Nucleobase classification
Does DNA usually contain uracil?
DNA
The nucleobases are classified into two types: the purines, A and G, being fused five- and six-membered heterocyclic compounds, and the pyrimidines, the six-membered rings C and T. A fifth pyrimidine nucleobase, uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. In addition to RNA and DNA a large number of artificial nucleic acid analogues have also been created to study the properties of nucleic acids, or for use in biotechnology. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. However in a number of bacteriophages – "Bacillus subtilis" bacteriophages PBS1 and PBS2 and "Yersinia" bacteriophage piR1-37 – thymine has been replaced by uracil. Another phage - Staphylococcal phage S6 - has been identified with a genome where thymine has been replaced by uracil. Base J (beta-d-glucopyranosyloxymethyluracil), a modified form of uracil, is also found in a number of organisms: the flagellates "Diplonema" and "Euglena", and all the kinetoplastid genera Biosynthesis of J occurs in two steps: in the first step a specific thymidine in DNA is converted into hydroxymethyldeoxyuridine; in the second HOMedU is glycosylated to form J. Proteins that bind specifically to this base have been identified. These proteins appear to be distant relatives of the Tet1 oncogene that is involved in the pathogenesis of acute myeloid leukemia. J appears to act as a termination signal for RNA polymerase II.