Dihydrothymidine and Thymidine Glycol Triphosphates As Substrates for DNA Polymerases: Differential Recognition of Thymine C5-C6 Bond Saturation and Sequence Specificity of Incorporation

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1988 Dec 9

PMID 3060857

Citations 7

Authors

H Ide

S S Wallace

Affiliations

Soon will be listed here.

Abstract

The ability of dihydrothymidine (DHdTTP) and thymidine glycol (dTTP-GLY) 5'-triphosphates to serve as substrates for different DNA polymerases was investigated. DHdTTP but not dTTP-GLY was used as a substrate by E. coli DNA polymerase I (Pol I). Within the detection limit of the assay used, neither T4 DNA polymerase nor avian myeloblastosis virus (AMV) reverse transcriptase used DHdTTP or dTTP-GLY as substrates. The ability of DHdTTP and dTTP-GLY to undergo enzyme-catalyzed turnover to the monophosphate paralleled their ability to serve as substrates for polymerization. These results, along with kinetic parameters for the incorporation of DHdTTP with Pol I, strongly suggest that the saturation of thymine C5-C6 bond and the substituent groups at C5 and C6 differentially exert effects on binding to DNA polymerases. DNA sequencing gel analysis of the polymerization products revealed that most single adenine sites were capable of templating DHdTTP, however, DNA synthesis was partially arrested at multiple adenine sites, suggesting that sequential incorporation of DHdTTP produced significant disorder in the primer terminus.

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References

Huang W, Lehman I . On the exonuclease activity of phage T4 deoxyribonucleic acid polymerase. J Biol Chem. 1972; 247(10):3139-46. View

Hayes R, Petrullo L, Huang H, Wallace S, LeClerc J . Oxidative damage in DNA. Lack of mutagenicity by thymine glycol lesions. J Mol Biol. 1988; 201(2):239-46. DOI: 10.1016/0022-2836(88)90135-0. View

Battula N, Loeb L . On the fidelity of DNA replication. Lack of exodeoxyribonuclease activity and error-correcting function in avian myeloblastosis virus DNA polymerase. J Biol Chem. 1976; 251(4):982-6. View

SANGER F, Nicklen S, Coulson A . DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977; 74(12):5463-7. PMC: 431765. DOI: 10.1073/pnas.74.12.5463. View

Singer B, FRAENKEL-CONRAT H, Kusmierek J . Preparation and template activities of polynucleotides containing O2- and O4-alkyluridine. Proc Natl Acad Sci U S A. 1978; 75(4):1722-6. PMC: 392411. DOI: 10.1073/pnas.75.4.1722. View

Clayton L, Goodman M, Branscomb E, Galas D . Error induction and correction by mutant and wild type T4 DNA polymerases. Kinetic error discrimination mechanisms. J Biol Chem. 1979; 254(6):1902-12. View

Kunkel T, Loeb L . On the fidelity of DNA replication. Effect of divalent metal ion activators and deoxyrionucleoside triphosphate pools on in vitro mutagenesis. J Biol Chem. 1979; 254(13):5718-25. View

Demple B, Linn S . DNA N-glycosylases and UV repair. Nature. 1980; 287(5779):203-8. DOI: 10.1038/287203a0. View

Rubin C, Schmid C . Pyrimidine-specific chemical reactions useful for DNA sequencing. Nucleic Acids Res. 1980; 8(20):4613-9. PMC: 324374. DOI: 10.1093/nar/8.20.4613. View

10.

Repine J, Pfenninger O, TALMAGE D, Berger E, PETTIJOHN D . Dimethyl sulfoxide prevents DNA nicking mediated by ionizing radiation or iron/hydrogen peroxide-generated hydroxyl radical. Proc Natl Acad Sci U S A. 1981; 78(2):1001-3. PMC: 319933. DOI: 10.1073/pnas.78.2.1001. View

11.

Alonso A, Medina A, Vicuna R, Venegas A, Valenzuela P, Yudelevich A . Molecular cloning and physical map of bacteriophage PM2 DNA. Gene. 1981; 13(1):115-8. DOI: 10.1016/0378-1119(81)90049-4. View

12.

Giloni L, Takeshita M, Johnson F, Iden C, Grollman A . Bleomycin-induced strand-scission of DNA. Mechanism of deoxyribose cleavage. J Biol Chem. 1981; 256(16):8608-15. View

13.

Langer P, Waldrop A, Ward D . Enzymatic synthesis of biotin-labeled polynucleotides: novel nucleic acid affinity probes. Proc Natl Acad Sci U S A. 1981; 78(11):6633-7. PMC: 349103. DOI: 10.1073/pnas.78.11.6633. View

14.

Joyce C, Kelley W, Grindley N . Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. J Biol Chem. 1982; 257(4):1958-64. View

15.

Demple B, Linn S . 5,6-Saturated thymine lesions in DNA: production by ultraviolet light or hydrogen peroxide. Nucleic Acids Res. 1982; 10(12):3781-9. PMC: 320752. DOI: 10.1093/nar/10.12.3781. View

16.

Watanabe S, Goodman M . Kinetic measurement of 2-aminopurine X cytosine and 2-aminopurine X thymine base pairs as a test of DNA polymerase fidelity mechanisms. Proc Natl Acad Sci U S A. 1982; 79(21):6429-33. PMC: 347139. DOI: 10.1073/pnas.79.21.6429. View

17.

Katcher H, Wallace S . Characterization of the Escherichia coli X-ray endonuclease, endonuclease III. Biochemistry. 1983; 22(17):4071-81. DOI: 10.1021/bi00286a013. View

18.

Makino K, Mossoba M, Riesz P . Formation of .OH and .H in aqueous solutions by ultrasound using clinical equipment. Radiat Res. 1983; 96(2):416-21. View

19.

Rajagopalan R, Melamede R, Laspia M, Erlanger B, Wallace S . Properties of antibodies to thymine glycol, a product of the radiolysis of DNA. Radiat Res. 1984; 97(3):499-510. View

20.

Revich G, Hillebrand G, Beattie K . High-performance liquid chromatographic purification of deoxynucleoside 5'-triphosphates and their use in a sensitive electrophoretic assay of misincorporation during DNA synthesis. J Chromatogr. 1984; 317:283-300. DOI: 10.1016/s0021-9673(01)91667-x. View