ArticleMethods in molecular biology (Clifton, N.J.)2014
The mutate-and-map protocol for inferring base pairs in structured RNA.
Article in Methods in molecular biology (Clifton, N.J.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- RNA tertiary structure and conformational dynamics revealed by BASH MaP.bioRxiv : the preprint server for biology · 2024Article
- Diversity and modularity of tyrosine-accepting tRNA-like structures.RNA (New York, N.Y.) · 2024Article
- Efficient 3'-pairing renders microRNA targeting less sensitive to mRNA seed accessibility.Nucleic acids research · 2023Article
- RNA:RNA interaction in ternary complexes resolved by chemical probing.RNA (New York, N.Y.) · 2023Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Retron reverse transcriptase termination and phage defense are dependent on host RNase H1.Nucleic acids research · 2022Article
- Mapping the Conformational Landscape of the Neutral Network of RNA Sequences That Connect Two Functional Distinctly Different Ribozymes.Chembiochem : a European journal of chemical biology · 2022Article
- Three-dimensional structure of a flavivirus dumbbell RNA reveals molecular details of an RNA regulator of replication.Nucleic acids research · 2021Article
- An expanded class of histidine-accepting viral tRNA-like structures.RNA (New York, N.Y.) · 2021Article
- Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses.RNA (New York, N.Y.) · 2021Article
- Folding heterogeneity in the essential human telomerase RNA three-way junction.RNA (New York, N.Y.) · 2020Article
- Hoogsteen base pairs increase the susceptibility of double-stranded DNA to cytotoxic damage.The Journal of biological chemistry · 2020Article
- Article
- An RNA pseudoknot stimulates HTLV-1RNA (New York, N.Y.) · 2020Article
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4 authors.
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Abstract
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single nucleotide resolution and used to constrain structural modeling. This experimental framework has been extensively revisited in the past decade with new strategies for high-throughput readouts, chemical modification, and rapid data analysis. Recently, we have coupled the technique to high-throughput mutagenesis. Point mutations of a base paired nucleotide can lead to exposure of not only that nucleotide but also its interaction partner. Systematically carrying out the mutation and mapping for the entire system gives an experimental approximation of the molecule's "contact map." Here, we give our in-house protocol for this "mutate-and-map" (M2) strategy, based on 96-well capillary electrophoresis, and we provide practical tips on interpreting the data to infer nucleic acid structure.
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