ArticleNature protocols2009
Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution.
Article in Nature protocols, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
69 citing papers in PubMed.
- Nucleotide-Resolution Mapping Reveals Specific MLE Binding Site on roX2 lncRNA.Journal of molecular biology · 2026Article
- Decoding the interactions and functions of non-coding RNA with artificial intelligence.Nature reviews. Molecular cell biology · 2025Review
- Sequential structure probing of cotranscriptional RNA folding intermediates.Nature communications · 2025Article
- Linker-Mediated Inactivation of the SAM-II Domain in the Tandem SAM-II/SAM-V Riboswitch.International journal of molecular sciences · 2024Article
- Identification of RNA structures and their roles in RNA functions.Nature reviews. Molecular cell biology · 2024Review
- RNA Secondary Structure Modeling Following the IPANEMAP Workflow.Methods in molecular biology (Clifton, N.J.) · 2024Article
- A Guide to Computational Cotranscriptional Folding Featuring the SRP RNA.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Observation of coordinated RNA folding events by systematic cotranscriptional RNA structure probing.Nature communications · 2023Article
- The Evaluation of SHAPE-MaP RNA Structure Probing Protocols Reveals a Novel Role of MnInternational journal of molecular sciences · 2023Article
- Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch.Nucleic acids research · 2022Article
- Programmable antivirals targeting critical conserved viral RNA secondary structures from influenza A virus and SARS-CoV-2.Nature medicine · 2022Article
- Role of Purine-Rich Regions in Mason-Pfizer Monkey Virus (MPMV) Genomic RNA Packaging and Propagation.Frontiers in microbiology · 2020Article
- Determinants of target prioritization and regulatory hierarchy for the bacterial small RNA SgrS.Molecular microbiology · 2019Article
- Unveiling the druggable RNA targets and small molecule therapeutics.Bioorganic & medicinal chemistry · 2019Review
- Stabilizing role of structural elements within the 5´ Untranslated Region (UTR) and gag sequences in Mason-Pfizer monkey virus (MPMV) genomic RNA packaging.RNA biology · 2019Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- Nucleotide and structural label identification in single RNA molecules with quantum tunneling spectroscopy.Chemical science · 2019Article
- SHAPE probing pictures Mg2+-dependent folding of small self-cleaving ribozymes.Nucleic acids research · 2018Article
- Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.The journal of physical chemistry. B · 2018Article
- New tRNA contacts facilitate ligand binding in aProceedings of the National Academy of Sciences of the United States of America · 2018Article
9 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
2 authors.
Funding
Abstract
RNA selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry exploits the discovery that conformationally dynamic nucleotides preferentially adopt configurations that facilitate reaction between the 2'-OH group and a hydroxyl-selective electrophile, such as benzoyl cyanide (BzCN), to form a 2'-O-adduct. BzCN is ideally suited for quantitative, time-resolved analysis of RNA folding and ribonucleoprotein (RNP) assembly mechanisms because this reagent both reacts with flexible RNA nucleotides and also undergoes auto-inactivating hydrolysis with a half-life of 0.25 s at 37 degrees C. RNA folding is initiated by addition of Mg(2+) or protein, or other change in solution conditions, and nucleotide resolution structural images are obtained by adding aliquots of the evolving reaction to BzCN and then 'waiting' for 1 second. Sites of the 2'-O-adduct formation are subsequently scored as stops to primer extension using reverse transcriptase. This time-resolved SHAPE protocol makes it possible to obtain 1-second structural snapshots in time-resolved kinetic studies for RNAs of arbitrary length and complexity in a straightforward and concise experiment.
Indexed as
Identifiers
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.