DNAmod: 5-(2-aminoethoxy)methyl-2'-deoxyuridine

Description

A pyrimidine 2'-deoxyribonucleoside that is 5-hydroxymethyl-2'-deoxyuridine in which the hydroxymethyl group at position 5 has been formally converted to the corresponding 2-aminoethyl ether. It is a thymidine hypermodification replacing 40% of thymidine nucleotides in the Salmonellaphage ViI.

Chemical properties

Chemical formula	Net charge	Average mass
C12H19N3O6	0	301.296

Recommended notation

Name	5-(2-aminoethoxy)methyluridine
Abbreviation	5-NeOmdU

Nomenclature

IUPAC	SMILES	InChI	InChIKey	Synonyms
5-[(2-aminoethoxy)methyl]-2'-deoxyuridine	N1(C(NC(C(=C1)COCCN)=O)=O)[C@H]2C[C@@H]([C@H](O2)CO)O	InChI=1S/C12H19N3O6/c13-1-2-20-6-7-4-15(12(19)14-11(7)18)10-3-8(17)9(5-16)21-10/h4,8-10,16-17H,1-3,5-6,13H2,(H,14,18,19)/t8-,9+,10+/m0/s1	YRTWGZACASMEIB-IVZWLZJFSA-N	5-neomdu 5-(2-aminoethoxymethyl)-1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione 5-[(2-aminoethoxy)methyl]-1-[(2r,4s,5r)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidine-2,4(1h,3h)-dione

Nature

Origin	Function	Functional detail	Organisms	References
natural	hypermodified nucleobase		Enterobacteria phage ViI	Lee, YJ, et al. 2018. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Proceedings of the National Academy of Sciences of the United States of America. 115(14).

Database references:

CHEBI:142164

Citations

Lee, YJ, et al. 2018. Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses. Proceedings of the National Academy of Sciences of the United States of America. 115(14).