Nucleic acid sequence and repair: Role of adduct, neighbor bases and enzyme specificity

Carcinogenesis

Volumn 21, Issue 6, 2000, Pages 1071-1078

  Singer, B ^a   Hang, B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA ADDUCT; DNA REPAIR; NOTE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; THERMOSTABILITY;

EID: 0034131114     PISSN: 01433334     EISSN: None     Source Type: Journal    
DOI: 10.1093/carcin/21.6.1071     Document Type: Note

References (94)

1. Benzer, S. (1961) On the topography of the genetic fine structure. Proc. Natl Acad. Sci. USA, 47, 403-416.
2. Koch, K.E. (1971) The influence of neighboring base-pairs upon base-pair substitution mutation rates. Proc. Natl Acad. Sci. USA, 68, 773-776.
3. Fuchs, R.P., Schwartz, N. and Daune, M.P. (1981) Hot spots of frameshift mutations induced by the ultimate carcinogen N-acetoxy-N-2-acetylaminofluorene. Nature, 294, 657-659.
4. Sukumar, S., Notario, V., Martin-Zanca, D. and Barbacid, M. (1983) Induction of mammary carcinomas in rats by nitroso-methylurea involves malignant activation of H-ras1 locus by single point mutations. Nature, 306, 658-661.
5. Zarbl, H., Sukumar, S., Arthur, A.V., Martin-Zanca, D. and Barbacid, M. (1985) Direct mutagenesis of Ha-ras-1 oncogenes by N-nitroso-N-methylurea during initiation of mammary carcinogenesis in rats. Nature, 315, 382-385.
6. Koffel-Schwartz, N., Verdier, J.M., Bichara, M., Freund, A.M., Daune, M.P. and Fuchs, R.P. (1984) Carcinogen-induced mutation spectrum in wild-type, uvrA and umuC strains of Escherichia coli. Strain specificity and mutation-prone sequences. J. Mol. Biol., 177, 33-51.
7. - strains of Escherichia coli. Genetics, 113, 811-819.
8. 6-methylguanine. J. Biol. Chem., 261, 9879-9885.
9. Schaaper, R.M. and Dunn, R.L. (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc. Natl Acad. Sci. USA, 84, 6220-6224.
10. 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.
11. Schaaper, R.M. and Dunn, R.L. (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc. Natl Acad. Sci. USA, 84, 6220-6224.
12. Burns, P.A., Gordon, A.J.E. and Glickman, B.W. (1987) Influence of neighbouring base sequence on N-melhyl-N′-nitro-N-nitrosoguanidine mutagenesis in the lacI gene of Escherichia coli. J. Mol. Biol., 194, 385-390.
13. Dolan, M.E., Oplinger, M. and Pegg, A.E (1988). Sequence specificity of guanine alkylation and repair. Carcinogenesis, 9, 2139-2143.
14. Burnouf, D., Koehl, P. and Fuchs, R.P. (1989) Single adduct mutagenesis: strong effect of the position of a single acetylaminofluorene adduct within a mutation hot spot. Proc. Natl Acad. Sci. USA, 86, 4147-4151.
15. 6-methyldeoxyguanosine at specific sites in a synthetic oligonudeotide designed to resemble a known mutagenic hotspot. J. Biol. Chem., 264, 838-841.
16. Schaaper, R.M. and Dunn, R.L. (1991) Spontaneous mutation in the Escherichia coli lacl gene. Genetics, 129, 317-326.
17. Bronstein, S.M., Cochrane, J.E., Craft, T.R., Swenberg, J.A. and Skopek, T.R. (1991) Toxicity, mutagenicity and mutational spectra of N-ethyl-N-nitrosourea in human cell lines with different DNA repair phenotypes. Cancer Res., 51, 5188-5197.
18. Daubersies, P., Galiegue-Zouitina, S., Koffel-Schwartz, N., Fuchs, R.P.P., Loucheux-Lefebvre, M.-H. and Bailleul, B. (1992) Mutation spectra of the two guanine adducts of the carcinogen 4-nitroquinoline 1-oxide in Escherichia coli. Influence of neighboring base sequence on mutagenesis. Carcinogenesis, 13, 349-354.
19. Cariello, N.F. and Skopek, T.R. (1993) Analysis of mutations occurring at the human hprt locus. J. Mol. Biol., 231, 41-57.
20. Carothers, A.M., Urlaub, G., Mucha, J., Yuan, W., Chasin, L.A. and Grunberger, D. (1993) Mutational hot spot induced by N-hydroxy-aminofluorene in dihydrofolate reductase mutants of Chinese hamster ovary cells. Carcinogenesis, 14, 2181-2194.
21. Singer, B. and Grunberger, D. (1983) Molecular Biology of Mutagens and Carcinogens. Plenum Press, New York, NY.
22. 6-guanine position of dGTP. Carcinogenesis, 4, 1591-1597.
23. Petruska, J. and Goodman, M.F. (1985) Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity. J. Biol. Chem., 260, 7533-7539.
24. Mendelman, L.V., Boosalis, M.S., Petruska, J. and Goodman, M.F. (1989) Nearest neighbor influences on DNA polymerase insertion fidelity. J. Biol. Chem., 264, 14415-14423.
25. 6-methylguanine in a defined primed oligonudeotide when Escherichia coli DNA polymerase 1 is used. Proc. Natl Acad. Sci. USA, 86, 8271-8274.
26. 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.
27. Jones, M., Wagner, R. and Radman, M. (1987) Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence. Genetics, 115, 605-610.
28. Seeberg, E. and Fuchs, R.P.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. USA, 87, 191-194.
29. Singer, B. and Essigmann, J.M. (1991) Site-specific mutagenesis: retrospective and prospective. Carcinogenesis, 12, 949-955.
30. Mu, D., Bertrand-Burggraf, E., Huang, J.-C., Fuchs, B.P.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.
31. Delagoutte, E., Bertrand-Burggraf, E., Dunand, J. and Fuchs, R.P.P. (1997) Sequence-dependent modulation of nucleotide excision repair: the efficiency of the incision reaction is inversely correlated with the stability of the pre-incision UvrB-DNA complex. J. Mol. Biol., 266, 703-710.
32. Mekhovich, O., Tang, M.-S. and Romano, L.J. (1998) Rate of incision of N-acetyl-2-aminofluorene and N-2-aminofluorene adducts by UvrABC nuclease is adduct- and sequence-specific: comparison of the rates of UvrABC nuclease incision and protein-DNA complex formation. Biochemistry, 37, 571-579.
33. Wei, D., Maher, V.M. and McCormick, J.J. (1995) Site-specific rates of excision repair of benzo[a]pyrene diol epoxide adducts in the hypoxanthine phosphoribosyltransferase gene of human fibroblasts: correlation with mutation spectra. Proc. Natl Acad. Sci. USA, 92, 2204-2208.
34. Svoboda, D.L., Smith, C.A., Taylor, J.-S.A. and Sancar, A. (1993) Effect of sequence, adduct type and opposing lesions on the binding and repair of ultraviolet photodamage by DNA photolyase and (A)BC excinuclease J. Biol. chem., 268, 10694-10700.
35. Tornaletti, S. and Pfeifer, G.P. (1994) Slow repair of pyrimidine dimers at p53 mutation hotspots in skin cancer. Science, 263, 1436-1438.
36. Gao, S., Drouin, R. and Holmquist, G.P. (1994) DNA repair rates mapped along the human PGK1 gene at nucleotide resolution. Science, 263, 1438-1440.
37. 6-ethenoadenine. J. Biol. Chem., 273, 33406-33413.
38. 6-benzethenodA, by the major human AP endonuclease MAP1 and Escherichia coli exonuclease III and endonuclease IV. Carcinogenesis, 19, 1339-1343.
39. 6-methylguanine residues in different positions in and around codon 12 of rat H-ras. Cancer Res., 51, 5843-5850.
40. 6-ethylguanine lesions. Mutat. Res., 255, 89-93.
41. Graves, R., Laval, J. and Pegg, A.E. (1992) Sequence specificity of DNA repair by Escherichia coli Fpg protein. Carcinogenesis, 13, 1455-1459.
42. 6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability. Biochemistry, 35, 15295-15301.
43. 6-alkylguanine-DNA alkyltransferase do not exhibit significant dependence on sequence context. Nucleic Acids Res., 24, 2087-2094.
44. Ye, N., Holmquist, G.P. and O'Connor, T.R. (1998) Heterogeneous repair of N-methylpurines at the nucleotide level in normal human cells. J. Mol. Biol., 284, 269-285.
45. Li, S. and Smerdon, M.J. (1999) Base excision repair of N-methylpurines in a yeast minichromosome. J. Biol. Chem., 274, 12201-12204.
46. Delaney, J.C. and Essigmann, J.M. (1999) Context-dependent mutagenesis by DNA lesions. Chem. Biol., 6, 743-753.
47. Ullah, S., Gallinari, P., Xu, Y.-Z., Goodman, M.F, Bloom, L.B., Jiricny, J. and Day, R.S. (1996) Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA-glycosylase. Biochemistry, 35, 12926-12932.
48. Saparbaev, M. and Laval, J. (1999) In Singer,B. and Bartsch,H. (eds) Enzymology of the Repair of Etheno Adducts in Mammalian Cells and in Escherichia coli, IARC Scientific Publications no. 150. IARC, Lyon, pp. 249-261.
49. Delort, A.M., Duplaa, A.M., Molko, D., Teoule, R., Leblanc , J.P. and Laval, J. (1985) Excision of uracil residues in DNA: mechanism of action of Escherichia coli and Micrococcus luteus uracil-DNA glycosylases. Nucleic Acids Res., 13, 319-335.
50. 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, 312-316.
51. Sági, J., Hang, B. and Singer, B. (1999) Sequence-dependent repair of synthetic AP sites in 15-mer and 35-mer oligonucleotides: role of thermodynamic stability imposed by neighbor bases. Chem. Res. Toxicol., 12, 917-923.
52. Bloom, L.B., Otto, M.R., Eritja, R., Reha-Krantz, L.J., Goodman, M.F. and Beechem, J.M. (1994) Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3́-exonuclease activity of bacteriophage T4 DNA polymerase. Biochemistry, 33, 7576-7586.
53. Modrich, P. (1994) Mismatch repair, genetic stability and cancer. Science, 266, 1959-1960.
54. Friedberg, E., Walker, G.C. and Seide, W. (1995) DNA Repair and Mutagenesis. ASM Press, Washington, DC.
55. Seeberg, E., Eide, L. and Bjoras, M. (1995) The base excision repair pathway. Trends Biochem. Sci., 20, 391-397.
56. Sancar, A. (1996) DNA excision repair. Annu. Rev. Biochem., 65, 43-81.
57. Modrich, P. and Lahue, R. (1996) Mismatch repair in replication fidelity, genetic recombination and cancer biology. Annu. Rev. Biochem., 65, 101-133.
58. Wood, R.D. (1996) DNA repair in eukaryotes. Annu. Rev. Biochem., 65, 135-167.
59. Singer, B. and Hang, B. (1997) What structural features determine repair enzyme specificity and mechanism in chemically modified DNA? Chem. Res. Toxicol., 10, 713-732.
60. Singer, B. and Bartsch, H. (1986) The Role of Cyclic Nucleic Acid Adducts in Carcinogenesis and Mutagenesis, IARC Scientific Publications no. 70. IARC, Lyon.
61. Marnett, L.J. and Burcham, P.C. (1993) Endogenous DNA adducts: potential and paradox. Chem. Res. Toxicol., 6, 771-785.
62. Singer, B. and Bartsch, H. (1999) Enzymology of the Repair of Etheno Adducts in Mammalian Cells and in Escherichia coli, IARC Scientific Publications no. 150. IARC, Lyon.
63. Koffel-Schwartz, N., Verdier, J.M., Bichara, M., Freund, A.M., Daune, M.P. and Fuchs, R.P. (1984) Carcinogen-induced mutation spectrum in wild-type, uvrA and umuC strains of Escherichia coli. Strain specificity and mutation-prone sequences. J. Mol. biol., 177, 33-51.
64. Radman, M. and Wagner, R. (1986) Mismatch repair in Escherichia coli. Annu. Rev. Genet., 20, 523-538.
65. Neddermann, P. and Jiricny, J. (1993) The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J. Biol. Chem., 268, 21218-21224.
66. Neddermann, P., Gallinari, P., Lettieri, T., Schmid, D., Truong, O., Hsuan, J.J., Wiebauer, K. and Jiricny, J. (1996) Cloning and expression of human G/T mismatch-specific thymine-DNA glycosylase. J. Biol. Chem., 271, 12767-12774.
67. Neddermann, P. and Jiricny, J. (1994) Efficient removal of uracil from G.U mispairs by the mismatch-specific thymine DNA glycosylase from HeLa cells. Proc. Natl Acad. Sci. USA, 91, 1642-1646.
68. 4-ethenocytosine and the G/T mismatch. Proc. Natl Acad. Sci. USA, 95, 13561-13566.
69. 4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase. Proc. Natl Acad. Sci. USA, 95, 8508-8513.
70. 6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequences. Biochemistry, 30, 11595-11599.
71. Bloom, L.B., Otto, M.R., Beechem, J.M. and Goodman, M.F. (1993) Influence of 5'-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment. Biochemistry, 32, 11247-11258.
72. Goodman, M.F., Cai, H., Bloom, L.B. and Eritja, R. (1994) Nucleotide insertion and primer extension at abasic template sites in different sequence contexts. Ann. N. Y. Acad. Sci., 726, 132-142.
73. Belguise-Valladier, P. and Fuchs, R.P. (1995) N-2-aminofluorene and N-2 acetylaminofluorene adducts: the local sequence context of an adduct and its chemical structure determine its replication properties. J. Mol. Biol., 249, 903-913.
74. Moriya, M., Spiegel, S., Fernandes, A., Amin, S., Liu, T., Geacintov, N. and Grollman, A.P. (1996) Fidelity of translesional synthesis past benzo[a]pyrene diol epoxide-2′-deoxyguanosine DNA adducts: marked effects of host cell, sequence context and chirality. Biochemistry, 35, 16646-16651.
75. 4-methylthymine.guanine basepairs. Mutat. Res., 356, 179-185.
76. Hashim, M.F. and Marnett, L.J. (1996) Sequence-dependent induction of base pair substitutions and frameshifts by propanodeoxyguanosine during in Vitro DNA replication. J. Biol. Chem., 271, 9160-9165.
77. 6-ethenodeoxyadenosine (εA): formation of εA base pairs and elongation in defined templates. Carcinogenesis, 18, 1609-1615.
78. Freemont, P.S., Friedman, J.M., Beese, L.S., Sanderson, M.R. and Steitz, T.A. (1988) Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. Natl Acad. Sci. USA, 85, 8924-8928.
79. Cowart, M., Gibson, K.J., Allen, D.J. and Benkovic, S.J. (1989) DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases. Biochemistry, 28, 1975-1983.
80. Beese, L.S., Derbyshire, V. and Steitz, T.A. (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA. Science, 260, 352-355.
81. 4-alkylthymine in Escherichia coli: the adaptive response and nucleotide excision repair. EMBO J., 7, 2261-2267.
82. 6-methylguanine by ABC excinuclease of Escherichia coli in vitro. J. Biol. Chem., 264, 5172-5176.
83. Daubersies, P., Galiegue-Zouitina, S., Koffel-Schwartz, N., Fuchs, R.P.P., Loucheux-Lefebvre, M.-H. and Bailleul, B. (1992) Mutation spectra of the two guanine adducts of the carcinogen 4-nitroquinoline 1-oxide in Escherichia coli. Influence of neighboring base sequence on mutagenesis. Carcinogenesis, 13, 349-354.
84. Kamiya, H., Murata-Kamiya, N., Koizume, S., Inoue, H., Nishimura, S. and Ohtsuka, E. (1995) 8-Hydroxyguanine (7,8-dihydro-8-oxoguanine) in hot spots of the c-Ha-ras gene: effects of sequence contexts on mutation spectra. Carcinogenesis, 16, 883-889.
85. Werntges, H., Steger, G., Riesner, D. and Fritz, H.-J. (1986) Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies. Nucleic Acids Res., 14, 3773-3790.
86. Fagan, P.A., Fàbrega, C., Eritja, R., Goodman, M.F. and Wemmer, D.E. (1996) NMR study of the conformation of the 2-aminopurine:cytosine mismatch in DNA. Biochemistry, 35, 4026-4033.
87. Gelfand, C.A., Plum, G.E., Grollman, A.P., Johnson, F. and Breslauer, K.J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry, 37, 7321-7327.
88. Allawi, H.T. and SantaLucia, J.Jr (1998) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. Biochemistry, 37, 9435-9444.
89. Peyret, N., Seneviratne, P.A., Allawi, H.T. and SantaLucia, J.Jr (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G and T.T mismatches. Biochemistry, 38, 3468-3477.
90. Stivers, J.T. (1998) 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Res., 26, 3837-3844.
91. 6-emenoadenine is preferred over 3-methyladenine as substrate by a cloned human N-methylpurine-DNA glycosylase (3-methyladenine-DNA glycosylase). Biochemistry, 33, 1624-1628.
92. Lindahl, T. (1982) DNA repair enzymes. Annu. Rev. Biochem., 51, 61-87.
93. 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.
94. Wilson, D.M., 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.