Biomaterial Database

Uracil glycol deoxynucleoside triphosphate is a better substrate for DNA polymerase I Klenow fragment than thymine glycol deoxynucleoside triphosphate. 1998

A A Purmal, and J P Bond, and B A Lyons, and Y W Kow, and S S Wallace

Department of Microbiology and Molecular Genetics, University of Vermont, Burlington 05405, USA.

A major stable oxidation product of DNA cytosine is 5,6-dihydroxy-5, 6-dihydrouracil (Ug). Ug can be formed directly in DNA or in the cellular nucleotide pools by deamination of the unstable primary product, cytosine glycol. Here, we synthesized dUgTP and showed that dUgTP was incorporated in place of dTTP and was a much better substrate for the model enzyme DNA polymerase I Klenow fragment lacking proofreading activity, Kf (exo-), than deoxythymidine glycol triphosphate (dTgTP). The relative efficiency for dUgTP insertion opposite A was 10 times higher than for dTgTP; however, the extension of a primer with 3' dUg was about 100 times more efficient than the extension of a primer with 3' dTg. At the insertion step, the differences in Vmax appeared to be responsible since the apparent Kms for dUgTP and dTgTP were about the same. In contrast, both the apparent Km and Vmax for elongation of dUg were markedly different from those of dTg. Molecular modeling was performed with both Tg and Ug and provides a rational structural explanation for these observations.

UI	MeSH Term	Description	Entries
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D010441	Peptide Chain Elongation, Translational	A process of GENETIC TRANSLATION, when an amino acid is transferred from its cognate TRANSFER RNA to the lengthening chain of PEPTIDES.	Chain Elongation, Peptide, Translational,Protein Biosynthesis Elongation,Protein Chain Elongation, Translational,Protein Translation Elongation,Translation Elongation, Genetic,Translation Elongation, Protein,Translational Elongation, Protein,Translational Peptide Chain Elongation,Biosynthesis Elongation, Protein,Elongation, Genetic Translation,Elongation, Protein Biosynthesis,Elongation, Protein Translation,Elongation, Protein Translational,Genetic Translation Elongation,Protein Translational Elongation
D003596	Cytosine	A pyrimidine base that is a fundamental unit of nucleic acids.
D003856	Deoxyuracil Nucleotides	Uracil nucleotides which contain deoxyribose as the sugar moiety.	Deoxyuridine Phosphates,Nucleotides, Deoxyuracil,Phosphates, Deoxyuridine
D004256	DNA Polymerase I	A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair.	DNA Polymerase alpha,DNA-Dependent DNA Polymerase I,Klenow Fragment,DNA Pol I,DNA Dependent DNA Polymerase I,Polymerase alpha, DNA
D004261	DNA Replication	The process by which a DNA molecule is duplicated.	Autonomous Replication,Replication, Autonomous,Autonomous Replications,DNA Replications,Replication, DNA,Replications, Autonomous,Replications, DNA
D013379	Substrate Specificity	A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.	Specificities, Substrate,Specificity, Substrate,Substrate Specificities
D013942	Thymine Nucleotides	Phosphate esters of THYMIDINE in N-glycosidic linkage with ribose or deoxyribose, as occurs in nucleic acids. (From Dorland, 28th ed, p1154)	Thymidine Phosphates,Nucleotides, Thymine,Phosphates, Thymidine
D014498	Uracil	One of four nucleotide bases in the nucleic acid RNA.