ArticleNature protocols2007
DMS footprinting of structured RNAs and RNA-protein complexes.
Article in Nature protocols, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 167 papers.
What it found
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Who cites it
167 citing papers in PubMed, 277 citations in OpenAlex.
- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- Mapping the Structure and Conformational Landscape of the 10-23 DNAzyme.ACS chemical biology · 2026Article
- Open questions on viral frameshifting: Exploiting the structural plasticity of the frameshifting element for therapeutic intervention.Biophysical journal · 2026Review
- Multi-site DMS probing reveals higher-order structure of RNA-protein complexes in living cells.Molecular cell · 2026Article
- A bifunctional H/ACA snoRNP mediates both pseudouridylation and rRNA scaffolding during ribosome assembly.bioRxiv : the preprint server for biology · 2026Article
- Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae.Journal of visualized experiments : JoVE · 2026Article
- Structures of the eIF4G-binding RNA domains among picornaviral IRES types are topologically conserved.Nature communications · 2026Article
- Structural probing of RNA hairpins quantifies protein occupancy on RNA and links it to function in human cells.bioRxiv : the preprint server for biology · 2026Article
- RNA Structure Analysis by Chemical Probing with DMS and CMCT.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Designing molecular RNA switches with Restricted Boltzmann machines.Nature communications · 2025Article
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- Energy-Dependent Changes in Ion Mobility Peak Width Reveal Stability Shifts in Ribonucleic Acid Stem Loops.Journal of the American Society for Mass Spectrometry · 2025Article
- Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.Nucleic acids research · 2025Article
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.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
- In vivo structure profiling reveals human cytosolic and mitochondrial tRNA structurome and interactome in response to stress.Nature communications · 2025Article
- Analysis of natural structures and chemical mapping data reveals local stability compensation in RNA.bioRxiv : the preprint server for biology · 2025Article
- Investigating the interplay between RNA structural dynamics and RNA chemical probing experiments.Nucleic acids research · 2025Article
- Structural switching dynamically controls the doubly pseudoknotted Rous sarcoma virus-programmed ribosomal frameshifting element.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- RNA infrastructure profiling illuminates transcriptome structure in crowded spaces.Cell chemical biology · 2024Article
107 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We describe a protocol in which dimethyl sulfate (DMS) modification of the base-pairing faces of unpaired adenosine and cytidine nucleotides is used for structural analysis of RNAs and RNA-protein complexes (RNPs). The protocol is optimized for RNAs of small to moderate size (< or = 500 nt). The RNA or RNP is first exposed to DMS under conditions that promote formation of the folded structure or complex, as well as 'control' conditions that do not allow folding or complex formation. The positions and extents of modification are then determined by primer extension, polyacrylamide gel electrophoresis and quantitative analysis. From changes in the extent of modification upon folding or protein binding (appearance of a 'footprint'), it is possible to detect local changes in the secondary and tertiary structure of RNA, as well as the formation of RNA-protein contacts. This protocol takes 1.5-3 d to complete, depending on the type of analysis used.
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What OpenQuestion holds
Registered trials
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.