The Use of DNA Glycosylases to Detect DNA Damage

  • Timothy R. O’Connor

Abstract

DNA glycosylases, first reported by Lindahl (1974), catalyze the scission of the glycosidic bond releasing damaged or mispaired bases as the first step of the base excision repair pathway (Fig. 12.1) (Dianov and Lindahl, 1994). Removal of damaged bases by a DNA glycosylase is generally associated with a specific type of damage (e.g., uracil-DNA glycosylase excises uracil bases formed by deamination or misincorporation into DNA; Lindahl, 1993). The specificity of DNA glycosylases, however, may also cross over to different types of DNA damage [e.g., AlkA protein, which excises a number of alkylated bases (Table I), also excises formyluracil and hydroxymethyluracil bases formed by oxidation (Bjelland et al., 1994)]. Proteins such as the uracil-DNA glycosylase, the AlkA protein, and the Tag protein leave abasic sites in DNA which are in turn processed by endonucleases cleaving the phosphodiester backbone hydrolytically at these sites (Dianov and Lindahl, 1994; Lloyd and Linn, 1993). In addition to this group of DNA glycosylases, the Fpg, Nth, and MutY proteins of E. coli and the UV endonuclease from bacteriophage T4 have physically associated activities incising DNA at abasic sites via β-elimination mechanisms (AP lyases) (Bailly and Verly, 1987; Gerlt, 1993), and as a consequence processing of these lesions may be slightly different than repair of abasic sites (Lloyd and Linn, 1993). The use of these enzymes in the detection of DNA damage is facilitated by the fact that DNA glycosylases are active in the presence of EDTA and function independent of any complex which may form in vivo. Table I summarizes several properties and damages recognized by DNA glycosylases.

Keywords

Modify Base Abasic Site Glycosylic Bond Hydrophobic Interaction Column AlkA Protein 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Asahara, H., Wistort, P. M., Bank, J. F., Bakerian, R. H., and Cunningham, R. P. (1989). Purification and characterization of Escherichia coli endonuclease III from the cloned nth gene. Biochemistry 28:4444–4449.PubMedCrossRefGoogle Scholar
  2. Au, K. G., Clark, S., Miller, J. H., and Modrich, P. (1989). Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs. Proc. Natl. Acad. Sci. USA 86:8877–8881.PubMedCrossRefGoogle Scholar
  3. Bailly, V., and Verly, W. G. (1987). Escherichia coli endonuclease III is not an endonuclease but a b-elimination catalyst. Biochem. J. 242:565–572.PubMedGoogle Scholar
  4. Bessho, T., Roy, R., Yamamoto, K., Kasai, H., Nishimura, S., Tano, K., and Mitra, S. (1993). Repair of 8-hydroxyguanine in DNA by mammalian N-methylpurine-DNA glycosylase. Proc. Natl. Acad. Sci. USA 90:8901–8904.PubMedCrossRefGoogle Scholar
  5. Bjelland, S., and Seeberg, E. (1987). Purification and characterization of 3-methyladenine-DNA glycosylase I from Escherichia coli. Nucleic Acids Res. 15:2787–2901.PubMedCrossRefGoogle Scholar
  6. Bjelland, S., Bjoras, M., and Seeberg, E. (1993). Excision of 3-methylguanine from alkylated DNA by 3-methyl-adenine DNA glycosylase I of Escherichia coli. Nucleic Acids Res. 21:2045–2049.PubMedCrossRefGoogle Scholar
  7. Bjelland, S., Birkeland, N. K., Benneche, T., Volden, G., and Seeberg, E. (1994). DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of the AlkA enzyme in Escherichia coli. J. Biol. Chem. 269:30489–30495.PubMedGoogle Scholar
  8. Boiteux, S. (1993). Properties and biological functions of the NTH and FPG proteins of Escherichia coli: Two DNA glycosylases that repair oxidative damage in DNA. J. Photochem. Photobiol. B:Biol. 19:87–96.CrossRefGoogle Scholar
  9. Boiteux, S., O’Connor, T. R., and Laval, J. (1987). Formamidopyrimidine-DNA glycosylase of Escherichia coli: Cloning and sequencing of the fpg structural gene and overproduction of the protein. EMBO J. 6:3177–3183.PubMedGoogle Scholar
  10. Boiteux, S., O’Connor, T. R., Lederer, F., Gouyette, A., and Laval, J. (1990). Homogeneous Fpg protein: A DNA glycosylase which excises imidazole ring-opened purines and nicks DNA at apurinic/apyrimidinic sites. J. Biol. Chem. 265:3916–3922.PubMedGoogle Scholar
  11. Boiteux, S., Gajewski, E., Laval, J., and Dizdaroglu, M. (1992). Substrate specificity of the Escherichia coli Fpg protein: Excision of purine lesions in DNA produced by ionizing radiation or photosensitization. Biochemistry 31:106–110.PubMedCrossRefGoogle Scholar
  12. Boorstein, R. J., Hilber, T. P., Cadet, J., Cunningham, R. P., and Teebor, G. W. (1989). UV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activities. Biochemistry 28:6164–6170.PubMedCrossRefGoogle Scholar
  13. Bradford, M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248–254.PubMedCrossRefGoogle Scholar
  14. Breimer, L. H. (1984). Enzymatic excision from γ-irradiated polydeoxyribonucleotide of adenine residues whose imidazole ring has been ruptured. Nucleic Acids Res. 12:6359–6367.PubMedCrossRefGoogle Scholar
  15. Cadet, J., and Weinfeld, M. (1993). Detecting DNA damage. Anal. Chem. 65:675A–682A.PubMedGoogle Scholar
  16. Carter, C. A., Habraken, Y., and Ludlum, D.B. (1988). Release of 7-alkylguanines from haloethylnitrosourea treated DNA by E. coli 3-methyladenine-DNA glycosylase II. Biochem. Biophys. Res. Commun. 155:1261–1265.PubMedCrossRefGoogle Scholar
  17. Chakravarti, D., Ibeanu, G.C., Tano, K., and Mitra, S. (1991). Cloning and expression in Escherichia coli of a human cDNA encoding the DNA repair protein N-methylpurine-DNA glycosylase. J. Biol. Chem. 266:15710–15715.PubMedGoogle Scholar
  18. Chetsanga, C.J., and Lindahl, T. (1979). Release of 7-methylguanine residues whose imidazole rings have been opened from damaged DNA by a DNA glycosylase from Escherichia coli. Nucleic Acids Res. 6:3673–3683.PubMedCrossRefGoogle Scholar
  19. Clarke, N. D., Kvaal, M., and Seeberg, E. (1984). Cloning of Escherichia coli genes encoding 3-methyladenine DNA glycosylases I and II. Mol. Gen. Genet. 197:368–372.PubMedCrossRefGoogle Scholar
  20. de Oliveira, R., Auffret van der Kemp, P., Thomas, D., Geiger, A., Nehls, P., and Boiteux, S. (1994). Formamidopyrimidine-DNA glycosylase in the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 22:3760–3764.PubMedCrossRefGoogle Scholar
  21. Demple, B., and Harrison, L. (1994). Repair of oxidative damage to DNA:Enzymology and biology. Annu. Rev. Biochem. 63:915–948.PubMedCrossRefGoogle Scholar
  22. Dianov, G., and Lindahl, T. (1994). Reconstitution of the DNA base excision-repair pathway. Curr. Biol. 4:1069–1076.PubMedCrossRefGoogle Scholar
  23. Dizdaroglu, M. (1991). Chemical determination of free radical-induced damage to DNA. Free Radical Biol. Med. 10:225–242.CrossRefGoogle Scholar
  24. Dizdaroglu, M., Laval, J., and Boiteux, S. (1993). Substrate specificity of the Escherichia coli endonuclease III:Excision of thymine-and cytosine-derived lesions in DNA produced by radiation-generated free radicals. Biochemistry 32:12105–12111.PubMedCrossRefGoogle Scholar
  25. Dodson, M. L., and Lloyd, R.S. (1989). Structure-function studies of the T4 endonuclease V repair enzyme. Mutat. Res. 218:49–65.PubMedCrossRefGoogle Scholar
  26. Dodson, M. L., Michaels, M. L., and Lloyd, R. S. (1994). Unified catalytic mechanism for DNA glycosylases. J. Biol. Chem. 269:32709–32712.PubMedGoogle Scholar
  27. Dosanjh, M. K., Chenna, A., Kim, E., Fraenkel-Conrat, H., Samson, L., and Singer, B. (1994). All four known cyclic adducts formed in DNA by the vinyl chloride metabolite chloracetaldehyde are released by a human DNA glycosylase. Proc. Natl. Acad. Sci. USA 91:1024–1028.PubMedCrossRefGoogle Scholar
  28. Floyd, R. A., West, M.S., Eneff, K.L., and Schneider, J.E. (1989). Methylene blue plus light mediates 8-hydroxy-guanine formation in DNA. Arch. Biochem. Biophys. 273:106–111.PubMedCrossRefGoogle Scholar
  29. Ganguly, T., Weems, K. M., and Duker, N. J. (1989). Ultraviolet-induced thymine hydrates are excised by bacterial and human DNA glycosylase activity. Biochemistry 29:7222–7228.CrossRefGoogle Scholar
  30. Gerlt, J. A. (1993). Mechanistic principles of enzyme-catalyzed cleavage of phosphodiester bonds, in:Nucleases (Linn, S., Roberts, R. J., and Lloyd, R. S, eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 1–34.Google Scholar
  31. Graves, R. J., Felzenswalb, L, Laval, J., and O’Connor, T. R. (1992). Excision of 5′-terminal deoxyribose phosphate from damaged DNA is catalysed by the Fpg protein of Escherichia coli. J. Biol. Chem. 267:14429–14435.PubMedGoogle Scholar
  32. Habraken, Y., Carter, C. A., Sekiguchi, M., and Ludlum, D. B. (1991). Release of N2,3-ethanoguanine from haloethylnitrosourea-treated DNA by Escherichia coli 3-methyladenine DNA glycosylase II. Carcinogenesis 12:1971–1973.PubMedCrossRefGoogle Scholar
  33. Hanawalt, P. C. (1994). Transcription-coupled repair and human disease. Science 266:1957–1958.PubMedCrossRefGoogle Scholar
  34. Hatahet, Z., Purmal, A. A., and Wallace, S. S. (1993). A novel method for site specific introduction of single model oxidative DNA lesions into oligodeoxyribonucleotides. Nucleic Acids Res. 21:1563–1568.PubMedCrossRefGoogle Scholar
  35. Hatahet, Z., Kow, Y W., Purmal, A. A., Cunningham, R. P., and Wallace, S. S. (1994). New substrates for old enzymes. J. Biol Chem. 269:18814–18820.PubMedGoogle Scholar
  36. Hegler, J., Bittner, D., Boiteux, S., and Epe, B. (1993). Quantification of oxidative DNA modifications in mitochondria. Carcinogenesis 14:2309–2312.PubMedCrossRefGoogle Scholar
  37. Holmes, J., Clark, S., and Modrich, P. (1990). Strand-specific mismatch correction in nuclear extracts of human and Drosophila melanogaster cell lines. Proc. Natl. Acad. Sci. USA 87:5837–5841.PubMedCrossRefGoogle Scholar
  38. Hsu, I.-C, Yang, Q., Kahng, M. W., and Xu, J.-F. (1994). Detection of DNA point mutations with DNA mismatch repair enzymes. Carcinogenesis 15:1657–1662.PubMedCrossRefGoogle Scholar
  39. Kow, Y W., and Wallace, S. S. (1987). Mechanism of action of Escherichia coli endonuclease III. Biochemistry 26:8200–8206.PubMedCrossRefGoogle Scholar
  40. Lindahl, T. (1974). An N-glycosidase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues. Proc. Natl. Acad. Sci. USA 71:3649–3653.PubMedCrossRefGoogle Scholar
  41. Lindahl, T. (1993). Instability and decay of the primary structure of DNA. Nature 362:709–715.PubMedCrossRefGoogle Scholar
  42. Lion, T., and Haas, O. A. (1990). Nonradioactive labeling of probe with digoxigenin by polymerase chain reaction. Anal. Biochem. 188:335–337.PubMedCrossRefGoogle Scholar
  43. Lloyd, R. S., and Linn, S. (1993). Nucleases involved in DNA repair, in:Nucleuses. (Linn, S., Roberts, R. J., and Lloyd, R. S., eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 263–316.Google Scholar
  44. Lu, A.-L., and Hsu, I.-C. (1992). Detection of single DNA base mutations with mismatch repair enzymes. Genomics 14:249–255.PubMedCrossRefGoogle Scholar
  45. Matijasevic, Z., Sekiguchi, M., and Ludlum, D. B. (1992). Release of N2,3-ethenoguanine from chloroacetaldehyde-treated DNA by Escherichia coli 3-methyladenine DNA glycosylase II. Proc. Natl. Acad. Sci. USA 89:9331–9334.PubMedCrossRefGoogle Scholar
  46. Mattes, W. B., Lee, C.-S., Laval, J., and O’Connor, T. R. (1996). Excision of DNA adducts of nitrogen mustards by bacterial and mammalian 3-methyladenine-DNA glycosylases. Carcinogenesis, in press..Google Scholar
  47. Maxam, A. M., and Gilbert, W. (1980). Sequencing end-labeled DNA with base-specific chemical cleavage. Methods Enzymol 65:499–559.PubMedCrossRefGoogle Scholar
  48. Müller, E., Boiteux, S., Cunningham, R. P., and Epe, B. (1990). Enzymatic recognition of DNA modifications induced by singlet oxygen and photosensitizers. Nucleic Acids Res. 18:5969–5973.PubMedCrossRefGoogle Scholar
  49. Neddermann, P., and Jiricny, J. (1993). Purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J. Biol. Chem. 268:21218–21224.PubMedGoogle Scholar
  50. O’Connor, T. (1993). Purification and characterisation of human 3-methyladenine-DNA glycosylase. Nucleic Acids Res. 21:5561–5569.PubMedCrossRefGoogle Scholar
  51. O’Connor, T. R., and Laval, J. (1989). Physical association of the formamidopyrimidine DNA glycosylase of Escherichia coli and an activity nicking DNA at apurinic/apyrimidinic sites. Proc. Natl. Acad. Sci. USA 86:5222–5226.PubMedCrossRefGoogle Scholar
  52. O’Connor, T. R., and Laval, F. (1990). Isolation and structure of a cDNA expressing a mammalian 3-methyladenine-DNA glycosylase. EMBO J. 9:3337–3342.PubMedGoogle Scholar
  53. O’Connor, T. R., and Laval, J. (1991). Human cDNA expressing a functional DNA glycosylase excising 3-methyladenine and 7-methylguanine. Biochem. Biophys. Res. Commun. 176:1170–1177.PubMedCrossRefGoogle Scholar
  54. O’Connor, T. R., Boiteux, S., and Laval, J. (1988). Ring-opened 7-methylguanine residues are a block to in vitro DNA synthesis. Nucleic Acids Res. 16:5879–5894.PubMedCrossRefGoogle Scholar
  55. O’Connor, T. R., Graves, R. J., de Murcia, G., Castaing, B., and Laval, J. (1993). Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. J. Biol. Chem. 268:9063–9070.PubMedGoogle Scholar
  56. Pfeifer, G. P., Drouin, R., and Holmquist, G.P. (1993). Detection of DNA adducts at the DNA sequence level by ligation-mediated PCR. Mutat. Res. 288:39–46.PubMedCrossRefGoogle Scholar
  57. Pierre, J., and Laval, J. (1980). Micrococcus luteus endonucleases for apurinic/apyrimidinic sites in deoxyribonucleic acid. 2. Further studies on the substrate specificity and mechanism of action. Biochemistry 19:5024–5029.PubMedCrossRefGoogle Scholar
  58. Sakumi, K., and Sekiguchi, M. (1990). Structures and functions of DNA glycosylases. Mutat. Res. 236:161–172.PubMedCrossRefGoogle Scholar
  59. Sakumi, K., Nakabeppu, Y., Yamamoto, Y, Kawabata, S., Iwanga, I., and Sekiguchi, M. (1986). Purification and structure of 3-methyladenine-DNA glycosylase I of Escherichia coli. J. Biol. Chem. 261:15761–15766.PubMedGoogle Scholar
  60. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989). Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.Google Scholar
  61. Samson, L., Derfler, B., Boosalis, M., and Call, K. (1991). Cloning and characterization of a 3-methyladenine DNA glycosylase cDNA from human cells whose gene maps to chromosome 16. Proc. Natl. Acad. Sci. USA 88:9127–9131.PubMedCrossRefGoogle Scholar
  62. Saparbaev, M., and Laval, J. (1994). Excision of hypoxanthine from DNA containing dIMP residues by the Escherichia coli, yeast, rat, and human alkylpurine DNA glycosylases. Proc. Natl. Acad. Sci. USA 91:5873–5877.PubMedCrossRefGoogle Scholar
  63. Schowalter, D. B., and Sommer, S. S. (1989). The generation of radiolabeled DNA and RNA probes with polymerase chain reaction. Anal. Biochem. 177:90–94.PubMedCrossRefGoogle Scholar
  64. Simha, D., Palejwala, V. A., and Humayun, M. Z. (1991). Mechanisms of mutagenesis by exocyclic DNA adducts. Construction and in vitro template characteristics of an oligonucleotide bearing a single site-specific ethenocytosine. Biochemistry 30:8727–8735.PubMedCrossRefGoogle Scholar
  65. Tsai-Wu, J. J., Liu, H. K., and Lu, A.-L. (1992). Escherichia coli MutY protein has both N-glycosylase and apurinic/ apyrimidinic endonuclease activities on A-C and A-G mispairs. Proc. Natl. Acad. Sci. USA 89:8779–8783.PubMedCrossRefGoogle Scholar
  66. Wang, W., Sitaram, A., and Scicchitano, D. A. (1995). 3-Methyladenine and 7-methylguanine exhibit no preferential removal from the transcribed strand of the dihydrofolate reductase gene in Chinese hamster ovary B11 cells. Biochemistry 34:1798–1804.PubMedCrossRefGoogle Scholar
  67. Yeh, Y C., Chang, D. Y, Masin, J., and Lu, A.-L. (1991). Two nicking enzyme systems specific for mismatch-containing DNA in nuclear extracts from human cells. J. Biol. Chem. 266:6480–6484.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1996

Authors and Affiliations

  • Timothy R. O’Connor
    • 1
  1. 1.Groupe ‘Réparation des lésions radio- et chimioinduites,’URA147 CNRS, Institut Gustave-Roussy PRIIVillejuif CedexFrance

Personalised recommendations