ArticleJournal of the American Chemical Society2010
Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 40 citations in OpenAlex.
- 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
- DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.Bioinformatics (Oxford, England) · 2019Article
- High-throughput determination of RNA structures.Nature reviews. Genetics · 2018Review
- Single-molecule FRET studies on the cotranscriptional folding of a thiamine pyrophosphate riboswitch.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.RNA (New York, N.Y.) · 2017Article
- Long-Range Interactions in Riboswitch Control of Gene Expression.Annual review of biophysics · 2017Review
- Transcriptional pausing at the translation start site operates as a critical checkpoint for riboswitch regulation.Nature communications · 2017Article
- The RNA Domain Vc1 Regulates Downstream Gene Expression in Response to Cyclic Diguanylate in Vibrio cholerae.PloS one · 2016Article
- Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells.Methods in enzymology · 2016Article
- Validating fragment-based drug discovery for biological RNAs: lead fragments bind and remodel the TPP riboswitch specifically.Chemistry & biology · 2014Article
- Safer one-pot synthesis of the 'SHAPE' reagent 1-methyl-7-nitroisatoic anhydride (1m7).RNA (New York, N.Y.) · 2013Article
- A personal perspective on chemistry-driven RNA research.Biopolymers · 2013Article
- The centrality of RNA for engineering gene expression.Biotechnology journal · 2013Review
- Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids.Molecular plant pathology · 2012Article
- Fingerprinting noncanonical and tertiary RNA structures by differential SHAPE reactivity.Journal of the American Chemical Society · 2012Article
- Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals.Nucleic acids research · 2012Article
- The mechanisms of RNA SHAPE chemistry.Journal of the American Chemical Society · 2012Article
- Folding energy landscape of the thiamine pyrophosphate riboswitch aptamer.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a powerful approach for characterizing RNA structure and dynamics at single-nucleotide resolution. However, SHAPE technology is limited, sometimes severely, because primer extension detection obscures structural information for approximately 15 nts at the 5' end and 40-60 nts at the 3' end of the RNA. Moreover, detection by primer extension is more complex than the actual structure-selective chemical interrogation step. Here we quantify covalent adducts in RNA directly by adduct-inhibited exoribonuclease degradation. RNA 2'-O-adducts block processivity of a 3'-->5' exoribonuclease, RNase R, to produce fragments that terminate three nucleotides 3' of the modification site. We analyzed the structure of the native thiamine pyrophosphate (TPP) riboswitch aptamer domain and identified large changes in local nucleotide dynamics and global RNA structure upon ligand binding. In addition to numerous changes that can be attributed to ligand recognition, we identify a single nucleotide bulge register shift, distant from the binding site, that stabilizes the ligand-bound structure. Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease (RNase-detected SHAPE) should prove broadly useful for facile structural analysis of small noncoding RNAs and for RNAs that have functionally critical structures at their 5' and 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.