hm5dC – 5'-hydroxymethyl-2'-deoxycytidine

Name
WID hm5dC View in model
Name 5'-hydroxymethyl-2'-deoxycytidine View in model
Traditional name 4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)pyrimidin-2-one
IUPAC name 4-amino-1-[4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-(hydroxymethyl)-1,2-dihydropyrimidin-2-one
Cross references PubChem: 10256919, CAS: 7226-77-9
 
Classification
Type modified_deoxyribonucleoside View in model
 
Structure
Empirical formula (pH 7.5) H15C10N3O5
SMILES (pH 7.5) C(C1=CN(C(=O)N=C1N)C2CC(C(O2)CO)O)O
Charge (pH 7.5) 0
Is hydrophobic False View in model
Molecular weight (Da) 257.24 View in model
van der Waals volume 
(pH 7.5; Å3 molecule‑1)		 218.01
pI 6.57
logP -2.78
logD (pH 7.5) -2.78
 
Function
Reaction participant View in model
 
Comments
Comments occurs in bacteriophage DNA [PUB_0477]; majority of m5dC in bacteria is due to action of restriction-modification systems [PUB_0478]; 100% replacement cytidine in E. coli phages T2, T4, T6 [PUB_0478]; hypermodification renders bacteriophage DNA resistant to several restriction endonucleases [PUB_078]
References

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

  2. 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