ArticleNature protocols2019
Isotope-dilution mass spectrometry for exact quantification of noncanonical DNA nucleosides.
Article in Nature protocols, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
33 citing papers in PubMed.
- Increasing TET Expression and 5-Hydroxymethylcytosine Formation by a Carbocyclic 5-Aza-2'-deoxy-cytidine Antimetabolite.Angewandte Chemie (International ed. in English) · 2026Article
- DNA adduct and mutational profiles reveal a threshold of cellular defenses againstNAR molecular medicine · 2026Article
- Long-term stability of RNA nucleoside standards for accurate LC-MS quantification.Nucleic acids research · 2026Article
- Metabolic isotopic labeling of (deoxy)ribose enables dual neutral loss scanning for profiling nucleic acid modifications.Nucleic acids research · 2026Article
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- Mass Spectrometry Quantification of Epigenetic Changes: A Scoping Review for Cancer and Beyond.International journal of molecular sciences · 2025Article
- Global DNA-methylation in quantitative epigenetics: orbitrap mass spectrometry.Frontiers in molecular biosciences · 2025Article
- Robust Bisulfite-Free Single-Molecule Real-Time Sequencing of Methyldeoxycytidine Based on a Novel hpTet3 Enzyme.Angewandte Chemie (International ed. in English) · 2024Article
- The type of DNA damage response after decitabine treatment depends on the level of DNMT activity.Life science alliance · 2024Article
- Enhanced ac4C detection in RNA via chemical reduction and cDNA synthesis with modified dNTPs.RNA (New York, N.Y.) · 2024Article
- Purine nucleosides replace cAMP in allosteric regulation of PKA in trypanosomatid pathogens.eLife · 2024Article
- Nucleoside Analogs: A Review of Its Source and Separation Processes.Molecules (Basel, Switzerland) · 2023Review
- Randomly incorporated genomic N6-methyldeoxyadenosine delays zygotic transcription initiation in a cnidarian.The EMBO journal · 2023Article
- Article
- Genome-wide deposition of 6-methyladenine in human DNA reduces the viability of HEK293 cells and directly influences gene expression.Communications biology · 2023Article
- Comprehensive comparison between azacytidine and decitabine treatment in an acute myeloid leukemia cell line.Clinical epigenetics · 2022Article
- Quantification of mRNA cap-modifications by means of LC-QqQ-MS.Methods (San Diego, Calif.) · 2022Article
- Spectroscopic and in vitro Investigations of FeChembiochem : a European journal of chemical biology · 2022Review
- Epigenetic Anti-Cancer Treatment With a Stabilized Carbocyclic Decitabine Analogue.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns.Communications biology · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA contains not only canonical nucleotides but also a variety of modifications of the bases. In particular, cytosine and adenine are frequently modified. Determination of the exact quantity of these noncanonical bases can contribute to the characterization of the state of a biological system, e.g., determination of disease or developmental processes, and is therefore extremely important. Here, we present a workflow that includes detailed description of critical sample preparation steps and important aspects of mass spectrometry analysis and validation. In this protocol, extraction and digestion of DNA by an optimized spin-column and enzyme-based method are described. Isotopically labeled standards are added in the course of DNA digestion, which allows exact quantification by isotope dilution mass spectrometry. To overcome the major bottleneck of such analyses, we developed a short (~14-min-per-sample) ultra-HPLC (UHPLC) and triple quadrupole mass spectrometric (QQQ-MS) method. Easy calculation of the modification abundance in the genome is possible with the provided evaluation sheets. Compared to alternative methods, the quantification procedure presented here allows rapid, ultrasensitive (low femtomole range) and highly reproducible quantification of different nucleosides in parallel. Including sample preparation and evaluation, quantification of DNA modifications can be achieved in less than a week.
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Registered trials
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