ArticleRNA (New York, N.Y.)2009
SHAMS: combining chemical modification of RNA with mass spectrometry to examine polypurine tract-containing RNA/DNA hybrids.
Article in RNA (New York, N.Y.), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain.ChemPlusChem · 2022Article
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- New windows into retroviral RNA structures.Retrovirology · 2018Review
- Structure-specific ribonucleases for MS-based elucidation of higher-order RNA structure.Journal of the American Society for Mass Spectrometry · 2014Article
- Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry.Nature structural & molecular biology · 2014Article
- Article
- The mechanisms of RNA SHAPE chemistry.Journal of the American Chemical Society · 2012Article
- Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come.Molecular biology international · 2012Article
- Viral reverse transcriptases show selective high affinity binding to DNA-DNA primer-templates that resemble the polypurine tract.PloS one · 2012Article
- Correlating SHAPE signatures with three-dimensional RNA structures.RNA (New York, N.Y.) · 2011Article
- MS analysis of nucleic acids in the post-genomic era.Analytical chemistry · 2011Article
- Investigation of the Reactivity of Oligodeoxynucleotides with Glyoxal and KMnO(4) Chemical Probes by Electrospray Ionization Mass Spectrometry.International journal of mass spectrometry · 2011Article
- Biophysical analysis of influenza A virus RNA promoter at physiological temperatures.The Journal of biological chemistry · 2011Article
- Characterization of oligodeoxynucleotides and modifications by 193 nm photodissociation and electron photodetachment dissociation.Analytical chemistry · 2010Article
- Infrared multiphoton dissociation of small-interfering RNA anions and cations.Journal of the American Society for Mass Spectrometry · 2010Article
- Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) has gained popularity as a facile method of examining RNA structure both in vitro and in vivo, exploiting accessibility of the ribose 2'-OH to acylation by N-methylisatoic anhydride (NMIA) in unpaired or flexible configurations. Subsequent primer extension terminates at the site of chemical modification, and these products are fractionated by high-resolution gel electrophoresis. When applying SHAPE to investigate structural features associated with the wild-type and analog-substituted polypurine tract (PPT)-containing RNA/DNA hybrids, their size (20-25 base pairs) rendered primer extension impractical. As an alternative method of detection, we reasoned that chemical modification could be combined with tandem mass spectrometry, relying on the mass increment of RNA fragments containing the NMIA adduct (M(r) = 133 Da). Using this approach, we demonstrate both specific modification of the HIV-1 PPT RNA primer and variations in its acylation pattern induced by replacing template nucleotides with a non-hydrogen-bonding thymine isostere. Our selective 2'-hydroxyl acylation analyzed by mass spectrometry strategy (SHAMS) should find utility when examining the structure of small RNA fragments or RNA/DNA hybrids where primer extension cannot be performed.
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