ArticleNucleic acids research2020
Broadly applicable oligonucleotide mass spectrometry for the analysis of RNA writers and erasers in vitro.
Article in Nucleic acids research, 2020. 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, 38 citations in OpenAlex.
- Silencing with precision: In silico strategies for antisense oligonucleotide engineering.Molecular biology reports · 2026Review
- Rapid Exonuclease-Based De Novo Sequencing Strategy for Long Oligonucleotides via Liquid-Phase Ion Trap Coupled With Mass Spectrometry.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Quantitative RNA modification mapping by mass spectrometry with isobaric tags and nucleobase fragment analysis.Nature communications · 2026Article
- Human 28S rRNA analysed by state-of-the-art oligonucleotide mass spectrometry: benchmarking current capabilities and a call to action for MS-Seq.bioRxiv : the preprint server for biology · 2026Article
- A nanogram-sensitive workflow for oligonucleotide mass spectrometry using ion-pair-free nanoflow HILIC and RNase benchmarking.Nucleic acids research · 2026Article
- Chemical reactivity of RNA and its modifications with hydrazine.Communications chemistry · 2025Article
- Stationary phase effects in hydrophilic interaction liquid chromatographic separation of oligonucleotides.The Analyst · 2024Article
- Direct sequencing of totalRNA (New York, N.Y.) · 2023Article
- Temporal resolution of NAIL-MS of tRNA, rRNA and Poly-A RNA is overcome by actinomycin D.RSC chemical biology · 2023Article
- Expanding the Epitranscriptomic RNA Sequencing and Modification Mapping Mass Spectrometry Toolbox with Field Asymmetric Waveform Ion Mobility and Electrochemical Elution Liquid Chromatography.Analytical chemistry · 2023Article
- Learning from the Invaders: What Viruses Teach Us about RNA-Based Regulation in Microbes.Microorganisms · 2022Article
- Opportunities and Challenges to Profile mRNA Modifications in Escherichia coli.Chembiochem : a European journal of chemical biology · 2022Article
- Quick Access to Nucleobase-Modified Phosphoramidites for the Synthesis of Oligoribonucleotides Containing Post-Transcriptional Modifications and Epitranscriptomic Marks.The Journal of organic chemistry · 2022Article
- Article
- Permethylation of Ribonucleosides Provides Enhanced Mass Spectrometry Quantification of Post-Transcriptional RNA Modifications.Analytical chemistry · 2022Article
- Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses.Angewandte Chemie (International ed. in English) · 2021Article
- A Compositional Model to Predict the Aggregated Isotope Distribution for Average DNA and RNA Oligonucleotides.Metabolites · 2021Article
- mInternational journal of molecular sciences · 2021Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
RNAs are post-transcriptionally modified by dedicated writer or eraser enzymes that add or remove specific modifications, respectively. Mass spectrometry (MS) of RNA is a useful tool to study the modification state of an oligonucleotide (ON) in a sensitive manner. Here, we developed an ion-pairing reagent free chromatography for positive ion detection of ONs by low- and high-resolution MS, which does not interfere with other types of small compound analyses done on the same instrument. We apply ON-MS to determine the ONs from an RNase T1 digest of in vitro transcribed tRNA, which are purified after ribozyme-fusion transcription by automated size exclusion chromatography. The thus produced tRNAValAAC is substrate of the human tRNA ADAT2/3 enzyme and we confirm the deamination of adenosine to inosine and the formation of tRNAValIACin vitro by ON-MS. Furthermore, low resolution ON-MS is used to monitor the demethylation of ONs containing 1-methyladenosine by bacterial AlkB in vitro. The power of high-resolution ON-MS is demonstrated by the detection and mapping of modified ONs from native total tRNA digested with RNase T1. Overall, we present an oligonucleotide MS method which is broadly applicable to monitor in vitro RNA (de-)modification processes and native RNA.
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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.