ArticleProceedings of the National Academy of Sciences of the United States of America2019
RNA base-pairing complexity in living cells visualized by correlated chemical probing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed.
- pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing.Nucleic acids research · 2026Article
- MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing.Nucleic acids research · 2026Article
- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- Mapping RNA structure assembly and remodeling in biomolecular condensates.bioRxiv : the preprint server for biology · 2026Article
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- Human lncRNAProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Article
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- RNA switch model for localization and translation of the myelin basic protein mRNA.bioRxiv : the preprint server for biology · 2025Article
- A small cationic probe for accurate, punctate discovery of RNA tertiary structure.bioRxiv : the preprint server for biology · 2025Article
- A portable poison exon for small-molecule control of mammalian gene expression.Nature methods · 2025Article
- Ribosome-induced mRNA pseudoknot interactions visualized by DMS MaP-Seq.bioRxiv : the preprint server for biology · 2025Article
- Functional Proximity across an mRNA.Biochemistry · 2025Article
- Structural analysis of the lncRNA SChLAP1 reveals protein binding interfaces and a conformationally heterogenous retroviral insertion.RNA (New York, N.Y.) · 2025Article
- Improving RNA Secondary Structure Prediction Through Expanded Training Data.bioRxiv : the preprint server for biology · 2025Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Structurally distinct manganese-sensing riboswitch aptamers regulate different expression platform architectures.Nucleic acids research · 2025Article
- Transcriptome-wide RNA accessibility mapping reveals structured RNA elements and pervasive conformational rearrangements under stress.bioRxiv : the preprint server for biology · 2025Article
17 more citing papers are in PubMed but not listed here.
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5 authors.
Funding
Abstract
RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base-pairing interactions in cells. PAIR-MaP has superior resolution compared to alternative experiments, can resolve multiple sets of pairing interactions for structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and 2 bacterial messenger RNA 5' untranslated regions reveals functionally important and complex structures undetected by prior analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.
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