ArticleNucleic acids research2014
Chemical probing of RNA with the hydroxyl radical at single-atom resolution.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- Hydroxyl radical-induced C1'-H abstraction reaction of different artificial nucleotides.Journal of molecular modeling · 2024Article
- Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.Nucleic acids research · 2023Article
- Photochemical and Single Electron Transfer Generation of 2'-Deoxycytidin-The Journal of organic chemistry · 2023Article
- Probing the dynamic RNA structurome and its functions.Nature reviews. Genetics · 2023Review
- Chemical Approaches To Analyzing RNA Structure Transcriptome-Wide.Chembiochem : a European journal of chemical biology · 2021Review
- Oxidative Modifications of RNA and Its Potential Roles in Biosystem.Frontiers in molecular biosciences · 2021Review
- The lncRNA Toolkit: Databases and In Silico Tools for lncRNA Analysis.Non-coding RNA · 2020Review
- Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.Nature protocols · 2018Article
- Mechanistic Studies on RNA Strand Scission from a C2'-Radical.The Journal of organic chemistry · 2016Article
- Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation.ACS chemical biology · 2016Review
- Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.Nature protocols · 2016Article
- Submolecular regulation of cell transformation by deuterium depleting water exchange reactions in the tricarboxylic acid substrate cycle.Medical hypotheses · 2016Article
- Progress and challenges for chemical probing of RNA structure inside living cells.Nature chemical biology · 2015Review
- Rapid RNA strand scission following C2'-hydrogen atom abstraction.Journal of the American Chemical Society · 2015Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
While hydroxyl radical cleavage is widely used to map RNA tertiary structure, lack of mechanistic understanding of strand break formation limits the degree of structural insight that can be obtained from this experiment. Here, we determine how individual ribose hydrogens of sarcin/ricin loop RNA participate in strand cleavage. We find that substituting deuterium for hydrogen at a ribose 5'-carbon produces a kinetic isotope effect on cleavage; the major cleavage product is an RNA strand terminated by a 5'-aldehyde. We conclude that hydroxyl radical abstracts a 5'-hydrogen atom, leading to RNA strand cleavage. We used this approach to obtain structural information for a GUA base triple, a common tertiary structural feature of RNA. Cleavage at U exhibits a large 5' deuterium kinetic isotope effect, a potential signature of a base triple. Others had noted a ribose-phosphate hydrogen bond involving the G 2'-OH and the U phosphate of the GUA triple, and suggested that this hydrogen bond contributes to backbone rigidity. Substituting deoxyguanosine for G, to eliminate this hydrogen bond, results in a substantial decrease in cleavage at G and U of the triple. We conclude that this hydrogen bond is a linchpin of backbone structure around the triple.
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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.