Sequence distribution of nucleobase adducts studied by isotope labeling of DNA–MASS spectrometry

Mass Spectrometry of Nucleosides and Nucleic Acids

Volumn , Issue , 2009, Pages 257-282

  Tretyakova, Natalia Y ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MASS SPECTROMETRY;

DNA REPLICATIONS; GENETIC CHANGES; HERITABLE MUTATIONS; ISOTOPE LABELING; NUCLEOBASE ADDUCTS; PROTO-ONCOGENES; SEQUENCE DISTRIBUTION; TUMOR SUPPRESSOR GENES;

DNA;

EID: 84896508078     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420044034     Document Type: Chapter

References (96)

1. Singer, B. and Grunberger, D., Molecular Biology of Mutagens and Carcinogens, Plenum Press, New York and London, 1983.
2. Malejka-Giganti, D. and Tretyakova, N., Molecular mechanisms of carcinogenesis, in Carcinogenic and Anticarcinogenic Food Components, W. Baer-Dubowska, A. Bartoszek, and D. Malejka-Giganti, eds, CRC Press, Boca Raton, FL, pp. 13-36, 2006.
3. Delaney, J.C. and Essigmann, J.M., Context-dependent mutagenesis by DNA lesions, Chem. Biol. 6, 743, 1999.
4. Loechler, E.L. et al., The role of carcinogen DNA adduct structure in the induction of mutations, Prog. Clin. Biol. Res. 340A, 51, 1990.
5. Delaney, J.C. and Essigmann, J.M., Effect of sequence context on O6-methylguanine repair and replication in vivo, Biochemistry 40, 14968, 2001.
6. Burrows, C.J. and Muller, J.G., Oxidative nucleobase modifications leading to strand scission, Chem. Rev. 98, 1109, 1998.
7. Denissenko, M.F. et al., Preferential formation of benzo[a]pyrene adducts at lung cancer mutational hotspots in p53, Science 274, 430, 1996.
8. Pfeifer, G.P., Denissenko, M.F., and Tang, M.S., PCR-based approaches to adduct analysis, Toxicol. Lett. 102-103, 447, 1998.
9. Jacobson, K.B. et al., Applications of mass spectrometry to DNA sequencing, Genet. Anal. Tech. Appl. 8, 223, 1991.
10. Tretyakova, N. et al., Locating nucleobase lesions within DNA sequences by MALDI-TOF mass spectral analysis of exonuclease ladders, Chem. Res. Toxicol. 14, 1058, 2001.
11. Brown, K. et al., Structural characterization of carcinogen-modified oligodeoxynucleotide adducts using matrix-assisted laser desorption/ionization mass spectrometry, J. Mass Spectrom. 38, 68, 2003.
12. Tretyakova, N. et al., Formation of benzo[a]pyrene diol epoxide-DNA adducts at specific guanines within K-ras and p53 gene sequences: Stable isotope-labeling mass spectrometry approach, Biochemistry 41, 9535, 2002.
13. Matter, B. et al., Formation of diastereomeric benzo[a]pyrene diol epoxide-guanine adducts in p53 genederived DNA sequences, Chem. Res. Toxicol. 17, 731, 2004.
14. Matter, B. et al., Quantitative analysis of the oxidative DNA lesion, 2,2-diamino-4-(2-deoxy-b-d- erythropentofuranosyl) amino]-5(2H)-oxazolone (oxazolone), in vitro and in vivo by isotope dilution-capillary HPLC-ESI-MS/MS, Nucleic Acids Res. 34, 5449, 2006.
15. Matter, B. et al., Sequence distribution of acetaldehyde-derived N2-ethyl-dG adducts along duplex DNA, Chem. Res. Toxicol. 20, 1379, 2007.
16. Kang, J.I., Jr. and Sowers, L.C., Examination of hypochlorous acid-induced damage to cytosine residues in a cpg dinucleotide in DNA, Chem. Res. Toxicol. 21, 1211-1218. 2008.
17. Gangl, E.T., Turesky, R.J., and Vouros, P., Detection of in vivo formed DNA adducts at the part-perbillion level by capillary liquid chromatography/microelectrospray mass spectrometry, Anal. Chem. 73, 2397, 2001.
18. Tretyakova, N.Y. et al., Formation of benzo[a]pyrene diol epoxide-DNA adducts at specific guanines within K-ras and p53 gene sequences: Stable isotope-labeling mass spectrometry approach, Biochemistry 41, 9535, 2002.
19. Ziegel, R. et al., K-ras gene sequence effects on the formation of 4-(methylnitrosamino)-1-(3-pyridyl)-1- butanone (NNK)-DNA adducts, Chem. Res. Toxicol. 16, 541, 2003.
20. Park, S. et al., 3’-Exonuclease resistance of DNA oligodeoxynucleotides containing O6-[4-oxo-4- (3-pyridyl)butyl]guanine, Nucleic Acids Res. 31, 1984, 2003.
21. Mao, B. et al., Opposite stereoselective resistance to digestion by phosphodiesterases I and II of benzo[a] pyrene diol epoxide-modified oligonucleotide adducts, Biochemistry 32, 11785, 1993.
22. Intenational Agency for Research on Cancer (IARC), IARC Monographs on the Evaluation of the Carcinogenic Risk of Chemicals to Humans: Polynuclear Aromatic Compounds, Part I, Chemical, Environmental, and Experimental Data, Vol. 32, Intenational Agency for Research on Cancer, Lyon, France, 1983.
23. Yang, S.K., Roller, P.P., and Gelboin, H.V., Enzymatic mechanism of benzo[a]pyrene conversion to phenols and diols and an improved high-pressure liquid chromatographic separation of benzo[a]pyrene derivatives, Biochemistry 16, 3680, 1977.
24. Osborne, M.R. et al., The reaction of (+/ -)-7a, 8b-dihydroxy-9b, 10b-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene with DNA, Int. J. Cancer 18, 362, 1976.
25. Talaska, G. et al., Chronic, topical exposure to benzo[a]pyrene induces relatively high steady-state levels of DNA adducts in target tissues and alters kinetics of adduct loss, Proc. Natl. Acad. Sci. USA 93, 7789, 1996.
26. Kriek, E. et al., Polycyclic aromatic hydrocarbon-DNA adducts in humans: Relevance as biomarkers for exposure and cancer risk, Mutat. Res. 400, 215, 1998.
27. Phillips, D.H., DNA adducts in human tissues: Biomarkers of exposure to carcinogens in tobacco smoke, Environ. Health Perspect. 104(Suppl 3), 453, 1996.
28. Randerath, E. et al., Covalent DNA damage in tissues of cigarette smokers as determined by 32P- postlabeling assay, J. Natl. Cancer Inst. 81, 341, 1989.
29. Johnson, R.E. et al., Bridging the gap: A family of novel DNA polymerases that replicate faulty DNA, Proc. Natl. Acad. Sci. USA 96, 12224, 1999.
30. Guengerich, F.P., Interactions of carcinogen-bound DNA with individual DNA polymerases, Chem. Rev. 106, 420, 2006.
31. Alekseyev, Y.O. and Romano, L.J., In vitro replication of primer-templates containing benzo[a]pyrene adducts by exonuclease-deficient Escherichia coli DNA polymerase I (Klenow fragment): Effect of sequence context on lesion bypass, Biochemistry 39, 10431, 2000.
32. Zhang, Y. et al., Error-prone lesion bypass by human DNA polymerase h, Nucleic Acids Res. 28, 4717, 2000.
33. Huang, X. et al., Effects of base sequence context on translesion synthesis past a bulky (+)-transanti- B[a]P-N2-dG lesion catalyzed by the Y-family polymerase pol k, Biochemistry 42, 2456, 2003.
34. Zhao, B. et al., Polh, Polz and Rev1 together are required for G to T transversion mutations induced by the (+)- and (-)-trans-anti-BPDE-N2-dG DNA adducts in yeast cells, Nucleic Acids Res., 34, 417, 2006.
35. Rodenhuis, S. and Slebos, R.J., Clinical significance of ras oncogene activation in human lung cancer, Cancer Res. 52, 2665s, 1992.
36. Westra, W.H. et al., K-ras oncogene activation in atypical alveolar hyperplasias of the human lung, Cancer Res. 56, 2224, 1996.
37. Harris, C.C., Structure and function of the p53 tumor suppressor gene: Clues for rational cancer therapeutic strategies, J. Natl. Cancer Inst. 88, 1442, 1996.
38. Denissenko, M.F. et al., Cytosine methylation determines hot spots of DNA damage in the human p53 gene, Proc. Natl. Acad. Sci. USA 94, 3893, 1997.
39. Hoffmann, D. and Hecht, S.S., Nicotine-derived N-nitrosamines and tobacco-related cancer: Current status and future directions, Cancer Res. 45, 935, 1985.
40. Hecht, S.S. et al., Induction of respiratory tract tumors in Syrian golden hamsters by a single dose of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and the effect of smoke inhalation, Carcinogenesis 4, 1287, 1983.
41. Hecht, S.S. et al., Comparative tumorigenicity and DNA methylation in F344 rats by 4-(methylnitrosamino)- 1-(3-pyridyl)-1-butanone and N-nitrosodimethylamine, Cancer Res. 46, 498, 1986.
42. Peterson, L.A. and Hecht, S.S., O6-methylguanine is a critical determinant of 4-(methylnitrosamino)-1- (3-pyridyl)-1-butanone tumorigenesis in A/J mouse lung, Cancer Res. 51, 5557, 1991.
43. Wang, L. et al., Pyridyloxobutyl adduct O6-[4-oxo-4-(3-pyridyl)butyl]guanine is present in 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone-treated DNA and is a substrate for O6-alkylguanine- DNA alkyltransferase, Chem. Res. Toxicol. 10, 562, 1997.
44. Wang, M. et al., Identification of adducts formed by pyridyloxobutylation of deoxyguanosine and DNA by 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone, a chemically activated form of tobacco specific carcinogens, Chem. Res. Toxicol. 16, 616, 2003.
45. Upadhyaya, P. et al., Identification of adducts produced by the reaction of 4-(acetoxymethylnitrosamino)- 1-(3-pyridyl)-1-butanol with deoxyguanosine and DNA, Chem. Res. Toxicol. 16, 180, 2003.
46. Hecht, S.S. et al., Identification of O2-substituted pyrimidine adducts formed in reactions of 4-(acetoxymethylnitrosamino)-1-(3-pyridyl)-1-butanone and 4-(acetoxymethylnitros-amino)-1-(3- pyridyl)-1-butanol with DNA, Chem. Res. Toxicol. 17, 588, 2004.
47. Sturla, S.J. et al., Mass spectrometric analysis of relative levels of pyridyloxobutylation adducts formed in the reaction of DNA with a chemically activated form of the tobacco-specific carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, Chem. Res. Toxicol. 18, 1048, 2005.
48. Gentil, A. et al., Mutagenic properties of a unique abasic site in mammalian cells, Biochem. Biophys. Res. Commun. 173, 704, 1990.
49. Takeshita, M. and Eisenberg, W., Mechanism of mutation on DNA templates containing synthetic abasic sites: Study with a double strand vector, Nucleic Acids Res. 22, 1897, 1994.
50. Ide, H. et al., On the mechanism of preferential incorporation of damp at abasic sites in translesional DNA synthesis. Role of proofreading activity of DNA polymerase and thermodynamic characterization of model template-primers containing an abasic site, Nucleic Acids Res. 23, 123, 1995.
51. Essigmann, J.M., Loechler, E.L. and Green, C.L., Genetic toxicology of O6-methylguanine, Prog. Clin. Biol. Res. 209A, 433, 1986.
52. Basu, A.K. and Essigmann, J.M., Site-specifically alkylated oligodeoxynucleotides: Probes for mutagenesis, DNA repair and the structural effects of DNA damage, Mutat. Res. 233, 189, 1990.
53. Tornaletti, S. and Pfeifer, G.P., Complete and tissue-independent methylation of cpg sites in the p53 gene: Implications for mutations in human cancers, Oncogene 10, 1493, 1995.
54. Rajesh, M. et al., Stable isotope labeling-mass spectrometry analysis of methyl- and pyridyloxobutylguanine adducts of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone in p53-derived DNA sequences, Biochemistry 44, 2197, 2005.
55. Sendowski, K. and Rajewsky, M.F., DNA sequence dependence of guanine-O6 alkylation by the N-nitroso carcinogens N-methyl- and N-ethyl-N-nitrosourea, Mutat. Res. 250, 153, 1991.
56. Hoffmann, D. and Hoffmann, I., The changing cigarette, 1950-1995, J. Toxicol. Environ. Health 50, 307, 1997.
57. Vaca, C.E., Fang, J.L., and Schweda, E.K., Studies of the reaction of acetaldehyde with deoxynucleosides, Chem. Biol. Interact. 98, 51, 1995.
58. Wang, M. et al., Identification of DNA adducts of acetaldehyde, Chem. Res. Toxicol. 13, 1149, 2000.
59. Fang, J.L. and Vaca, C.E., Detection of DNA adducts of acetaldehyde in peripheral white blood cells of alcohol abusers, Carcinogenesis 18, 627, 1997.
60. Wang, M. et al., Identification of an acetaldehyde adduct in human liver DNA and quantitation as N2-ethyldeoxyguanosine, Chem. Res. Toxicol. 19, 319, 2006.
61. Zhang, S. et al., Analysis of crotonaldehyde- and acetaldehyde-derived 1, N2-propanodeoxyguanosine adducts in DNA from human tissues using liquid chromatography electrospray ionization tandem mass spectrometry, Chem. Res. Toxicol. 19, 1386, 2006.
62. Terashima, I. et al., Miscoding potential of the N2-ethyl-2′-deoxyguanosine DNA adduct by the exonuclease-free Klenow fragment of Escherichia coli DNA polymerase I, Biochemistry 40, 4106, 2001.
63. Perrino, F.W. et al., The N2-ethylguanine and the O6-ethyl- and O6-methylguanine lesions in DNA: Contrasting responses from the “bypass” DNA polymerase h and the replicative DNA polymerase a, Chem. Res. Toxicol. 16, 1616, 2003.
64. Pryor, W.A., Prier, D.G., and Church, D.F., Electron-spin resonance study of mainstream and sidestream cigarette smoke: Nature of the free radicals in gas-phase smoke and in cigarette tar, Environ. Health Perspect. 47, 345, 1983.
65. Shafirovich, V. et al., Nitrogen dioxide as an oxidizing agent of 8-oxo-7,8-dihydro-2′-deoxyguanosine but not of 2′-deoxyguanosine, Chem. Res. Toxicol. 14, 233, 2001.
66. Kim, S.G. and Novak, R.F., Role of P450IIE1 in the metabolism of 3-hydroxypyridine, a constituent of tobacco smoke: Redox cycling and DNA strand scission by the metabolite 2,5-dihydroxypyridine, Cancer Res. 50, 5333, 1990.
67. Yu, D. et al., Reactive oxygen species generated by PAH o-quinones cause change-in-function mutations in p53, Chem. Res. Toxicol. 15, 832, 2002.
68. Park, J.H. et al., Formation of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dguo) by PAH o-quinones: Involvement of reactive oxygen species and copper(II)/copper(I) redox cycling, Chem. Res. Toxicol. 18, 1026, 2005.
69. Park, J.H. et al., Polycyclic aromatic hydrocarbon (PAH) o-quinones produced by the aldo-keto-reductases (akrs) generate abasic sites, oxidized pyrimidines, and 8-oxo-dguo via reactive oxygen species, Chem. Res. Toxicol. 19, 719, 2006.
70. Alvarez, M.N., Trujillo, M., and Radi, R., Peroxynitrite formation from biochemical and cellular fluxes of nitric oxide and superoxide, Methods Enzymol. 359, 353, 2002.
71. Halliwell, B., Gutteridge, J.M., and Cross, C.E., Free radicals, antioxidants, and human disease: Where are we now?, J. Lab. Clin. Med. 119, 598, 1992.
72. Prat, F., Houk, K.N., and Foote, C.S., Effect of guanine stacking on the oxidation of 8-oxoguanine in B-DNA, J. Am. Chem. Soc. 120, 845, 1998.
73. Cadet, J. and Treoule, R., Comparative study of oxidation of nucleic acid components by hydroxyl radicals, singlet oxygen and superoxide anion radicals, Photochem. Photobiol. 28, 661, 1978.
74. Douki, T. and Cadet, J., Peroxynitrite mediated oxidation of purine bases of nucleosides and isolated DNA, Free Radical Res. 24, 369, 1996.
75. Luo, W. et al., Characterization of spiroiminodihydantoin as a product of one-electron oxidation of 8-oxo-7,8-dihydroguanosine, Org. Lett. 2, 613, 2000.
76. Luo, W. et al., Characterization of hydantoin products from one-electron oxidation of 8-oxo-7,8- dihydroguanosine in a nucleoside model, Chem. Res. Toxicol, 14, 927, 2001.
77. Yermilov, V. et al., Formation of 8-nitroguanine by the reaction of guanine with peroxynitrite in vitro, Carcinogenesis 16, 2045, 1995.
78. Sakumi, K. et al., Ogg1 knockout-associated lung tumorigenesis and its suppression by Mth1 gene disruption, Cancer Res. 63, 902, 2003.
79. Saito, I. et al., The most electron-donating sites in duplex DNA: Guanine-guanine stacking rule, Nucl. Acids Symp. Ser. 191, 1995.
80. Bennett, W.P. et al., Molecular epidemiology of human cancer risk: Gene-environment interactions and p53 mutation spectrum in human lung cancer, J. Pathol. 187, 8, 1999.
81. Ziegel, R. et al., Endogenous 5-methylcytosine protects neighboring guanines from N7 and O6-methylation and O6-pyridyloxobutylation by the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone, Biochemistry 43, 540, 2004.
82. Fowles, J. and Dybing, E., Application of toxicological risk assessment principles to the chemical constituents of cigarette smoke, Tob. Control 12, 424, 2003.
83. Cochrane, J.E. and Skopek, T.R., Mutagenicity of butadiene and its epoxide metabolites: I. Mutagenic potential of 1,2-epoxybutene, 1,2,3,4-diepoxybutane and 3,4-epoxy-1,2-butanediol in cultured human lymphoblasts, Carcinogenesis 15, 713, 1994.
84. Recio, L. et al., Mutational spectrum of 1,3-butadiene and metabolites 1,2-epoxybutene and 1,2,3,4-diepoxybutane to assess mutagenic mechanisms, Chem. Biol. Interact. 135-136, 325, 2001.
85. Verly, W.G., Brakier, L., and Feit, P.W., Inactivation of the T7 coliphage by the diepoxybutane stereoisomers, Biochim. Biophys. Acta 228, 400, 1971.
86. Matagne, R., Induction of chromosomal aberrations and mutations with isomeric forms of L-threitol-I,4- bismethanesulfonate in plant materials, Mutat. Res. 7, 241, 1969.
87. Bianchi, A. and Contin, M., Mutagenic activity of isomeric forms of diepoxybutane in maize, J. Heredity 53, 277, 1962.
88. Tretyakova, N. et al., Adenine adducts with diepoxybutane: Isolation and analysis in exposed calf thymus DNA, Chem. Res. Toxicol. 10, 1171, 1997.
89. Tretyakova, N.Y., et al., Synthesis, characterization, and in vitro quantitation of N-7-guanine adducts of diepoxybutane, Chem. Res. Toxicol. 10, 779, 1997.
90. Park, S. and Tretyakova, N., Structural characterization of the major DNA-DNA cross-link of 1,2,3,4- diepoxybutane, Chem. Res. Toxicol. 17, 129, 2004.
91. Rajski, S.R. and Williams, R.M., DNA cross-linking agents as antitumor drugs, Chem. Rev. 98, 2723, 1998.
92. Park, S. et al., Interstrand and intrastrand DNA-DNA cross-linking by 1,2,3,4-diepoxybutane: Role of stereochemistry, J. Am. Chem. Soc. 127, 14355, 2005.
93. Boger, D.L. et al., Bifunctional alkylating agents derived from duocarmycin SA: Potent antitumor activity with altered sequence selectivity, Bioorg. Med. Chem. Lett. 10, 495, 2000.
94. Frelon, S. et al., High-performance liquid chromatography-tandem mass spectrometry measurement of radiation-induced base damage to isolated and cellular DNA, Chem. Res. Toxicol. 13, 1002, 2000.
95. Tretyakova, N.Y. et al., Quantitative analysis of 1,3-butadiene-induced DNA adducts in vivo and in vitro using liquid chromatography electrospray ionization tandem mass spectrometry, J. Mass Spectrom. 33, 363, 1998.
96. Knize, M.G. et al., Liquid chromatography-tandem mass spectrometry method of urine analysis for determining human variation in carcinogen metabolism, J. Chromatogr. A 914, 95, 2001.