Quantification of 5-(hydroxymethyl)uracil in DNA by gas chromatography/mass spectrometry: Problems and solutions

Chemical Research in Toxicology

Volumn 11, Issue 7, 1998, Pages 786-793

  LaFrancois, Christopher J ^a   Yu, Kin ^a   Sowers, Lawrence C ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

URACIL DERIVATIVE;

ANIMAL TISSUE; ARTICLE; DNA DAMAGE; DNA DETERMINATION; MASS SPECTROMETRY; NONHUMAN; NUCLEOTIDE SEQUENCE; OXIDATION; QUANTITATIVE ASSAY;

DNA; FORMIC ACIDS; GAS CHROMATOGRAPHY-MASS SPECTROMETRY; HYDROLYSIS; INDICATORS AND REAGENTS; OLIGONUCLEOTIDES; PENTOXYL; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 0031829530     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx970233c     Document Type: Article

References (55)

1. Imlay, J. A., and Linn, S. (1988) DNA damage and oxygen radical toxicity. Science 240, 1302-1309.
2. Loeb, L. A. (1989) Endogenous carcinogenesis: molecular oncology into the twenty-first century - Presidential address. Cancer Res. 49, 5489-5496.
3. Mullaart, E., Lohman, P. H. M., Berends, F., and Vijg, J. (1990) DNA damage metabolism and aging. Mutat. Res. 237, 189-210.
4. Ames, B. N., Shigenaga, M. K., and Hagen, T. M. (1993) Oxidants, antioxidants, and the degenerative diseases of aging. Proc. Natl. Acad. Sci. U.S.A. 90, 7915-7922.
5. Ames, B. N., Gold, L. S., and Willett, W. C. (1995) The causes and prevention of cancer. Proc. Natl. Acad. Sci. U.S.A. 92, 5258-5265.
6. Dizdaroglu, M. (1984) The use of capillary gas chromatography-mass spectrometry for identification of radiation-induced DNA hase damage and DNA base-amino acid cross-links. J. Chromatogr. 295, 103-121.
7. Teebor, G. W., Frenkel, K., and Goldstein, M. S. (1984) Ionizing radiation and tritium transmutation both cause formation of 5-hydroxymethyl-2′-deoxyuridine in cellular DNA. Proc. Natl. Acad. Sci. U.S.A. 81, 318-321.
8. Hollstein, M. C., Brooks, P., Linn, S., and Ames, B. N. (1984) Hydroxymethyluracil DNA glycosylase in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 81, 4003-4007.
9. Frenkel, K., Cummings, A., Solomon, J., Cadet, J., Steinberg, J. J., and Teebor, G. W. (1985) Quantitative determination of the 5-(hydroxymethyl)uracil moiety in the DNA of gamma-irradiated cells. Biochemistry 24, 4527-4533.
10. Cannon-Carlson, S. V., Gokhaie, H., and Teebor, G. W. (1989) Purification and characterization of 5-hydroxymethyluracil-DNA glycosylase from calf thymus. J. Biol. Chem. 264, 13306-13312.
11. Frenkel, K., and Klein, C. B. (1993) Methods used for analysis of "environmentally" damaged nucleic acids. J. Chromatogr. 618, 289-314.
12. Mellac, S., Fazakerley, G. V., and Sowers, L. C. (1993) Structures of base pairs with 5-(hydroxymethyl)-2′-deoxyuridine in DNA determined by NMR spectroscopy. Biochemistry 32, 7779-7786.
13. Grollman, A. P., and Moriya, M. (1993) Mutagenesis by 8-oxoguanine: an enemy within. TIG 9, 246-249.
14. Wallace, S. S. (1994) DNA damages processed by base excision repair: biological consequences. Int. J Radiat. Biol. 66, 579-589.
15. Feig, D. I., Sowers, L. C., and Loeb, L. A. (1994) Reverse chemical mutagenesis: Identification of the mutagenic lesions resulting from reactive oxygen species-mediated damage to DNA. Proc. Natl. Acad. Sci. U.S.A. 91, 6609-6613.
16. Vilpo, J. A., and Vilpo, L. M. (1995) Restriction, methylation and ligation of 5-hydroxymethyluracil-containing DNA. Mutat. Res. 316, 123-131.
17. Fazakerley, G. V., and Boulard, Y. (1995) DNA mismatches and modified bases. Methods Enzymol. 261, 145-163.
18. Henle, E., and Linn, S. (1997) Formation, prevention and repair of DNA damage by iron/hydrogen peroxide. J. Biol. Chem. 272, 19095-19098.
19. Djuric, Z., Heilbrun, L. K., Reading, B. A., Boomer, A., Valeriote, F. A., and Martino, S. (1991) Effects of a low-fat diet on levels of oxidative damage to DNA in human peripheral nucleated blood cells. J. Natl. Cancer Inst. 83, 766-769.
20. Frenkel, K., Karkoszka, J., Kim, E., and Taioli, E. (1993) Recognition of oxidized DNA bases by sera of patients with inflammatory diseases. Free Radical Biol. Med. 14, 483-494.
21. Djuric, Z., Heilbrun, L. K., Simon, M. S., Smith, D., Luongo, D. A., LoRusso, P. M., and Martino, S. (1996) Levels of 5-hydroxymethyl-2′-deoxyuridine in DNA from blood as a marker of breast cancer. Cancer 77, 691-696.
22. Fuciarelli, A., Wegher, B. J., Gajewski, E., Dizdaroglu, M., and Blakely, W. F. (1989) Quantitative measurement of radiation-induced base products in DNA using gas chromatography- mass spectrometry. Radiat. Res. 119, 219-231.
23. Kresbach, G M., Itani, M., Saha, M., Rogers, E. J., Vouros, P., and Giese, R. W. (1989) Ester and related derivatives of ring N-pentafluorobenzylated 5-hydroxymethyluracil. Hydrolytic stability, mass spectral properties, and trace detection by gas chromatogaphy-electron capture detection, gas chromatography-electron-capture negative ion mass spectrometry, and movingbelt liquid chromatography-electron-capture negative ion mass spectrometry. J. Chromatogr. 476, 423-438.
24. Annan, R. S., Kresbach, G. M., Giese, R. W., and Vouros, P. (1989) Trace detection of modified DNA bases via moving-belt liquid chromatography-mass spectrometry using electrophoric derivitization and negative chemical ionization. J. Chromatogr. 465, 285-296.
25. Gajewski, E., Rao, G., Nackerdien, Z., and Dizdaroglu, M. (1990) Modification of DNA bases in mammalian chromatin by radiation-generated free radicals. Biochemistry 29, 7876-7882.
26. Cattley, R. C., Dietze, S. R., Richardson, F. C., and Popp, J. A. (1990) Detection of 5-hydroxymethyl-2′-deoxyuridine in DNA from calf thymus, Hela cells, and rat liver nuclei. Nucleosides Nucleotides 9, 179-187.
27. Frenkel, K., Zhong, Z., Wei, H., Karkoszka, J., Patel, U., Rashid, K., Georgescu, M., and Solomon, J. J. (1991) Quantitative high-performance liquid chromatography analysis of DNA oxidized in vitro and in vivo. Anal. Biochem. 196, 126-136.
28. Djuric, Z., Luongo, D. A., and Harper, D. A. (1991) Quantitation of 5-(hydroxymethyl)uracil in DNA by gas chromatography with mass spectral detection. Chem. Res. Toxicol. 4, 687-691.
29. Akman, S. A., Doroshow, J. H., Burke, T. G., and Dizdaroglu, M. (1992) DNA base modifications induced in isolated human chromatin by NADH dehydrogenase-catalyzed reduction of doxorubicin. Biochemistry 31, 3500-3506.
30. Nackerdien, Z., Olinski, R., and Dizdaroglu, M. (1992) DNA base damage in chromatin of gamma-irradiated cultured human cells. Free Radical Res. Commun. 16, 259-273.
31. Claycamp, H. G. (1992) Phenol sensitization of DNA to subsequent oxidative damage in 8-hydroxyguanine assays. Carcinogenesis 13, 1289-1292.
32. 32P-postlabeling and GC/MS-selective ion monitoring assays. IARC 124, 271-276.
33. Hamberg, M., and Zhang, L.-Y (1995) Quantitative determination of 8-hydroxyguanine and guanine by isotope dilution mass spectrometry. Anal. Biochem. 229, 336-344.
34. Ravanat, J.-L., Turesky, R. J., Gremaud, E., Trudel, L. J., and Stadler, R. H. (1995) Determination of 8-oxoguanine in DNA by gas chromatography-mass spectrometry and HPLC-electrochemical detection: overestimation of the background level of the oxidized base by the gas chromatography-mass spectrometry assay. Chem. Res. Toxicol. 8, 1039-1045.
35. Swarts, S. G., Smith, G. S., Miao, L., and Wheeler, K. T. (1996) Effects of formic acid hydrolysis on the quantitative analysis of radiation-induced DNA base damage products assayed by gas chromatography. Radiat. Environ. Biophys. 35, 41-53.
36. Douki, T., Delatour, T., Paganon, F., and Cadet, J., (1996) Measurement of oxidative damage at pyrimidine bases in gamma-irradiated DNA. Chem. Res. Toxicol. 9, 1145-1151.
37. Herbert, K. E., Evans, M. D., Finnegan, M. T. V., Farooq, S., Mistry, N., Podmore, I. D., Farmer, P., and Lunec, J (1996) A novel HPLC procedure for the analysis of 8-oxoguanine in DNA. Free Radical Biol. Med. 20, 467-473.
38. Collins, A., Cadet, J., Epe, B., and Gedik, C. (1997) Problems in the measurement of 8-oxoguanine in human DNA. Report of a workshop, DNA oxidation, held in Aberdeen, UK, 19-21 January, 1997. Carcinogenesis 18, 1833-1836.
39. Bodepudi, V., Iden, C. R., and Johnson, F. (1991) An improved method for the preparation of the phosphoramidites of modified 2′-deoxynucleotides: incorporation of 8-oxo-2′-dooxy-7H-guanosine into synthetic oligomers. Nucleosides Nucleotides 10, 755-761.
40. Beaucage, S., and Iyer, R. (1993) The synthesis of modified oligonucleotides by the phosphoramidite approach and their applications. Tetrahedron 49, 6123-6194.
41. Sowers, L. C., and Beardsley, G. P (1993) Synthesis of oligonucleotides containing 5-(hydroxymethyl)-2′-deoxyuridine at defined sites. J. Org. Chem. 58, 1664-1665.
42. Matray, T. J., Haxton, K. J., and Greenberg, M. M. (1995) The effects of the ring fragmentation product of thymidine C5-hydrate on phosphodiesterases and Klenow (exo-) fragment. Nucleic Acids Res. 23, 4642-4648.
43. Tardy-Planechaud, S., Fujimoto, J., Lin, S. S., and Sowers, L. C. (1997) Solid phase synthesis and restriction endonuclease cleavage of oligodeoxynucleotides containing 5-(hydroxymethyl)-cytosine. Nucleic Acids Res. 25, 553-558.
44. Fujimoto, J., Tran, L., and Sowers, L. C. (1997) Synthesis and cleavage of oligodeoxynucleotides containing a 5-hydroxyuracil residue at a defined site. Chem. Res. Toxicol. 10, 1254-1258.
45. LaFrancois, C. J., Fujimoto, J., and Sowers, L. C. (1998) Synthesis and characterization of isotopically enriched pyrimidine deoxynucleoside oxidation damage products. Chem. Res. Toxicol. 11, 75-83.
46. Dickerson, R, E., and Drew, H. R. (1981) Structure of a B-DNA dodecamer II. Influence of base sequence on helix structure. J. Mol. Biol. 149, 761-786.
47. Cantor, C. R., Warshaw, M. M., and Shapiro, H. (1970) Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9, 1059-1077.
48. Shiau, G. T., Schinazi, R. F., Chen, M. S., and Prusoff, W. H. (1980) Synthesis and biological activities of 5-(hydroxymethyl, azidomethyl, or aminomethyl)-2′-deoxyuridine and related 5′-substituted analogues. J. Med. Chem. 23, 127-133.
49. Handbook of Biochemistry and Molecular Biology, 3rd. ed. (1975) (Fasman, G. D., Ed.) Nucleic Acids Vol 1, CRC Press Inc., Cleveland, OH.
50. Chang, P. K. (1958) Synthesis of some 5-alkyl-6-azauracils. J. Org. Chem. 23, 1951-1953.
51. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning, a Laboratory Manual, 2nd ed., p C.1, Cold Spring Harbor Laboratory Press, Plainview, NY.
52. Cline, R. E., Fink, R. M., and Fink, K. (1959) Synthesis of 5-substituted pyrimidines via formaldehyde addition. J. Am. Chem. Soc. 81, 2521-2527.
53. Scheit, K. H. (1966) Die synthese der 5′-diphosphate von 5-methyluridin, 5-hydroxymethyl-uridin und 3,4-dimethyl-uridin. (Synthesis of the 5′-diphosphate of 5-methyluridine, 5-(hydroxymethyl)-uridine and 3,5-dimethyluridine.) Chem. Ber. 99, 3884-3890.
54. McCloskey, J. A. (1990) Calculation of isotopic abundance distributions. Methods Enzymol. 193, 882-886.
55. Falcone, J. M., and Box, H. C. (1997) Selective hydrolysis of damaged DNA by nuclease P1. Biochim. Biophys. Acta 1337, 267-275.