ArticleRNA (New York, N.Y.)2017
Direct identification of base-paired RNA nucleotides by correlated chemical probing.
Article in RNA (New York, N.Y.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- Article
- The role of structure in regulatory RNA elements.Bioscience reports · 2024Review
- RNA tertiary structure and conformational dynamics revealed by BASH MaP.bioRxiv : the preprint server for biology · 2024Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.Nucleic acids research · 2023Article
- Nano-DMS-MaP allows isoform-specific RNA structure determination.Nature methods · 2023Article
- Mutation signature filtering enables high-fidelity RNA structure probing at all four nucleobases with DMS.bioRxiv : the preprint server for biology · 2023Article
- Single-Molecule Correlated Chemical Probing: A Revolution in RNA Structure Analysis.Accounts of chemical research · 2023Article
- Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications.JACS Au · 2023Review
- Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function.Nucleic acids research · 2023Article
- Discovery of a large-scale, cell-state-responsive allosteric switch in the 7SK RNA using DANCE-MaP.Molecular cell · 2022Article
- Thoughts on how to think (and talk) about RNA structure.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Review
- SHAPE Directed Discovery of New Functions in Large RNAs.Accounts of chemical research · 2021Review
- Chemical Approaches To Analyzing RNA Structure Transcriptome-Wide.Chembiochem : a European journal of chemical biology · 2021Review
- Time-Resolved, Single-Molecule, Correlated Chemical Probing of RNA.Journal of the American Chemical Society · 2020Article
- Advances in RNA 3D Structure Modeling Using Experimental Data.Frontiers in genetics · 2020Review
- RNA base-pairing complexity in living cells visualized by correlated chemical probing.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Single-molecule correlated chemical probing reveals large-scale structural communication in the ribosome and the mechanism of the antibiotic spectinomycin in living cells.PLoS biology · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Many RNA molecules fold into complex secondary and tertiary structures that play critical roles in biological function. Among the best-established methods for examining RNA structure are chemical probing experiments, which can report on local nucleotide structure in a concise and extensible manner. While probing data are highly useful for inferring overall RNA secondary structure, these data do not directly measure through-space base-pairing interactions. We recently introduced an approach for single-molecule correlated chemical probing with dimethyl sulfate (DMS) that measures RNA interaction groups by mutational profiling (RING-MaP). RING-MaP experiments reveal diverse through-space interactions corresponding to both secondary and tertiary structure. Here we develop a framework for using RING-MaP data to directly and robustly identify canonical base pairs in RNA. When applied to three representative RNAs, this framework identified 20%-50% of accepted base pairs with a <10% false discovery rate, allowing detection of 88% of duplexes containing four or more base pairs, including pseudoknotted pairs. We further show that base pairs determined from RING-MaP analysis significantly improve secondary structure modeling. RING-MaP-based correlated chemical probing represents a direct, experimentally concise, and accurate approach for detection of individual base pairs and helices and should greatly facilitate structure modeling for complex RNAs.
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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.