Home LiteratureArticle Details
PMID: 3906566 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Thymine glycols and urea residues in M13 DNA constitute replicative blocks in vitro.

Nucleic acids research ·Vol. 13 ·No. 22 ·1985-11-25 ·Pages 8035-52

Ide H, Kow YW, Wallace SS

Abstract

Thymine glycols were produced in M13 DNA in a concentration dependent manner by treating the DNA with osmium tetroxide (OsO4). For the formation of urea-containing M13 DNA, OsO4-oxidized DNA was hydrolyzed in alkali (pH 12) to convert the thymine glycols to urea residues. With both thymine glycol- and urea-containing M13 DNA, DNA synthesis catalyzed by Escherichia coli DNA polymerase I Klenow fragment was decreased in proportion to the number of damages present in the template DNA. Sequencing gel analysis of the products synthesized by E. coli DNA polymerase I and T4 DNA polymerase showed that DNA synthesis terminated opposite the putative thymine glycol site and at one nucleotide before the putative urea site. Substitution of manganese for magnesium in the reaction mix resulted in increased processivity of DNA synthesis so that a base was incorporated opposite urea. With thymine glycol-containing DNA, processivity in the presence of manganese was strongly dependent on the presence of a pyrimidine 5' to the thymine glycol in the template.

MeSH Terms
Bacterial Proteins/metabolism Coliphages/physiology DNA Replication DNA, Single-Stranded/metabolism DNA, Viral/metabolism DNA-Directed DNA Polymerase/metabolism Escherichia coli/enzymology Osmium Tetroxide/pharmacology T-Phages/enzymology Templates, Genetic/drug effects Thymine/analogs & derivatives,metabolism Urea/metabolism Viral Proteins/metabolism Virus Replication
Chemicals
Bacterial Proteins DNA, Single-Stranded DNA, Viral Viral Proteins thymine glycol Urea DNA-Directed DNA Polymerase Osmium Tetroxide Thymine
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ide H
Kow Y W
Wallace S S
References (29)
29 references, click to expand
  1. Determination of base sequence in nucleic acids with the electron microscope. V. The thymine-specific reactions of osmium tetroxide with deoxyribonucleic acid and its components.
    Biochemistry. 1966 Jul;5(7):2283-8 PMID: 5959451
  2. Metabolism of intermediate pyrimidine reduction products in vitro.
    J Biol Chem. 1956 Jan;218(1):1-7 PMID: 13278308
  3. The permanganate oxidation of thymidine and thymidylic acid.
    Biochim Biophys Acta. 1971 Jan 1;228(1):1-8 PMID: 5546561
  4. Letter: Gamma-ray induced thymine damage in mammalian cells.
    Int J Radiat Biol Relat Stud Phys Chem Med. 1974 Apr;25(4):413-7 PMID: 4545839
  5. Excision of damaged thymine residues from gamma-irradiated poly(dA-dT) by crude extracts of Escherichia coli.
    Proc Natl Acad Sci U S A. 1974 Sep;71(9):3532-6 PMID: 4610578
  6. Biological effect of thymine ring saturation in coliphage phiX174-DNA.
    Radiat Res. 1977 Feb;69(2):375-8 PMID: 841010
  7. Thymine fragment damage retained in the DNA polynucleotide chain after gamma irradiation in aerated solutions. II.
    Radiat Res. 1977 Nov;72(2):190-200 PMID: 918256
  8. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  9. Sites of inhibition of in vitro DNA synthesis in carcinogen- and UV-treated phi X174 DNA.
    Nature. 1979 Apr 12;278(5705):664-6 PMID: 450070
  10. The effect of template secondary structure on vaccinia DNA polymerase.
    J Biol Chem. 1979 Aug 25;254(16):7820-6 PMID: 381293
  11. Determination of thymine ring saturation products of the 5,6-dihydroxydihydrothymine type by the alkali degradation assay.
    Radiat Res. 1980 Mar;81(3):496-8 PMID: 7360899
  12. Two types of replication proteins increase the rate at which T4 DNA polymerase traverses the helical regions in a single-stranded DNA template.
    J Biol Chem. 1981 Apr 25;256(8):4087-94 PMID: 6971292
  13. Depurination causes mutations in SOS-induced cells.
    Proc Natl Acad Sci U S A. 1981 Mar;78(3):1773-7 PMID: 6453349
  14. Sites of termination of in vitro DNA synthesis on ultraviolet- and N-acetylaminofluorene-treated phi X174 templates by prokaryotic and eukaryotic DNA polymerases.
    Proc Natl Acad Sci U S A. 1981 Jan;78(1):110-4 PMID: 6165985
  15. Identification of the cis-thymine glycol moiety in chemically oxidized and gamma-irradiated deoxyribonucleic acid by high-pressure liquid chromatography analysis.
    Biochemistry. 1981 Dec 22;20(26):7566-71 PMID: 7326245
  16. The role of DNA polymerase in base substitution mutagenesis on non-instructional templates.
    Biochimie. 1982 Aug-Sep;64(8-9):829-38 PMID: 6215955
  17. Escherichia coli xth mutants are hypersensitive to hydrogen peroxide.
    J Bacteriol. 1983 Feb;153(2):1079-82 PMID: 6337115
  18. Characterization of the Escherichia coli X-ray endonuclease, endonuclease III.
    Biochemistry. 1983 Aug 16;22(17):4071-81 PMID: 6351916
  19. Insertion of nucleotides opposite apurinic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides.
    Biochemistry. 1983 Sep 13;22(19):4518-26 PMID: 6354260
  20. Arrest of DNA elongation by DNA polymerases at guanine adducts on 4-hydroxyaminoquinoline 1-oxide-modified DNA template.
    Cancer Res. 1984 May;44(5):1867-70 PMID: 6424933
  21. Properties of antibodies to thymine glycol, a product of the radiolysis of DNA.
    Radiat Res. 1984 Mar;97(3):499-510 PMID: 6729026
  22. Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage.
    Proc Natl Acad Sci U S A. 1984 Sep;81(18):5633-7 PMID: 6592579
  23. A role for DNA polymerase in the specificity of nucleotide incorporation opposite N-acetyl-2-aminofluorene adducts.
    J Mol Biol. 1984 Sep 25;178(3):569-94 PMID: 6492159
  24. Influence of template primary and secondary structure on the rate and fidelity of DNA synthesis.
    J Biol Chem. 1985 Mar 10;260(5):3116-25 PMID: 3972819
  25. Sequence context effects in DNA replication blocks induced by aflatoxin B1.
    Proc Natl Acad Sci U S A. 1985 May;82(10):3096-100 PMID: 3923472
  26. Abasic sites from cytosine as termination signals for DNA synthesis.
    Nucleic Acids Res. 1985 Jun 25;13(12):4285-98 PMID: 3892486
  27. Artefacts in the chromatography of mixtures of amino- acids containing cysteine.
    Nature. 1951 Dec 22;168(4288):1090-1 PMID: 14910653
  28. Separation of the phosphoric esters on the filter paper chromatogram.
    Nature. 1949 Dec 31;164(4183):1107-12, illust PMID: 15398090
  29. The permanganate oxidation of thymine.
    Biochim Biophys Acta. 1970 Jul 16;213(1):1-13 PMID: 5488924
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/13.22.8035
Published
1985-11-25
Pages
8035-52
Language
English
Region
England
NLM ID
0411011
PMCID
PMC322108
Subset
IM
Grants
NCI NIH HHS · CA3367 · United States
External Links
PubMed source DOI: 10.1093/nar/13.22.8035 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2