ArticleNature protocols2011
Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) for direct analysis of covalent adducts and of nucleotide flexibility in RNA.
Article in Nature protocols, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Reversible 2'-OH acylation enhances RNA stability.Nature chemistry · 2023Article
- Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities.RNA (New York, N.Y.) · 2022Article
- Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation.Nucleic acids research · 2021Article
- The chemistry and applications of RNA 2'-OH acylation.Nature reviews. Chemistry · 2020Article
- Non-Coding Variants inCancers · 2018Review
- Regulatory RNAs in Virulence and Host-Microbe Interactions.Microbiology spectrum · 2018Review
- lncRNA PAPAS tethered to the rDNA enhancer recruits hypophosphorylated CHD4/NuRD to repress rRNA synthesis at elevated temperatures.Genes & development · 2018Article
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation.Nature communications · 2017Article
- A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8.Nucleic acids research · 2016Article
- Opportunities in the design and application of RNA for gene expression control.Nucleic acids research · 2016Review
- A unified analytic framework for prioritization of non-coding variants of uncertain significance in heritable breast and ovarian cancer.BMC medical genomics · 2016Article
- The RNA Domain Vc1 Regulates Downstream Gene Expression in Response to Cyclic Diguanylate in Vibrio cholerae.PloS one · 2016Article
- SHAPE analysis of the RNA secondary structure of the Mouse Hepatitis Virus 5' untranslated region and N-terminal nsp1 coding sequences.Virology · 2015Article
- Progress and outlook in structural biology of large viral RNAs.Virus research · 2014Review
- High-throughput mutate-map-rescue evaluates SHAPE-directed RNA structure and uncovers excited states.RNA (New York, N.Y.) · 2014Article
- A view of pre-mRNA splicing from RNase R resistant RNAs.International journal of molecular sciences · 2014Review
- SHAPE analysis of small RNAs and riboswitches.Methods in enzymology · 2014Article
- Principles of translational control: an overview.Cold Spring Harbor perspectives in biology · 2012Review
- Insights into the regulatory landscape of the lysine riboswitch.Journal of molecular biology · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
RNA SHAPE chemistry yields quantitative, single-nucleotide resolution structural information based on the reaction of the 2'-hydroxyl group of conformationally flexible nucleotides with electrophilic SHAPE reagents. However, SHAPE technology has been limited by the requirement that sites of RNA modification be detected by primer extension. Primer extension results in loss of information at both the 5' and 3' ends of an RNA and requires multiple experimental steps. Here we describe RNase-detected SHAPE that uses a processive, 3'→5' exoribonuclease, RNase R, to detect covalent adducts in 5'-end-labeled RNA in a one-tube experiment. RNase R degrades RNA but stops quantitatively three and four nucleotides 3' of a nucleotide containing a covalent adduct at the ribose 2'-hydroxyl or the pairing face of a nucleobase, respectively. We illustrate this technology by characterizing ligand-induced folding for the aptamer domain of the Escherichia coli thiamine pyrophosphate riboswitch RNA. RNase-detected SHAPE is a facile, two-day approach that can be used to analyze diverse covalent adducts in any RNA molecule, including short RNAs not amenable to analysis by primer extension and RNAs with functionally important structures at their 5' or 3' ends.
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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.