ArticleRNA (New York, N.Y.)2011
A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- De novo design of RNA pseudoknots with deep learning.bioRxiv : the preprint server for biology · 2026Article
- Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.Nucleic acids research · 2025Article
- Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression.Molecular systems biology · 2024Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Review
- An RNA pseudoknot stimulates HTLV-1RNA (New York, N.Y.) · 2020Article
- Computational design of three-dimensional RNA structure and function.Nature nanotechnology · 2019Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Allele-specific SHAPE-MaP assessment of the effects of somatic variation and protein binding on mRNA structure.RNA (New York, N.Y.) · 2018Article
- Updates to the RNA mapping database (RMDB), version 2.Nucleic acids research · 2018Article
- RNA structure inference through chemical mapping after accidental or intentional mutations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo.Biophysical journal · 2017Article
- Classification of RNA structure change by 'gazing' at experimental data.Bioinformatics (Oxford, England) · 2017Article
- Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.PLoS computational biology · 2015Article
- Computational analysis of RNA structures with chemical probing data.Methods (San Diego, Calif.) · 2015Review
- Article
- High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.RNA (New York, N.Y.) · 2014Article
- The mutate-and-map protocol for inferring base pairs in structured RNA.Methods in molecular biology (Clifton, N.J.) · 2014Article
- HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis.Nucleic acids research · 2013Article
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3 authors.
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Abstract
We present a rapid experimental strategy for inferring base pairs in structured RNAs via an information-rich extension of classic chemical mapping approaches. The mutate-and-map method, previously applied to a DNA/RNA helix, systematically searches for single mutations that enhance the chemical accessibility of base-pairing partners distant in sequence. To test this strategy for structured RNAs, we have carried out mutate-and-map measurements for a 35-nt hairpin, called the MedLoop RNA, embedded within an 80-nt sequence. We demonstrate the synthesis of all 105 single mutants of the MedLoop RNA sequence and present high-throughput DMS, CMCT, and SHAPE modification measurements for this library at single-nucleotide resolution. The resulting two-dimensional data reveal visually clear, punctate features corresponding to RNA base pair interactions as well as more complex features; these signals can be qualitatively rationalized by comparison to secondary structure predictions. Finally, we present an automated, sequence-blind analysis that permits the confident identification of nine of the 10 MedLoop RNA base pairs at single-nucleotide resolution, while discriminating against all 1460 false-positive base pairs. These results establish the accuracy and information content of the mutate-and-map strategy and support its feasibility for rapidly characterizing the base-pairing patterns of larger and more complex RNA systems.
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