ArticleNucleic acids research2019
The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 27 citations in OpenAlex.
- 1-Deazainosine-impact on RNA structure and role in exploring ribozyme catalysis.Chemical science · 2026Article
- C‑Nucleosides Stabilize RNA by Reducing Nucleophilicity at 2'-OH.ACS central science · 2025Article
- Article
- Novabeads: Stimuli-Responsive Signal-Amplifying Hydrogel Microparticles for Enzymeless Fluorescence-Based Detection of microRNA Biomarkers.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- The intrinsic preference of guanosine bases for cleavage-facilitating interactions with phosphodiester moieties in RNA anions revealed by base modifications and mass spectrometry.Nucleic acids research · 2025Article
- FAST MS: Software for the Automated Analysis of Top-Down Mass Spectra of Polymeric Molecules Including RNA, DNA, and Proteins.Journal of the American Society for Mass Spectrometry · 2025Article
- Resolving the intricate binding of neomycin B to multiple binding motifs of a neomycin-sensing riboswitch aptamer by native top-down mass spectrometry and NMR spectroscopy.Nucleic acids research · 2024Article
- Effect of Protonation on the Molecular Structure of Adenosine 5'-Triphosphate: A Combined Theoretical and Near Edge X-ray Absorption Fine Structure Study.The journal of physical chemistry letters · 2023Article
- Review of fragmentation of synthetic single-stranded oligonucleotides by tandem mass spectrometry from 2014 to 2022.Rapid communications in mass spectrometry : RCM · 2023Review
- SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome.Nucleic acids research · 2023Article
- Native Top-Down Mass Spectrometry Uncovers Two Distinct Binding Motifs of a Functional Neomycin-Sensing Riboswitch Aptamer.Journal of the American Chemical Society · 2023Article
- RNA Chemical Labeling with Site-Specific, Relative Quantification by Mass Spectrometry for the Structural Study of a Neomycin-Sensing Riboswitch Aptamer Domain.ChemPlusChem · 2022Article
- 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis.Journal of the American Chemical Society · 2022Article
- Studying the Key Intermediate of RNA Autohydrolysis by Cryogenic Gas-Phase Infrared Spectroscopy.Angewandte Chemie (International ed. in English) · 2022Article
- pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31.Biophysical chemistry · 2022Article
- Impact of 3-deazapurine nucleobases on RNA properties.Nucleic acids research · 2021Article
- Radical Transfer Dissociation for De Novo Characterization of Modified Ribonucleic Acids by Mass Spectrometry.Angewandte Chemie (International ed. in English) · 2020Article
- Changed reactivity of secondary hydroxy groups in C8-modified adenosine - lessons learned from silylation.Beilstein journal of organic chemistry · 2020Article
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4 authors at 1 institution in 1 country.
Funding
Abstract
The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5'-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.
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