hm5dU – 5-hydroxymethyl-2'-deoxyuridine

Name
WID hm5dU View in model
Name 5-hydroxymethyl-2'-deoxyuridine View in model
Traditional name 1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-3H-pyrimidine-2,4-dione
IUPAC name 1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2,3,4-tetrahydropyrimidine-2,4-dione
Cross references ChEBI: 472579, PubChem: 85661900
 
Classification
Type modified_deoxyribonucleoside View in model
 
Structure
Empirical formula (pH 7.5) H14C10N2O6
SMILES (pH 7.5) C1C(C(OC1N2C=C(C(=O)NC2=O)CO)CO)O
Charge (pH 7.5) 0
Is hydrophobic False View in model
Molecular weight (Da) 258.23 View in model
van der Waals volume 
(pH 7.5; Å3 molecule‑1)		 214.52
pI 3.55
logP -2.40
logD (pH 7.5) -2.40
 
Function
Reaction participant View in model
 
Comments
Comments 75 lesions per 10^6 bases [PUB_0479]; occurs in bacteriophage DNA [PUB_0477]; dT is completely replaced by hm5dU in some bacteriophage at the nucleotide precursor level, dCMP ==> dUMP ==> hm5dUMP ==> hm5dUTP, by dCMP deaminase, dUMP hydroxymethylase (not present in M. genitalium), deoxynucleotide monophosphate kinase, and nucleotide diphosphate kinase [PUB_0478];
References

  1. Gommers-Ampt JH, Borst P. Hypermodified bases in DNA. FASEB J 9, 1034-42 (1995). WholeCell: PUB_0478, PubMed: 7649402

  2. Guetens G, De Boeck G, Highley M, van Oosterom AT, de Bruijn EA. Oxidative DNA damage: biological significance and methods of analysis. Crit Rev Clin Lab Sci 39, 331-457 (2002). WholeCell: PUB_0479, PubMed: 12385502

  3. Warren RA. Modified bases in bacteriophage DNAs. Annu Rev Microbiol 34, 137-58 (1980). WholeCell: PUB_0477, PubMed: 7002022
 
Metadata
Created 2012-10-01 15:07:00
Last updated 2012-10-01 15:12:15