DNAmod: (beta-D-glucopyranosyloxymethyl)deoxyuridine

Description

A pyrimidine 2'-deoxyribonucleoside having beta-D-glucopyranosyloxymethyluracil (base J) as the nucleobase.

Chemical properties

Chemical formula	Net charge	Average mass
C16H24N2O11	0	420.369

(beta-D-glucopyranosyloxymethyl)deoxyuridine

Recommended notation

Name	β-glucosyl-hydroxymethyluracil
Abbreviation	base J
Symbol	J

Nomenclature

IUPAC	SMILES	InChI	InChIKey	Synonyms
2'-deoxy-5-[(beta-D-glucopyranosyloxy)methyl]uridine	C1=C(CO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)C(NC(N1[C@@H]3O[C@H](CO)[C@H](C3)O)=O)=O	InChI=1S/C16H24N2O11/c19-3-8-7(21)1-10(28-8)18-2-6(14(25)17-16(18)26)5-27-15-13(24)12(23)11(22)9(4-20)29-15/h2,7-13,15,19-24H,1,3-5H2,(H,17,25,26)/t7-,8+,9+,10+,11+,12-,13+,15+/m0/s1	LHASLBSEALHFGO-URARBOGNSA-N	5-(beta-d-glucopyranosyloxymethyl)-2'-deoxyuridine (beta-d-glucosyloxymethyl)deoxyuridine dj beta-d-glucosyl-homedu beta-ghmu alpha-(beta-d-glucopyranosyloxy)thymidine 5-((glucopyranosyloxy)methyl)uridine

Mapping techniques

Method	Method detail	Resolution	Qualifier	References
(GLIB/CMS)-seq	chemical conversion and immunoprecipitation	low		Kawasaki, F, et al. 2017. Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania. Genome Biology. 18(1).
SMRT	direct detection	single-base	target sequences	Genest, PA, et al. 2015. Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing. Nucleic Acids Research. 43(4).
immunodetection	affinity-based	low		van Leeuwen, F, et al. 1998. Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. Genes & Development. 11(23).

Nature

Origin	Function	Functional detail	Organisms	References
natural	hypermodified nucleobase	transcription terminator	Crithidia fasciculata Euglena gracilis Leishmania donovani Leishmania major Leishmania tarentolae Trypanoplasma borreli Trypanosoma brucei Trypanosoma cruzi Trypanosoma equiperdum	Gommers-Ampt, JH, et al. 1993. beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T brucei. Cell. 75(6). Dooijes, D, et al. 2000. Base J originally found in kinetoplastida is also a minor constituent of nuclear DNA of Euglena gracilis. Nucleic Acids Research. 28(16). Genest, PA, et al. 2007. Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania. Nucleic Acids Research. 35(7). Ekanayake, DK, et al. 2011. Epigenetic regulation of transcription and virulence in Trypanosoma cruzi by O-linked thymine glucosylation of DNA. Molecular and Cellular Biology. 31(8). Kawasaki, F, et al. 2017. Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania. Genome Biology. 18(1).

Database references:

CHEBI:111513

Citations

Borst, P, et al. 2008. Base J: discovery, biosynthesis, and possible functions. Annual Review of Microbiology. 62.
Cliffe, LJ, et al. 2009. JBP1 and JBP2 are two distinct thymidine hydroxylases involved in J biosynthesis in genomic DNA of African trypanosomes. Nucleic Acids Research. 37(5).
Dooijes, D, et al. 2000. Base J originally found in kinetoplastida is also a minor constituent of nuclear DNA of Euglena gracilis. Nucleic Acids Research. 28(16).
Ekanayake, DK, et al. 2011. Epigenetic regulation of transcription and virulence in Trypanosoma cruzi by O-linked thymine glucosylation of DNA. Molecular and Cellular Biology. 31(8).
Genest, PA, et al. 2007. Telomeric localization of the modified DNA base J in the genome of the protozoan parasite Leishmania. Nucleic Acids Research. 35(7).
Genest, PA, et al. 2015. Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing. Nucleic Acids Research. 43(4).
Gommers-Ampt, JH, et al. 1993. beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei. Cell. 75(6).
Kawasaki, F, et al. 2017. Genome-wide mapping of 5-hydroxymethyluracil in the eukaryote parasite Leishmania. Genome Biology. 18(1).
van Leeuwen, F, et al. 1998. Localization of the modified base J in telomeric VSG gene expression sites of Trypanosoma brucei. Genes & Development. 11(23).