Measurement of formamidopyrimidines in DNA

Free Radical Biology and Medicine

Volumn 45, Issue 12, 2008, Pages 1601-1609

  Jaruga, Pawel ^a   Kirkali, Güldal ^b   Dizdaroglu, Miral ^a  

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b DOKUZ EYLUL UNIVERSITY   (Turkey)

Author keywords

Formamidopyrimidines; Gas chromatography mass spectrometry; Hydroxyl radical; Isotope dilution

Indexed keywords

2,6 DIAMINO 4 HYDROXY 5 FORMAMIDOPYRIMIDINE; 4,6 DIAMINO 5 FORMAMIDOPYRIMIDINE; DNA GLYCOSYLTRANSFERASE; PYRIMIDINE DERIVATIVE; UNCLASSIFIED DRUG;

DNA DAMAGE; DNA ISOLATION; EXCISION REPAIR; GAS CHROMATOGRAPHY; GENE MUTATION; MASS SPECTROMETRY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SENSITIVITY AND SPECIFICITY; SHORT SURVEY;

DNA; DNA DAMAGE; DNA GLYCOSYLASES; FAMILIAL MEDITERRANEAN FEVER; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HUMANS; LYMPHOCYTES; PYRIMIDINES;

EUKARYOTA; PROKARYOTA;

EID: 56349157373     PISSN: 08915849     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.freeradbiomed.2008.09.019     Document Type: Short Survey

References (75)

1. Halliwell B., and Gutteridge J.M.C. Free radicals in biology and medicine. fourth ed. (2007), Oxford University Press, Oxford
2. von Sonntag C. Free-radical-induced DNA damage and its repair (2006), Springer, Hiedelberg
3. Dizdaroglu M. Oxidative damage to DNA in mammalian chromatin. Mutat. Res. 275 (1992) 331-342
4. Breen A.P., and Murphy J.A. Reactions of oxyl radicals with DNA. Free Radic. Biol. Med. 18 (1995) 1033-1077
5. Sutherland B.M., Bennett P.V., Sidorkina O., and Laval J. Clustered DNA damages induced in isolated DNA and in human cells by low doses of ionizing radiation. Proc. Natl. Acad. Sci. USA 97 (2000) 103-108
6. Evans M.D., Dizdaroglu M., and Cooke M.S. Oxidative DNA damage and disease: induction, repair and significance. Mutat. Res. 567 (2004) 1-61
7. Cadet J., Berger M., Douki T., and Ravanat J.L. Oxidative damage to DNA: formation, measurement, and biological significance. Rev. Physiol. Biochem. Pharmacol. 131 (1997) 1-87
8. Friedberg E.C., Walker G.C., Siede W., Wood R.D., Schultz R.A., and Ellenberger T. DNA repair and mutagenesis (2005), ASM Press, Washington, DC
9. Wallace S.S. Biological consequences of free radical-damaged DNA bases. Free Radic. Biol. Med. 33 (2002) 1-14
10. Dizdaroglu M., Kirkali G., and Jaruga P. Formamidopyrimidines in DNA: mechanisms of formation, repair and biological effects. Free Radic. Biol. Med. 45 (2008) 1610-1621
11. Hems G. Effect of ionizing radiation on aqueous solutions of guanylic acid and guanosine. Nature 181 (1958) 1721-1722
12. Hems G. Chemical effects of ionizing radiation on deoxyribonucleic acid in dilute aqueous solution. Nature 186 (1960) 710-712
13. Hems G. Effects of ionizing radiation on aqueous solutions of inosine and adenosine. Radiat. Res. 13 (1960) 777-787
14. Conlay J.J. Effect of ionizing radiation on adenine in aerated and de-aerated aqueous solutions. Nature 197 (1963) 555-557
15. van Hemmen J.J., and Bleichrodt J.F. The decomposition of adenine by ionizing radiation. Radiat. Res. 46 (1971) 444-456
16. Bonicel A., Mariaggi N., Hughes E., and Téoule R. In vitro gamma irradiation of DNA: identification of radioinduced chemical modifications of the adenine moiety. Radiat. Res. 83 (1980) 19-26
17. Chetsanga C.J., and Grigorian C. A dose-response study on opening of imidazole ring of adenine in DNA by ionizing radiation. Int. J. Radiat. Biol. 44 (1983) 321-331
18. Berger M., and Cadet J. Isolation and characterization of the radiation-induced degradation products of 2′-deoxyguanosine in oxygen free aqueous solutions. Z. Naturforsch. [B] 40b (1985) 1519-1531
19. Douki T., Delatour T., Bianchini F., and Cadet J. Observation and prevention of an artefactual formation of oxidized DNA bases and nucleosides in the GC-EIMS method. Carcinogenesis 17 (1996) 347-353
20. McCloskey J.A. Constituents of nucleic acids: overview and strategy. Methods Enzymol. 193 (1990) 771-781
21. Dizdaroglu M. Application of capillary gas chromatography-mass spectrometry to chemical characterization of radiation-induced base damage of DNA; implications for assessing DNA repair processes. Anal. Biochem. 144 (1985) 593-603
22. Dizdaroglu M. Characterization of free radical-induced base damage in DNA by the combined use of enzymatic hydrolysis and gas chromatography-mass spectrometry. J. Chromatogr. 367 (1986) 357-366
23. Dizdaroglu M. Quantitative determination of oxidative base damage in DNA by stable isotope-dilution mass spectrometry. FEBS Lett. 315 (1993) 1-6
24. Schram K.H. Preparation of trimethylsilyl derivatives of nucleic acid components for analysis by mass spectrometry. Methods Enzymol. 193 (1990) 791-796
25. Nelson V.C. Synthesis of isotopically labelled DNA degradation products for use in mass spectrometric studies of cellular DNA damage. J. Label. Comp. Radiopharm. 38 (1996) 713-723
26. Watson J.T. Selected-ion measurements. Methods Enzymol. 193 (1990) 86-106
27. Dizdaroglu M., Jaruga P., Birincioglu M., and Rodriguez H. Free radical-induced damage to DNA: mechanisms and measurement. Free Radic. Biol. Med. 32 (2002) 1102-1115
28. Lunec J. ESCODD: European Standards Committee on oxidative DNA damage. Free Radic. Res. 29 (1998) 601-608
29. ESCODD. Comparison of different methods of measuring 8-oxoguanine as a marker of oxidative DNA damage. Free Radic. Res. 32 (2000) 333-341
30. ESCODD. Comparative analysis of baseline 8-oxo-7,8-dihydroguanine in mammalian cell DNA, by different methods in different laboratories: an approach to consensus. Carcinogenesis 23 (2002) 2129-2133
31. ESCODD. Measurement of DNA oxidation in human cells by chromatographic and enzymic methods. Free Radic. Biol. Med. 34 (2003) 1089-1099
32. Collins A.R., Cadet J., Moller L., Poulsen H.E., and Vina J. Are we sure we know how to measure 8-oxo-7,8-dihydroguanine in DNA from human cells?. Arch. Biochem. Biophys. 423 (2004) 57-65
33. Jenner A., England T.G., Aruoma O.I., and Halliwell B. Measurement of oxidative DNA damage by gas chromatography-mass spectrometry: ethanethiol prevents artifactual generation of oxidized DNA bases. Biochem. J. 331 (1998) 365-369
34. Sentürker S., and Dizdaroglu M. The effect of experimental conditions on the levels of oxidatively modified bases in DNA as measured by gas chromatography-mass spectrometry: how many modified bases are involved? Prepurification or not?. Free Radic Biol. Med. 27 (1999) 370-380
35. Halliwell B., and Dizdaroglu M. The measurement of oxidative damage to DNA by HPLC and GC/MS techniques. Free Radic. Res. Commun. 16 (1992) 75-87
36. Dizdaroglu M. Facts about the artifacts in the measurement of oxidative DNA base damage by gas chromatography-mass spectrometry. Free Radic. Res. 29 (1998) 551-563
37. Douki T., Martini R., Ravanat J.L., Turesky R.J., and Cadet J. Measurement of 2,6-diamino-4-hydroxy-5-formamidopyrimidine and 8-oxo-7,8-dihydroguanine in isolated DNA exposed to gamma radiation in aqueous solution. Carcinogenesis 18 (1997) 2385-2391
38. Swarts S.G., Smith G.S., Miao L., and Wheeler K.T. Effects of formic acid hydrolysis on the quantitative analysis of radiation-induced DNA base damage products assayed by gas chromatography/mass spectrometry. Radiat. Environ. Biophys. 35 (1996) 41-53
39. Douki T., Spinelli S., Ravanat J.-L., and Cadet J. Hydroxyl radical-induced degradation of 2′-deoxyguanosine under reducing conditions. J. Chem. Soc. Perkin Trans. 2 (1999) 1875-1880
40. Douki T., Bretonniere Y., and Cadet J. Protection against radiation-induced degradation of DNA bases by polyamines. Radiat. Res. 153 (2000) 29-35
41. Pouget J.-P., Douki T., Richard M., and Cadet J. DNA damage induced in cells by gamma and UVA radiation as measured by HPLC/GC-MS and HPLC-EC and comet assay. Chem. Res. Toxicol. 13 (2000) 541-549
42. Frelon S., Douki T., Ravanat J.L., Pouget J.P., Tornabene C., and Cadet J. High-performance liquid chromatography-tandem mass spectrometry measurement of radiation-induced base damage to isolated and cellular DNA. Chem. Res. Toxicol. 13 (2000) 1002-1010
43. Douki T., Ravanat J.-L., Frelon S., Bourdat A.-G., Pouget J.-P., and Cadet J. Critical reviews of oxidative stress and aging. Advances in basic science, diagnostics and intervention (2003), World Scientific, NJ
44. Pouget J.P., Frelon S., Ravanat J.L., Testard I., Odin F., and Cadet J. Formation of modified DNA bases in cells exposed either to gamma radiation or to high-LET particles. Radiat. Res. 157 (2002) 589-595
45. Frelon S., Douki T., Favier A., and Cadet J. Hydroxyl radical is not the main reactive species involved in the degradation of DNA bases by copper in the presence of hydrogen peroxide. Chem. Res. Toxicol. 16 (2003) 191-197
46. Kaur H., and Halliwell B. Measurement of oxidized and methylated DNA bases by HPLC with electrochemical detection. Biochem. J. 318 (1996) 21-23
47. Kasai H. Analysis of a form of oxidative DNA damage, 8-hydroxy-2′- deoxyguanosine, as a marker of cellular oxidative stress during carcinogenesis. Mutat. Res. Rev. Mutat. Res. 387 (1997) 147-163
48. Xue L., and Greenberg M.M. Facile quantification of lesions derived from 2′-deoxyguanosine in DNA. J. Am. Chem. Soc. 129 (2007) 7010-7011
49. Malayappan B., Garrett T.J., Segal M., and Leeuwenburgh C. Urinary analysis of 8-oxoguanine, 8-oxoguanosine, fapy-guanine and 8-oxo-2′-deoxyguanosine by high-performance liquid chromatography-electrospray tandem mass spectrometry as a measure of oxidative stress. J. Chromatogr. A 1167 (2007) 54-62
50. Jaruga P., Speina E., Gackowski D., Tudek B., and Olinski R. Endogenous oxidative DNA base modifications analysed with repair enzymes and GC/MS technique. Nucleic Acids Res. 28 (2000) E16
51. Rodriguez H., Jurado J., Laval J., and Dizdaroglu M. Comparison of the levels of 8-hydroxyguanine in DNA as measured by gas chromatography mass spectrometry following hydrolysis of DNA by Escherichia coli Fpg protein or formic acid. Nucleic Acids Res. 28 (2000) E75
52. Dizdaroglu M., Jaruga P., and Rodriguez H. Measurement of 8-hydroxy-2′-deoxyguanosine in DNA by high-performance liquid chromatography-mass spectrometry: comparison with measurement by gas chromatography-mass spectrometry. Nucleic Acids Res. 29 (2001) E12
53. Boiteux S., Gajewski E., Laval J., and Dizdaroglu M. 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 (1992) 106-110
54. Dizdaroglu M. Base-excision repair of oxidative DNA damage by DNA glycosylases. Mutat. Res. 591 (2005) 45-59
55. Karakaya A., Jaruga P., Bohr V.A., Grollman A.P., and Dizdaroglu M. Kinetics of excision of purine lesions from DNA by Escherichia coli Fpg protein. Nucleic Acids Res. 25 (1997) 474-479
56. Birincioglu M., Jaruga P., Chowdhury G., Rodriguez H., Dizdaroglu M., and Gates K.S. DNA base damage by the antitumor agent 3-amino-1,2,4-benzotriazine 1,4-dioxide (tirapazamine). J. Am. Chem. Soc. 125 (2003) 11607-11615
57. Hu J., de Souza-Pinto N.C., Haraguchi K., Hogue B.A., Jaruga P., Greenberg M.M., Dizdaroglu M., and Bohr V.A. Repair of formamidopyrimidines in DNA involves different glycosylases: role of the OGG1, NTH1, and NEIL1 enzymes. J. Biol. Chem. 280 (2005) 40544-40551
58. Malins D.C., Anderson K.M., Stegeman J.J., Jaruga P., Green V.M., Gilman N.K., and Dizdaroglu M. Biomarkers signal contaminant effects on the organs of English sole (Parophrys vetulus) from Puget Sound. Environ. Health Perspect. 114 (2006) 823-829
59. Nyaga S.G., Jaruga P., Lohani A., Dizdaroglu M., and Evans M.K. Accumulation of oxidatively induced DNA damage in human breast cancer cell lines following treatment with hydrogen peroxide. Cell Cycle 6 (2007) 1472-1478
60. Kirkali G., Tunca M., Genc S., Jaruga P., and Dizdaroglu M. Oxidative DNA damage in polymorphonuclear leukocytes of patients with familial Mediterranean fever. Free Radic. Biol. Med. 44 (2008) 386-393
61. Dizdaroglu M. The use of capillary gas chromatography-mass spectrometry for identification of radiation-induced DNA base damage and DNA base-amino acid crosslinks. J. Chromatogr. 295 (1984) 103-121
62. White E., Krueger V.P., and McCloskey J.A. Mass spectra of trimethylsilyl derivatives of pyrimidine and purine bases. J. Org. Chem. 37 (1972) 430-438
63. Dizdaroglu M. Formation of an 8-hydroxyguanine moiety in deoxyribonucleic acid on gamma-irradiation in aqueous solution. Biochemistry 24 (1985) 4476-4481
64. Dizdaroglu M. Free-radical-induced formation of an 8,5′-cyclo-2′-deoxyguanosine moiety in deoxyribonucleic acid. Biochem. J. 238 (1986) 247-254
65. Dirksen M.L., Blakely W.F., Holwitt E., and Dizdaroglu M. Effect of DNA conformation on the hydroxyl radical-Induced formation of 8,5′-cyclopurine-2′-deoxyribonucleoside residues in DNA. Int. J. Radiat. Biol. 54 (1988) 195-204
66. Jaruga P., Birincioglu M., Rodriguez H., and Dizdaroglu M. Mass spectrometric assays for the tandem lesion 8,5′-cyclo-2′-deoxyguanosine in mammalian DNA. Biochemistry 41 (2002) 3703-3711
67. Dizdaroglu M. Substrate specificities and excision kinetics of DNA glycosylases involved in base-excision repair of oxidative DNA damage. Mutat. Res. 531 (2003) 109-126
68. Jaruga P., Birincioglu M., Rosenquist T.A., and Dizdaroglu M. Mouse NEIL1 protein is specific for excision of 2,6-diamino-4-hydroxy-5-formamidopyrimidine and 4,6-diamino-5-formamidopyrimidine from oxidatively damaged DNA. Biochemistry 43 (2004) 15909-15914
69. Hazra T.K., Izumi T., Boldogh I., Imhoff B., Kow Y.W., Jaruga P., Dizdaroglu M., and Mitra S. Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA. Proc. Natl. Acad. Sci. USA 99 (2002) 3523-3528
70. Roy L.M., Jaruga P., Wood T.G., McCullough A.K., Dizdaroglu M., and Lloyd R.S. Human polymorphic variants of the NEIL1 DNA glycosylase. J. Biol. Chem. 282 (2007) 15790-15798
71. Miller S.A., Dykes D.D., and Polesky H.F. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res. 16 (1988) 1215
72. Asami S., Hirano T., Yamaguchi R., Tomioka Y., Itoh H., and Kasai H. Increase of a type of oxidative DNA damage, 8-hydroxyguanine, and its repair activity in human leukocytes by cigarette smoking. Cancer Res. 56 (1996) 2546-2549
73. Helbock H.J., Beckman K.B., Shigenaga M.K., Walter P.B., Woodall A.A., Yeo H.C., and Ames B.N. DNA oxidation matters: The HPLC-electrochemical detection assay of 8-oxo-deoxyguanosine and 8-oxo-guanine. Proc. Natl. Acad. Sci. USA 95 (1998) 288-293
74. Lenton K.J., Therriault H., Fulop T., Payette H., and Wagner J.R. Glutathione and ascorbate are negatively correlated with oxidative DNA damage in human lymphocytes. Carcinogenesis 20 (1999) 607-613
75. Jaruga P., Theruvathu J., Dizdaroglu M., and Brooks P.J. Complete release of (5′S)-8,5′-cyclo-2′-deoxyadenosine from dinucleotides, oligodeoxynucleotides and DNA, and direct comparison of its levels in cellular DNA with other oxidatively induced DNA lesions. Nucleic Acids Res. 32 (2004) e87