ArticleJournal of the American Chemical Society2014
Nanopores discriminate among five C5-cytosine variants in DNA.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it, 104 citations in OpenAlex.
- Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA.Clinical epigenetics · 2021Pooled it
- Targeted native long-read sequencing of DNA methylation alterations following CRISPR-Cas9-induced double-strand breaks in human cells.BMC research notes · 2026Article
- The potential of mRNA markers in body fluids and personal source analysis based on the QNome nanopore sequencing.International journal of legal medicine · 2026Article
- CRISPR-Cas9-induced double-strand breaks disrupt maintenance of epigenetic information.Genome biology · 2025Article
- Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae.Ecology and evolution · 2025Article
- Nanopores map the acid-base properties of a single site in a single DNA molecule.Nucleic acids research · 2024Article
- Decoding the Epigenetic Landscape: Insights into 5mC and 5hmC Patterns in Mouse Cortical Cell Types.bioRxiv : the preprint server for biology · 2024Article
- Review
- Whole-Genome Sequencing of 5-Hydroxymethylcytosine at Base Resolution by Bisulfite-Free Single-Step Deamination with Engineered Cytosine Deaminase.ACS central science · 2023Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores.Journal of the American Chemical Society · 2023Article
- Factors and Methods for the Detection of Gene Expression Regulation.Biomolecules · 2023Review
- Labeling and sequencing nucleic acid modifications using bio-orthogonal tools.RSC chemical biology · 2022Review
- Modification mapping by nanopore sequencing.Frontiers in genetics · 2022Review
- Current and Emerging Technologies for the Analysis of the Genome-Wide and Locus-Specific DNA Methylation Patterns.Advances in experimental medicine and biology · 2022Article
- Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides.International journal of molecular sciences · 2021Review
- Recent advances in biological nanopores for nanopore sequencing, sensing and comparison of functional variations in MspA mutants.RSC advances · 2021Review
- Quantification and mapping of DNA modifications.RSC chemical biology · 2021Review
- Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double-mutant AML.Blood · 2021Article
- RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control.Biomolecules · 2021Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Individual DNA molecules can be read at single nucleotide precision using nanopores coupled to processive enzymes. Discrimination among the four canonical bases has been achieved, as has discrimination among cytosine, 5-methylcytosine (mC), and 5-hydroxymethylcytosine (hmC). Two additional modified cytosine bases, 5-carboxylcytosine (caC) and 5-formylcytosine (fC), are produced during enzymatic conversion of hmC to cytosine in mammalian cells. Thus, an accurate picture of the cytosine epigenetic status in target cells should also include these C5-cytosine variants. In the present study, we used a patch clamp amplifier to acquire ionic current traces caused by phi29 DNA polymerase-controlled translocation of DNA templates through the M2MspA pore. Decision boundaries based on three consecutive ionic current states were implemented to call mC, hmC, caC, fC, or cytosine at CG dinucleotides in ∼4400 individual DNA molecules. We found that the percentage of correct base calls for single pass reads ranged from 91.6% to 98.3%. This accuracy depended upon the identity of nearest neighbor bases surrounding the CG dinucleotide.
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What OpenQuestion holds
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.