Description
A primary alcohol that is uracil bearing a hydroxymethyl substituent at the 5-position.
Chemical properties
| Chemical formula | Net charge | Average mass |
|---|---|---|
| C5H6N2O3 | 0 | 142.11282 |
Recommended notation
| Name | 5-hydroxymethyluracil |
|---|---|
| Abbreviation | 5hmU |
| Symbol | g |
Nomenclature
| IUPAC | SMILES | InChI | InChIKey | Synonyms |
|---|---|---|---|---|
| 5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione | OCc1c[nH]c(=O)[nH]c1=O | InChI=1S/C5H6N2O3/c8-2-3-1-6-5(10)7-4(3)9/h1,8H,2H2,(H2,6,7,9,10) | JDBGXEHEIRGOBU-UHFFFAOYSA-N |
|
Mapping techniques
| Method |
Method detail
|
Resolution
|
Qualifier
|
References |
|---|---|---|---|---|
| Hardisty-labelling | chemical tagging | single-base | target sequences |
|
SMRT | direct detection | single-base | target sequences |
|
Yu-labelling | chemical tagging | single-base | 5hmU:G mismatch only |
|
Nature
| Origin | Function | Functional detail |
Organisms
|
References |
|---|---|---|---|---|
| natural | damage, demethylation intermediate, and possible epigenetic mark |
|
|
Citations
- Bianchini, F, et al. 1998. Urinary excretion of 5-(hydroxymethyl) uracil in healthy volunteers: effect of active and passive tobacco smoke. International Journal of Cancer. 77(1).
- Cathcart, R, et al. 1984. Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage. Proceedings of the National Academy of Sciences of the United States of America. 81(18).
- Chen, HJ, et al. 2005. Measurement of urinary excretion of 5-hydroxymethyluracil in human by GC/NICI/MS: correlation with cigarette smoking, urinary TBARS and etheno DNA adduct. Toxicology Letters. 155(3).
- Clark, TA, et al. 2011. Direct detection and sequencing of damaged DNA bases. Genome Integrity. 2.
- Djuric, Z, et al. 1991. Quantitation of 5-(hydroxymethyl)uracil in DNA by gas chromatography with mass spectral detection. Chemical Research in Toxicology. 4(6).
- Frenkel, K, et al. 1985. Quantitative determination of the 5-(hydroxymethyl)uracil moiety in the DNA of gamma-irradiated cells. Biochemistry. 24(17).
- Hardisty, RE, et al. 2015. Selective Chemical Labeling of Natural T Modifications in DNA. Journal of the American Chemical Society. 137(29).
- Kawasaki, F, et al. 2017. Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania. Genome Biology. 18(1).
- Klungland, A, et al. 2001. 5-Formyluracil and its nucleoside derivatives confer toxicity and mutagenicity to mammalian cells by interfering with normal RNA and DNA metabolism. Toxicology Letters. 119(1).
- Kow, YW, et al. 2002. Repair of deaminated bases in DNA. Free Radical Biology & Medicine. 33(7).
- LaFrancois, CJ, et al. 1998. Quantification of 5-(hydroxymethyl)uracil in DNA by gas chromatography/mass spectrometry: problems and solutions. Chemical Research in Toxicology. 11(7).
- Pfaffeneder, T, et al. 2014. Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA. Nature Chemical Biology. 10(7).
- Rae, PM, et al. 1973. 5-Hydroxymethyluracil in the DNA of a dinoflagellate. Proceedings of the National Academy of Sciences of the United States of America. 70(4).
- Ravanat, JL, et al. 1999. Simultaneous determination of five oxidative DNA lesions in human urine. Chemical Research in Toxicology. 12(9).
- Yu, M, et al. 2014. Detection of mismatched 5-hydroxymethyluracil in DNA by selective chemical labeling. Methods (San Diego, Calif.). 72.