What structural features determine repair enzyme specificity and mechanism in chemically modified DNA?

Chemical Research in Toxicology

Volumn 10, Issue 7, 1997, Pages 713-732

  Singer, B ^a   Hang, B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA GLYCOSYLTRANSFERASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

DNA DAMAGE; DNA REPAIR; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; EUKARYOTE; HUMAN; NONHUMAN; PROKARYOTE; REVIEW; STRUCTURE ACTIVITY RELATION;

ANIMALS; CARBON-OXYGEN LYASES; DEOXYRIBONUCLEASE IV (PHAGE T4-INDUCED); DNA ADDUCTS; DNA GLYCOSYLASES; DNA LIGASES; DNA REPAIR; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; DNA-FORMAMIDOPYRIMIDINE GLYCOSYLASE; HUMANS; N-GLYCOSYL HYDROLASES; O(6)-METHYLGUANINE-DNA METHYLTRANSFERASE; SUBSTRATE SPECIFICITY; URACIL-DNA GLYCOSIDASE;

EUKARYOTA; PROKARYOTA;

EID: 0030787013     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx970011e     Document Type: Review

References (192)

1. Lindahl, T. (1982) DNA repair enzymes. Annu. Rev. Biochem. 51, 61-87.
2. Singer, B. (1986) O-Alkyl pyrimidines in mutagenesis and carcinogenesis: occurrence and significance. Cancer Res. 46, 4879-4885.
3. Lindahl, T., Sedgwick, B., Sekiguchi, M., and Nakabeppu, Y. (1988) Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 57, 133-157.
4. Wallace, S. S. (1988) AP endonucleases and DNA glycosylases that recognize oxidative DNA damage. Environ. Mol. Mutagen. 12, 431-477.
5. Myles, G. M., and Sancar, A. (1989) DNA repair. Chem. Res. Toxicol. 2, 197-226.
6. Singer, B. (1989) Structure-function relationships in alkylation damage and repair. In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells (Lambert, M. W., Laval, J., Eds.) pp 1-17, Plenum Press, New York.
7. 6-alkylguanine-DNA alkyl-transferase: regulation and importance in response to alkylating carcinogenic and therapeutic agents. Cancer Res. 50, 6119-6129.
8. Van Houten, B. (1990) Nucleotide excision repair in Escherichia coli. Microbiol. Rev. 54, 18-51.
9. Samson, L. D. (1992) The repair of DNA alkylation damage by methyltransferases and glycosylases. Essays Biochem. 27, 69-78.
10. Barnes, D. E., Lindahl, T., and Sedgwick, B. (1993) DNA repair. Curr. Opin. Cell Biol. 5, 424-433.
11. Demple, B., and Harrison, L. (1994) Repair of oxidative damage to DNA: enzymology and biology. Annu. Rev. Biochem. 63, 915-948.
12. Sancar, A. (1994) Mechanisms of DNA excision repair. Science 266, 1954-1956.
13. Modrich, P. (1994) Mismatch repair, genetic stability, and cancer. Science 266, 1959-1960.
14. Friedberg, E., Walker, G. C., and Seide, W. (1995) DNA Repair and Mutagenesis, ASM Press, Washington, DC.
15. Seeberg, E., Eide, L., and Bjoras, M. (1995) The base excision repair pathway. Trends Biochem. Sci. 20, 391-397.
16. Sancar, A. (1996) DNA excision repair. Annu. Rev. Biochem. 65, 43-81.
17. Modrich, P., and Lahue, R. (1996) Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu. Rev. Biochem. 65, 101-133.
18. Wood, R. D. (1996) DNA repair in eukaryotes. Annu. Rev. Biochem. 65, 135-167.
19. Varshney, U., Hutcheon, T., and van de Sande, J. H. (1988) Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung). J. Biol. Chem. 263, 7776-7784.
20. Olsen, L. C., Aasland, R., Wittwer, C. U., Krokan, H. E., and Heiland, D. E. (1989) Molecular cloning of human uracil-DNA glycosylase, a highly conserved DNA repair enzyme. EMBO J. 8, 3121-3125.
21. Savva, R., McAuley-Hecht, K., Brown, T., and Pearl, L. (1995) The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature 373, 487-493.
22. Mol, C. D., Arvai, A. S., Slupphaug, G., Kavli, B., Alseth, I., Krokan, H. E., and Tainer, J. A. (1995) Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell 80, 869-878 (see comments).
23. Nakabeppu, Y., Miyata, T., Kondo, H., Iwanaga, S., and Sekiguchi, M. (1984) Structure and expression of the alkA gene of Escherichia coli involved in adaptive response to alkylating agents. J. Biol. Chem. 259, 13730-13736.
24. 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. U.S.A. 88, 9127-9131.
25. 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.
26. Vickers, M. A., Vyas, P., Harris, P. C., Simmons, D. L., and Higgs, D. R. (1993) Structure of the human 3-methyladenine DNA glycosylase gene and localization close to the 16p telomere. Proc. Natl. Acad. Sci. U.S.A. 90, 3437-3441.
27. 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.
28. Yamagata, Y., Kato, M., Odawara, K., Tokuno, Y., Nakashima, Y., Matsushima, N., Yasumura, K., Tomita, K., Ihara, K., Fujii, Y., Nakabeppu, Y., Sekiguchi, M., and Fujii, S. (1996) Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glyeosylase II, from Escherichia coli. Cell 86, 311-319.
29. Labahn, J., Scharer, O. D., Long, A., Ezaz-Nikpay, K., Verdine, G. L., and Ellenberger, T. E. (1996) Structural basis for the excision repair of alkylation-damaged DNA. Cell 86, 321-329.
30. 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.
31. Kuo, C. F., McRee, D. E., Fisher, C. L., O'Handley, S. F., Cunningham, R. P., and Tainer, J. A. (1992) Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III. Science 258, 434-440.
32. Roldán-Arjona, T., Anselmino, C., and Lindahl, T. (1996) Molecular cloning and functional analysis of a Schizosaccharomyces pombe homologue of Escherichia coli endonuclease III. Nucleic Acids Res. 24, 3307-3312.
33. Rogers, S. G., and Weiss, B. (1980) Cloning of the exonuclease III gene of Escherichia coli. Gene 11, 187-195.
34. Robson, C. N., and Hickson, I. D. (1991) Isolation of cDNA clones encoding a human apurinic/apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in E. coli xth (exonuclease III) mutants. Nucleic Acids Res. 19, 5519-5523.
35. Demple, B., Herman, T., and Chen, D. S. (1991) Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Proc. Natl. Acad. Sci. U.S.A. 88, 11450-11454.
36. Seki, S., Hatsushika, M., Watanabe, S., Akiyama, K., Nagao, K., and Tsutsui, K. (1992) cDNA cloning, sequencing, expression and possible domain structure of human APEX nuclease homologous to Escherichia coli exonuclease III. Biochim. Biophys. Acta 1131, 287-299.
37. Mol, C. D., Kuo, C. F., Thayer, M. M., Cunningham, R. P., and Tainer, J. A. (1995) Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374, 381-386.
38. Sedgwick, B. (1983) Molecular cloning of a gene which regulates the adaptive response to alkylating agents in Escherichia coli. Mol. Gen. Genet. 191, 466-472.
39. 6-methylguanine-DNA methyltransferase. cDNA expression in Escherichia coli and gene expression in human cells. J. Biol. Chem. 265, 9563-9569.
40. 6-alkylguanine. Proc. Natl. Acad. Sci. U.S.A. 87, 686-690.
41. 6-methylguanine-DNA methyltransferase from E. coli. EMBO J. 13, 1495-1501.
42. Lawley, P. D., and Orr, D. J. (1970) Specific excision of methylation products from DNA of Escherichia coli treated with N-methyl-N′-nitro-N-nitrosoguanidine. Chem. Biol. Interact. 2, 154-157.
43. Lawley, P. D., and Warren, W. (1975) Specific excision of ethylated purines from DNA of Escherichia coli treated with N-ethyl-N-nitrosourea. Chem. Biol. Interact. 11, 55-57.
44. Margison, G. P., Capps, M. J., O'Connor, P. J., and Craig, A. W. (1973) Loss of 7-methylguanine from rat liver DNA after methylation in vivo with methylmethanesulphonate or dimethylnitrosamine. Chem. Biol. Interact. 6, 119-124.
45. 6-ethylguanine from rat liver DNA. Br. J. Cancer 40, 809-813.
46. Shooter, K. V., Slade, T. A., and O'Connor, P. J. (1977) The formation and stability of methyl phosphotriesters in the DNA of rat tissues after treatment with the carcinogen N,N-dimethylnitrosamine. Chem. Biol. Interact. 19, 363-367.
47. Shooter, K. V., and Slade, T. A. (1977) The stability of methyl and ethyl phosphotriesters in DNA in vivo. Chem. Biol. Interact. 19, 353-361.
48. Bodell, W. J., Singer, B., Thomas, G. H., and Cleaver, J. E. (1979) Evidence for removal at different rates of O-ethyl pyrimidines and ethylphosphotriesters in two human fibroblast cell lines. Nucleic Acids Res. 6, 2819-2829.
49. Singer, B., Spengler, S., and Bodell, W. J. (1981) Tissue-dependent enzyme-mediated repair or removal of O-ethyl pyrimidines and ethyl purines in carcinogen-treated rats. Carcinogenesis 2, 1069-1073.
50. Dolan, M. E., Scicchitano, D., Singer, B., and Pegg, A. E. (1984) Comparison of repair of methylated pyrimidines in poly(dT) by extracts from rat liver and Escherichia coli. Biochem. Biophys. Res. Commun. 123, 324-330.
51. Kriek, E. (1972) Persistent binding of a new reaction product of the carcinogen N-hydroxy-N-2-acetylaminofluorene with guanine in rat liver DNA in vivo. Cancer Res. 32, 2042-2048.
52. Wang, T. C., and Cerutti, P. A. (1979) Formation and removal of aflatoxin B1-induced DNA lesions in epithelioid human lung cells. Cancer Res. 39, 5165-5170.
53. 2-deoxyguanosine DNA adduct formed in human fibroblasts by (+/-)-7β,8α-dihydroxy-9α,-10a-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene. Proc. Natl. Acad. Sci. U.S.A. 77, 5933-5937.
54. 6-ethylguanine in DNA. J. Mol. Biol. 154, 169-175.
55. 6-alkylguanine-DNA alkyltransferases from rat liver and E. coli. Carcinogenesis 6, 1027-1031.
56. McCarthy, T. V., Karran, P., and Lindahl, T. (1984) Inducible repair of O-alkylated DNA pyrimidines in Escherichia coli. EMBO J. 3, 545-550.
57. 2-methylthymine DNA glycosylase. Biochem. Biophys. Res. Commun. 120, 1-8.
58. 4-alkylthymidine following exposure to methylating and ethylating hepatocarcinogens. Carcinogenesis 6, 625-629.
59. 6-methylguanine-DNA methyltransferase. Nucleic Acids Res. 11, 7743-7758.
60. 6-alkylguanine-DNA alkyltransferase. Cancer Res. 46, 3353-3357.
61. 6-alkylguanine-DNA alkyltransferase by alkylating agents or alkylated DNA. Cancer Res. 46, 2320-2323.
62. 6-methylguanine-DNA methyltransferase and chloroethylnitrosourea-treated DNA. Cancer Res. 52, 6052-6058.
63. McCarthy, T. V., and Lindahl, T. (1985) Methyl phosphotriesters in alkylated DNA are repaired by the Ada regulatory protein of E. coli. Nucleic Acids Res. 13, 2683-2698.
64. + extract. Nucleic Acids Res. 13, 7067-7077.
65. Carter, C. A., Kirk, M. C., and Ludlum, D. B. (1988) Phosphotriester formation by the haloethylnitrosoureas and repair of these lesions by E. coli BS21 extracts. Nucleic Acids Res. 16, 5661-5672.
66. Brent, T. P., Dolan, M. E., Fraenkel-Conrat, H., Hall, J., Karran, P., Laval, L., Margison, G. P., Montesano, R., Pegg, A. E., Potter, P. M., Singer, B., Swenberg, J. A., and Yarosh, D. B. (1988) Repair of O-alkylpyrimidines in mammalian cells: a present consensus. Proc. Natl. Acad. Sci. U.S.A. 85, 1759-1762.
67. Sedgwick, B., Robins, P., Totty, N., and Lindahl, T. (1988) Functional domains and methyl acceptor sites of the Escherichia coli ada protein. J. Biol. Chem. 263, 4430-4433.
68. Yamamoto, Y., and Sekiguchi, M. (1979) Pathways for repair of DNA damaged by alkylating agent in Escherichia coli. Mol. Gen. Genet. 171, 251-256.
69. Laval, J., Pierre, J., and Laval, F. (1981) Release of 7-methylguanine residues from alkylated DNA by extracts of Micrococcus luteus and Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 78, 852-855.
70. 6-alkylguanines or 1-alkyladenines. Proc. Natl. Acad. Sci. U.S.A. 78, 856-860.
71. Margison, G. P., and Pegg, A. E. (1981) Enzymatic release of 7-methylguanine from methylated DNA by rodent liver extracts. Proc. Natl. Acad. Sci. U.S.A. 78, 861-865.
72. Gallagher, P. E., and Brent, T. P. (1984) Further purification and characterization of human 3-methyladenine-DNA glycosylase. Evidence for broad specificity. Biochim. Biophys. Acta 782, 394-401.
73. Hall, J., and Karran, P. (1986) O-Methylated pyrimidines-important lesions in cytotoxicity and mutagenicity in mammalian cells. In Repair of DNA Lesions Introduced by N-Nitroso Compounds (Myrnes, M. B., Krokan, H., Eds.) pp 77-86, Norwegian University Press, Oslo.
74. Habraken, Y., and Ludlum, D. B. (1989) Release of chloroethyl ethyl sulfide-modified DNA bases by bacterial 3-methyladenine-DNA glycosylases I and II. Carcinogenesis 10, 489-492.
75. 6-ethenodeoxyadenosine. Cancer Res. 52, 1377-1379.
76. 6-ethenoadenine and 3-methyladenine. Proc. Natl. Acad. Sci. U.S.A. 89, 9386-9390.
77. 2,3-ethenoguanine from chloroacetaldehyde-treated DNA by Escherichia coli 3-methyladenine DNA glycosylase II. Proc. Natl. Acad. Sci. U.S.A. 89, 9331-9334.
78. 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 chloroacetaldehyde are released by a human DNA glycosylase. Proc. Natl. Acad. Sci. U.S.A. 91, 1024-1028.
79. 2,3-ethanoguanine from haloethylnitrosourea-treated DNA by Escherichia coli 3-methyladenine DNA glycosylase II. Carcinogenesis 12, 1971-1973.
80. 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. U.S.A. 91, 5873-5877.
81. 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.
82. 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. U.S.A. 90, 8901-8904.
83. 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 17, 643-648.
84. Matijasevic, Z., Stering, A., Niu, T.-q., Austin-Ritchie, P., and Ludlum, D. B. (1996) Release of sulfur mustard-modified bases from DNA by 3-methyladenine DNA glycosylase II. Carcinogenesis 17, 2249-2252.
85. 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, 3673-3684.
86. Breimer, L. H. (1984) Enzymatic excision from gamma-irradiated polydeoxyribonucleotides of adenine residues whose imidazole rings have been ruptured. Nucleic Acids Res. 12, 6359-6367.
87. Chetsanga, C. J., and Frenette, G. P. (1983) Excision of aflatoxin Bl-imidazole ring opened guanine adducts from DNA by formamidopyrimidine-DNA glycosylase. Carcinogenesis 4, 997-1000.
88. Boiteux, S., Bichara, M., Fuchs, R. P., and Laval, J. (1989) Excision of the imidazole ring-opened form of N-2-aminofluorene-C(8)-guanine adduct in poly(dG-dC) by Escherichia coli formamidopyrimidine-DNA glycosylase. Carcinogenesis 10, 1905-1909.
89. Tchou, J., Kasai, H., Shibutani, S., Chung, M. H., Laval, J., Grollman, A. P., and Nishimura, S. (1991) 8-Oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity. Proc. Natl. Acad. Sci. U.S.A. 88, 4690-4694.
90. Boiteux, S., Gajewski, E., Laval, J., and Dizdaroglu, M. (1992) Substrate specificity of the Escherichia coli Fpg protein (formamidopyrimidine-DNA glycosylase): excision of purine lesions in DNA produced by ionizing radiation or photosensitization. Biochemistry 31, 106-110.
91. Michaels, M. L., Pham, L., Cruz, C., and Miller, J. H. (1991) MutM, a protein that prevents G·C→T·A transversions, is formamidopyrimidine-DNA glycosylase. Nucleic Acids Res. 19, 3629-3632.
92. Cabrera, M., Nghiem, Y., and Miller, J. H. (1988) mutM, a second mutator locus in Escherichia coli that generates G·C→T·A transversions. J. Bacteriol. 170, 5405-5407.
93. 4-alkylthymine in Escherichia coli: the adaptive response and nucleotide excision repair. EMBO J. 7, 2261-2267.
94. 6-methylguanine by ABC excinuclease of Escherichia coli in vitro. J. Biol. Chem. 264, 5172-5176.
95. 6-alkylguanine-DNA alkyl-transferase and nucleotide excision repair activities in human cells. Cancer Res. 52, 2008-2011 (see comments).
96. 4-alkylthymines in human cells. J. Biol. Chem. 269, 25521-25528.
97. Lin, J. J., and Sancar, A. (1989) A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA. Biochemistry 28, 7979-7984.
98. Snowden, A., Row, Y. W., and Van Houten, B. (1990) Damage repertoire of the Escherichia coli UvrABC nuclease complex includes abasic sites, base-damage analogues, and lesions containing adjacent 5′ or 3′ nicks. Biochemistry 29, 7251-7259.
99. Kow, Y. W., Wallace, S. S., and Van Houten, B. (1990) UvrABC nuclease complex repairs thymine glycol, an oxidative DNA base damage. Mutat. Res. 235, 147-156.
100. Huang, J. C., Hsu, D. S., Kazantsev, A., and Sancar, A. (1994) Substrate spectrum of human excinuclease: repair of abasic sites, methylated bases, mismatches, and bulky adducts. Proc. Natl. Acad. Sci. U.S.A. 91, 12213-12217.
101. 4-methylthymine, or the cisplatin-d(GpG) adduct. Proc. Natl. Acad. Sci. U.S.A. 93, 6443-6447.
102. Singer, B., and Grunberger, D. (1983) Molecular Biology of Mutagens and Carcinogens, Plenum Press, New York.
103. Lindahl, T. (1974) An N-glycosidase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues. Proc. Natl. Acad. Sci. U.S.A. 71, 3649-3653.
104. Warner, H. R., and Rockstroh, P. A. (1980) Incorporation and excision of 5-fluorouracil from deoxyribonucleic acid in Escherichia coli. J. Bacteriol. 141, 680-686.
105. Hatahet, Z., Kow, Y. W., Purmal, A. A., Cunningham, R. P., and Wallace, S. S. (1994) New substrates for old enzymes. 5-Hydroxy-2′-deoxycytidine and 5-hydroxy-2′-deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase, while 5-hydroxy-2′-deoxyuridine is a substrate for uracil DNA N-glycosylase. J. Biol. Chem. 269, 18814-18820.
106. Dizdaroglu, M., Karakaya, A., Jaruga, P., Slupphaug, G., and Krokan, H. E. (1996) Novel activities of human uracil DNA N-glycosylase for cytosine-derived products of oxidative DNA damage. Nucleic Acids Res. 24, 418-422.
107. 6-ethenoadenine when present in DNA. Nucleic Acids Res. 23, 3750-3755.
108. Bjørås, M., Klungland, A., Johansen, R. F., and Seeberg, E. (1995) Purification and properties of the alkylation repair DNA glycosylase encoded the MAG gene from Saccharomyces cerevisiae. Biochemistry 34, 4577-4582.
109. Rydberg, B., and Lindahl, T. (1982) Nonenzymatic methylation of DNA by the intracellular methyl group donor S-adenosyl-L-methionine is a potentially mutagenic reaction. EMBO J. 1, 211-216.
110. 6-Ethenoadenine is preferred over 3-methyladenine as substrate by a cloned human N-methylpurine-DNA glycosylase (3-methyl-adenine-DNA glycosylase). Biochemistry 33, 1624-1628.
111. Chen, H. J., and Chung, F. L. (1994) Formation of etheno adducts in reactions of enals via autoxidation. Chem. Res. Toxicol. 7, 857-860.
112. 4-ethenocytosine by lipid peroxidation products and nucleic acid bases. Chem. Res. Toxicol. 8, 278-283.
113. Chung, F.-L., Chen, H.-J. C., and Nath, R. G. (1996) Lipid peroxidation as a potential endogenous source for the formation of exocyclic DNA adducts. Carcinogenesis 17, 2105-2111.
114. Habraken, Y., Carter, C. A., Kirk, M. C., and Ludlum, D. B. (1991) Release of 7-alkylguanines from N-(2-chloroethyl)-N′-cyclohexyl-N-nitrosourea-modified DNA by 3-methyladenine DNA glycosylase II. Cancer Res. 51, 499-503.
115. Singer, B. (1975) Methylation and ethylation of uridylic acid and thymidylic acid. Reactivity of the ring and phosphate as a function of pH and alkyl group. Biochemistry 14, 4353-4357.
116. 2-Alkylcytidine - a new major product of neutral, aqueous reaction of cytidine with carcinogens. FEBS Lett. 63, 85-88.
117. 4-alkyl products. Nucleic Acids Res. 3, 989-1000.
118. Singer, B. (1976) All oxygens in nucleic acids react with carcinogenic ethylating agents. Nature 264, 333-339.
119. Singer, B., Bodell, W. J., Cleaver, J. E., Thomas, G. H., Rajewsky, M. F., and Thon, W. (1978) Oxygens in DNA are main targets for ethylnitrosourea in normal and xeroderma pigmentosum fibroblasts and fetal rat brain cells. Nature 276, 85-88.
120. 4-methyldeoxythymidine in place of deoxythymidine in primed poly-(dA-dT)·poly(dA-dT) synthesis. Proc. Natl. Acad. Sci. U.S.A. 80, 4884-4888.
121. Singer, B., Spengler, S. J., Chavez, F., Sagi, J., Kuśmierek, J. T., Preston, B. D., and Loeb, L. A. (1987) O-Alkyl deoxythymidines are recognized by DNA polymerase I as deoxythymidine or deoxycytidine. In N-Nitroso Compounds: Occurrence, Biological Effects and Relevance to Human Cancer (O'Neill, J. K., et al., Eds.) Vol. 84, pp 37-41, IARC, Lyon, France.
122. Preston, B. D., Zakour, R. A., Singer, B., and Loeb, L. A. (1988) Fidelity of Base Selection by DNA Polymerases: Studies on Site-Specific Incorporation of Base Analogues. In DNA Replication and Mutagenesis (Moses, R. E., and Summers, W. C., Eds.) pp 196-207, American Society of Microbiology, Washington, DC.
123. Preston, B. D., Singer, B., and Loeb, L. A. (1987) Comparison of the relative mutagenicities of O-alkylthymines site-specifically incorporated into φX 174 DNA. J. Biol. Chem. 262, 13821-13827.
124. 4-alkyl pyrimidine nueleosides: stability of the glycosyl bond and of the alkyl group as a function of pH. Biochemistry 17, 1246-1250.
125. Boiteux, S., Bichara, M., Fuchs, R. P. P., and Lavai, J. (1989) Substrate specificity of the formamidopyrimidine-DNA glycosylase of E. coli: repair of the imidazole ring-opened form N-hydroxy-2-amino-fluorene-guanine adducts in DNA. In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cells (Lambert, M. W., Laval, J., Eds.) pp 37-44, Plenum Publishing Corp., New York.
126. Boiteux, S., Belleney, J., Roques, B. P., and Laval, J. (1984) Two rotameric forms of open ring 7-methylguanine are present in alkylated polynucleotides. Nucleic Acids Res. 12, 5429-5439.
127. Chetsanga, C. J., Polidori, G., and Mainwaring, M. (1982) Analysis and excision of ring-opened phosphoramide mustard-deoxyguanine adducts in DNA. Cancer Res. 42, 2616-2621.
128. 4-methylthymine repair by eukaryotic methyltransferases. J. Biol. Chem. 266, 2767-2771.
129. Iyama, A., Sakumi, K., Nakabeppu, Y., and Sekiguchi, M. (1994) A unique structural feature of rabbit DNA repair methyltransferase as revealed by cDNA cloning. Carcinogenesis 15, 627-633.
130. Demple, B., Sedgwick, B., Robins, P., Totty, N., Waterfield, M. D., and Lindahl, T. (1985) Active site and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 82, 2688-2692.
131. Samson, L. (1992) The suicidal DNA repair methyltransferases of microbes. Mol. Microbiol. 6, 825-831.
132. Myers, L. C., Verdine, G. L., and Wagner, G. (1993) Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada. Biochemistry 32, 14089-14094.
133. Habazettl, J., Myers, L. C., Yuan, F., Verdine, G. L., and Wagner, G. (1996) Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR. Biochemistry 35, 9335-9348.
134. 6-methylguanine in DNA. J. Mol. Biol. 213, 739-747.
135. 6-methylguanine-DNA methyltransferase with that encoded by a cloned cDNA. J. Biol. Chem. 266, 1064-1070.
136. Den Engelse, L., Menkveld, G. J., De Brij, R. J., and Tates, A. D. (1986) Formation and stability of alkylated pyrimidines and purines (including imidazole ring-opened 7-alkylguanine) and alkylphosphotriesters in liver DNA of adult rats treated with ethylnitrosourea or dimethylnitrosamine. Carcinogenesis 7, 393-403.
137. 4-ethylthymine and the ethylphosphotriester dTp(Et)dT are highly persistent DNA modifications in slowly dividing tissues of the ethylnitrosourea-treated rat. Carcinogenesis 8, 751-757.
138. Pegg, A. E., and Dolan, M. E. (1989) Investigation of sequence specificity in DNA alkylation and repair using oligodeoxynucleotide substrates. In DNA Repair Mechanisms and Their Biological Implications in Mammalian Cell (Lambert, M. W., Laval, J., Eds.) pp 45-59, Plenum Press, New York.
139. 6-benzylguanine provides a means to evaluate the role of this protein in protection against carcinogenic and therapeutic alkylating agents. Proc. Natl. Acad. Sci. U.S.A. 87, 5368-5372.
140. 6-alkylguanine-DNA alkyltransferase. J. Med. Chem. 35, 4486-4491.
141. 6-benzylguanine. Biochemistry 32, 11998-12006.
142. 6-alkylguanine-DNA alkyltransferase. J. Med. Chem. 37, 342-347.
143. 6-alkylguanine-DNA alkyltransferase. Cancer Res. 54, 5123-5130.
144. 6-benzyl-2′-deoxyguanosine in Sprague-Dawley rats. Chem. Res. Toxicol. 7, 762-769.
145. 6-alkylguanine-DNA alkyltransferase. J. Med. Chem. 38, 359-365.
146. 6-benzylguanine. Biochem. J. 298, 231-235.
147. 6-alkylguanine-DNA alkyltransferase. Prog. Nucleic Acid Res. Mol. Biol. 51, 167-223.
148. Ludlum, D. B. (1990) DNA alkylation by the haloethylnitrosoureas: nature of modifications produced and their enzymatic repair or removal. Mutat. Res. 233, 117-126.
149. Doetsch, P. W., and Cunningham, R. P. (1990) The enzymology of apurinic/apyrimidinic endonucleases. Mutat. Res. 236, 173-201.
150. Xanthoudakis, S., and Curran, T. (1992) Identification and characterization of Ref-1, a nuclear protein that facilitates AP-1 DNA-binding activity. EMBO J. 11, 653-665.
151. Barzilay, G., and Hickson, I. D. (1995) Structure and function of apurinic/apyrimidinic endonucleases. Bioessays 17, 713-719.
152. Chenna, A., Hang, B., Rydberg, B., Kim, E., Pongracz, K., Bodell, W. J., and Singer, B. (1995) The benzene metabolite p-benzoquinone forms adducts with DNA bases that are excised by a repair activity from human cells that differs from an ethenoadenine glycosylase. Proc. Natl. Acad. Sci. U.S.A. 92, 5890-5894.
153. Hang, B., Chenna, A., Fraenkel-Conrat, H., and Singer, B. (1996) An unusual mechanism for the major human AP endonuclease involving 5' cleavage of DNA containing a benzene-derived exocyclic adduct in the absence of an AP site. Proc. Natl. Acad. Sci. U.S.A. 93, 13737-13741.
154. Kow, Y. W., and Wallace, S. S. (1985) Exonuclease III recognizes urea residues in oxidized DNA. Proc. Natl. Acad. Sci. U.S.A. 82, 8354-8358.
155. Ide, H., Tedzuka, K., Shimzu, H., Kimura, Y., Purmal, A. A., Wallace, S. S., and Kow, Y. W. (1994) Alpha-deoxyadenosine, a major anoxic radiolysis product of adenine in DNA, is a substrate for Escherichia coli endonuclease IV. Biochemistry 33, 7842-7847.
156. Takeshita, M., Chang, C. N., Johnson, F., Will, S., and Grollman, A. P. (1987) Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/ apyrimidinic endonucleases. J. Biol. Chem. 262, 10171-10179.
157. Sanderson, B. J., Chang, C. N., Grollman, A. P., and Henner, W. D. (1989) Mechanism of DNA cleavage and substrate recognition by a bovine apurinic endonuclease. Biochemistry 28, 3894-3901.
158. Wilson, D. M. R., Takeshita, M., Grollman, A. P., and Demple, B. (1995) Incision activity of human apurinic endonuclease (Ape) at abasic site analogs in DNA. J. Biol. Chem. 270, 16002-16007.
159. Kalnik, M. W., Chang, C.-N., Johnson, P., Grollman, A. P., and Patel, D. J. (1989) NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite acyclic lesions. Biochemistry 28, 3373-3383.
160. Weiss, B. (1976) Endonuclease II of Escherichia coli is exonuclease III. J. Biol. Chem. 251, 1896-1901.
161. Kow, Y. W. (1989) Mechanism of action of Escherichia coli exonuclease III. Biochemistry 28, 3280-3287.
162. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E., and Tainer, J. A. (1996) A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 384, 87-92.
163. Kunkel, T. A., and Wilson, S. H. (1996) Push and pull of base flipping. Nature 384, 25-26.
164. Pearl, L. H., and Savva, R. (1995) DNA repair in three dimensions. Trends Biochem. Sci. 20, 421-426.
165. Roberts, R. J. (1995) On base flipping. Cell 82, 9-12.
166. 5dC) in B and Z forms. Carcinogenesis 6, 805-807.
167. 6-methylguanine residues when present in Z-DNA. J. Biol. Chem. 260, 8711-8715.
168. Lagravère, C., Malfoy, B., Leng, M., and Laval, J. (1984) Ring-opened alkylated guanine is not repaired in Z-DNA. Nature 310, 798-800.
169. 6-ethenodeoxyadenosine adduct (εLA) opposite thymidine in a DNA duplex. Nonplanar alignment of εdA(anti) and dT(anti) at the lesion site. Biochemistry 30, 1820-1828.
170. 6-ethenodeoxyadenosine adduct (εdA) opposite deoxyguanosine in a DNA duplex. εdA(syn)·dG(anti) pairing at the lesion site. Biochemistry 30, 1828-1835.
171. Korobka, A., Cullinan, D., Cosman, M., Grollman, A. P., Patel, D. J., Eisenberg, M., and de los Santos, C. (1996) Solution structure of an oligodeoxynucleotide duplex containing the exocyclic lesion 3,N4-etheno-2'-deoxycytidine opposite 2′-deoxyadenosine, determined by NMR spectroscopy and restrained molecular dynamics. Biochemistry 35, 13310-13318.
172. 4-etheno-2′-deoxycytidine opposite thymidine: comparison with the duplex containing deoxyadenosine opposite the adduct. Biochemistry 35, 13319-13327.
173. 4-ethenocytosine, and 4-amino-5-(imidazol-2-yl)imidazole. Biochemistry 32, 12793-12801.
174. 4-ethenocytosine are excised by separate human DNA glycosylases. Carcinogenesis 16, 155-157.
175. 4-ethano-2′-deoxycytidine, and 3-(2-hydroxyethyl)-2′-deoxyuridine. Chem. Res. Toxicol. 8, 157-163.
176. 6-alkylguanine-DNA alkyltransferase. Cancer Res. 44, 3806-3811.
177. 2,3-etheno-deoxyguanosine, using a site-directed kinetic assay. Carcinogenesis 12, 745-747.
178. 2,3-ethenoguanine produces G→A transitions in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 88, 9974-9978.
179. 2,3-ethenodeoxyguanosine 5′-triphosphate. Stability of the glycosyl bond in the monomer and in poly(dG,εdG-dC). Chem. Res. Toxicol. 2, 230-233.
180. Sukumar, S., Notario, V., Martin-Zanca, D., and Barbacid, M. (1983) Induction of mammary carcinomas in rats by nitrosomethylurea involves malignant activation of H-ras-1 locus by single point mutations. Nature 306, 658-661.
181. Mattes, W. B., Hartley, J. A., and Kohn, K. W. (1986) DNA sequence selectivity of guanine-N7 alkylation by nitrogen mustards. Nucleic Acids Res. 14, 2971-2987.
182. - strains of Escherichia coli. Genetics 113, 811-819.
183. Richardson, K. K., Richardson, F. C., Crosby, R. M., Swenberg, J. A., and Skopek, T. R. (1987) DNA base changes and alkylation following in vivo exposure of Escherichia coli to N-methyl-N-nitrosourea or N-ethyl-N-nitrosourea. Proc. Natl. Acad. Sci. U.S.A. 84, 344-348.
184. Burns, P. A., Gordon, A. J., and Glickman, B. W. (1987) Influence of neighbouring base sequence on N-methyl-N'-nitro-N-nitrosoguanidine mutagenesis in the lacI gene of Escherichia coli. J. Mol. Biol. 194, 385-390.
185. Dolan, M. E., Oplinger, M., and Pegg, A. E. (1988) Sequence specificity of guanine alkylation and repair. Carcinogenesis 9, 2139-2143.
186. Haseltine, W. A., Gordon, L. K., Lindan, C. P., Grafstrom, R. H., Shaper, N. L., and Grossman, L. (1980) Cleavage of pyrimidine dimers in specific DNA sequences by a pyrimidine dimer DNA-glycosylase of M. luteus. Nature 285, 634-641.
187. Seeberg, E., and Fuchs, R. P. (1990) Acetylaminofluorene bound to different guanines of the sequence -GGCGCC-is excised with different efficiencies by the UvrABC excision nuclease in a pattern not correlated to the potency of mutation induction. Proc. Natl. Acad. Sci. U.S.A. 87, 191-194.
188. Mu, D., Bertrand-Burggraf, E., Huang, J. C., Fuchs, R. P., and Sancar, A. (1994) Human and E. coli excinucleases are affected differently by the sequence context of acetylaminofluorene-guanine adduct. Nucleic Acids Res. 22, 4869-4871 [published erratum appears in Nucleic Acids Res. 23 (3), 540, 1995].
189. Eftedal, I., Volden, G., and Krokan, H. E. (1994) Excision of uracil from double-stranded DNA by uracil-DNA glycosylase is sequence specific. Ann. N. Y. Acad. Sci. 726, 312-314.
190. Sander, M., and Benhaim, D. (1996) Drosophila Rrp1 3′-exo-nuclease: demonstration of DNA sequence dependence and DNA strand specificity. Nucleic Acids Res. 24, 3926-3933.
191. Walker, L. J., Robson, C. N., Black, E., Gillespie, D., and Hickson, I. D. (1993) Identification of residues in the human DNA repair enzyme HAP1 (Ref-1) that are essential for redox regulation of Jun DNA binding. Mol. Cell Biol. 13, 5370-5376.
192. 6-ethyldeoxyguanosine, accumulates in hepatocyte DNA of rats exposed continuously to diethylnitrosamine. Proc. Natl. Acad. Sci. U.S.A. 81, 1692-1695.