ArticleJournal of the American Chemical Society2016
Sequencing of DNA Lesions Facilitated by Site-Specific Excision via Base Excision Repair DNA Glycosylases Yielding Ligatable Gaps.
Article in Journal of the American Chemical Society, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
21 citing papers in PubMed, 39 citations in OpenAlex.
- Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability.Nature methods · 2025Article
- Pioneering contribution of Professor Bruce Ames to early development in biochemical aspects of oxidatively generated damage to DNA.Frontiers in molecular biosciences · 2025Review
- Recognition of 8-Oxo-2'-deoxyguanosine in DNA Using the Triphosphate of 2'-Deoxycytidine Connecting the 1,3-Diazaphenoxazine Unit, dCdapTP.Molecules (Basel, Switzerland) · 2024Article
- Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0.Chemical communications (Cambridge, England) · 2023Article
- PromotersRSC chemical biology · 2023Article
- DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol.Journal of the American Chemical Society · 2022Article
- Base-Resolution Analysis of Deoxyuridine at the Genome Scale Based on the Artificial Incorporation Modified Nucleobase.ACS central science · 2021Article
- Detection of Genomic Uracil Patterns.International journal of molecular sciences · 2021Review
- HumanJournal of the American Chemical Society · 2019Article
- Sequencing abasic sites in DNA at single-nucleotide resolution.Nature chemistry · 2019Article
- Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress.Nucleic acids research · 2019Article
- Oxidative Modification of Guanine in a Potential Z-DNA-Forming Sequence of a Gene Promoter Impacts Gene Expression.Chemical research in toxicology · 2019Article
- Genome-wide mapping reveals that deoxyuridine is enriched in the human centromeric DNA.Nature chemical biology · 2018Article
- Mapping three guanine oxidation products along DNA following exposure to three types of reactive oxygen species.Free radical biology & medicine · 2018Article
- Chemical Analysis of DNA Damage.Analytical chemistry · 2018Review
- Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.Genome research · 2017Article
- 8-Oxo-7,8-dihydroguanine in the Context of a Gene Promoter G-Quadruplex Is an On-Off Switch for Transcription.ACS chemical biology · 2017Article
- Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Sequencing DNA for the Oxidatively Modified Base 8-Oxo-7,8-Dihydroguanine.Methods in enzymology · 2017Article
- The use of an artificial nucleotide for polymerase-based recognition of carcinogenic O6-alkylguanine DNA adducts.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Modifications to nucleotides in the genome can lead to mutations or are involved in regulation of gene expression, and therefore, finding the site of modification is a worthy goal. Robust methods for sequencing modification sites on commercial sequencers have not been developed beyond the epigenetic marks on cytosine. Herein, a method to sequence DNA modification sites was developed that utilizes DNA glycosylases found in the base excision repair pathway to excise the modification. This approach yields a gap at the modification site that is sealed by T4-DNA ligase, yielding a product strand missing the modification. Upon sequencing, the modified nucleotide is reported as a deletion mutation, identifying its location. This approach was used to detect a uracil (U) or 8-oxo-7,8-dihydroguanine (OG) in codon 12 of the KRAS gene in synthetic oligodeoxynucleotides. Additionally, an OG modification site was placed in the VEGF promoter in a plasmid and sequenced. This method requires only commercially available materials and can be put into practice on any sequencing platform, allowing this method to have broad potential for finding modifications in DNA.
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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.