-MaP: Chemical Mapping of RNA Structures Using Primer-less Sequencing.bioRxiv : the preprint server for biology · 2026Article
- MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing.Nucleic acids research · 2026Article
- Long-range mRNA folding shapes expression and sequence of bacterial genes.Molecular cell · 2026Article
- Article
- Comparative analysis of flavivirus sfRNA dynamics and secondary structure.Journal of virology · 2026Article
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- SARS-CoV-2 5'-UTR stem-loops activate the antiviral protein oligoadenylate synthetase 1 (OAS1).The Journal of biological chemistry · 2026Article
- Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis.Nature biotechnology · 2026Article
- Conserved structural features of the lncRNA HOTAIR in breast cancer cells.bioRxiv : the preprint server for biology · 2026Article
- SARS-CoV-2 5'-UTR stem-loops activate the antiviral protein oligoadenylate synthetase 1 (OAS1).bioRxiv : the preprint server for biology · 2026Article
- Mechanistically Defined Epoxide- and Aziridine-2-carboxamide Electrophiles Enable Stereoselective Covalent Ribonucleic Acid Modulation.Journal of the American Chemical Society · 2026Article
- Comparative analysis of flavivirus sfRNA dynamics and secondary structure.bioRxiv : the preprint server for biology · 2026Article
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Deep learning for RNA secondary structure determination: gauging generalizability and broadening the scope of traditional methods.RNA (New York, N.Y.) · 2026Review
- The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.Nucleic acids research · 2026Article
- Site-Selective Ligand Selection by Mutational Profiling for Covalent RNA Targeting.Angewandte Chemie (International ed. in English) · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Long-range mRNA folding shapes expression and sequence of bacterial genes.bioRxiv : the preprint server for biology · 2025Article
18 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Due to the mounting evidence that RNA structure plays a critical role in regulating almost any physiological as well as pathological process, being able to accurately define the folding of RNA molecules within living cells has become a crucial need. We introduce here 2-aminopyridine-3-carboxylic acid imidazolide (2A3), as a general probe for the interrogation of RNA structures in vivo. 2A3 shows moderate improvements with respect to the state-of-the-art selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) reagent NAI on naked RNA under in vitro conditions, but it significantly outperforms NAI when probing RNA structure in vivo, particularly in bacteria, underlining its increased ability to permeate biological membranes. When used as a restraint to drive RNA structure prediction, data derived by SHAPE-MaP with 2A3 yields more accurate predictions than NAI-derived data. Due to its extreme efficiency and accuracy, we can anticipate that 2A3 will rapidly take over conventional SHAPE reagents for probing RNA structures both in vitro and in vivo.
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