Impact of cytosine 5-halogens on the interaction of DNA with restriction endonucleases and methyltransferase

Chemical Research in Toxicology

Volumn 19, Issue 4, 2006, Pages 556-562

  Valinluck, Victoria ^a   Wu, Winnie ^a   Liu, Pingfang ^a,b,c   Neidigh, Jonathan W ^a   Sowers, Lawrence C ^a,b  

^a LOMA LINDA UNIVERSITY SCHOOL OF MEDICINE   (United States)

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

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 CHLOROCYTOSINE; BACTERIAL ENZYME; BROMINE; CHLORINE; CYTOSINE DERIVATIVE; DNA BINDING PROTEIN; FLUCYTOSINE; HALOGEN; IODINE; METHYL GROUP; METHYLTRANSFERASE; OLIGONUCLEOTIDE; PYRIMIDINE; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE MSPI; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BINDING SITE; COMPLEX FORMATION; COVALENT BOND; ENZYME DEGRADATION; ENZYME INHIBITION; ENZYME INHIBITOR INTERACTION; EUKARYOTE; HALOGENATION; INFLAMMATION; METHYLATION; MOLECULAR RECOGNITION; PROKARYOTE; PROTEIN DNA INTERACTION; STEREOSPECIFICITY; SUBSTITUTION REACTION;

CYTOSINE; DNA; DNA RESTRICTION ENZYMES; HALOGENS; METHYLTRANSFERASES;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 33646107882     PISSN: 0893228X     EISSN: None     Source Type: Journal    
DOI: 10.1021/tx050341w     Document Type: Article

References (36)

1. Henderson, J. P., Byun, J., and Heinecke, J. W. (1999) Molecular chlorine generated by the myeloperoxidase-hydrogen peroxide-chloride system of phagocytes produces 5-chlorocytosine in bacterial RNA. J. Biol. Chem. 274, 33440-33448.
2. Whiteman, M., Jenner, A., and Halliwell, B. (1997) Hypochlorous acid-induced base modifications in isolated calf thymus DNA. Chem. Res. Toxicol. 10, 1240-1246.
3. Henderson, J. P., Byun, J., Williams, M. V., Mueller, D. M., McCormick, M. L., and Heinecke, J. W. (2001) Production of brominating intermediates by myeloperoxidase: A transhalogenation pathway for generating mutagenic nucleobases during inflammation. J. Biol. Chem. 276, 7867-7875.
4. Henderson, J. P., Byun, J., Williams, M. V., McCormick, M., Parks, W. C., Ridnour, L. A., and Heinecke, J. W. (2001) Bromination of deoxycytidine by eosinophil peroxidase: A mechanism for mutagenesis by oxidative damage of nucleotide precursors. Proc. Natl. Acad. Sci. U.S.A. 98, 1631-1636.
5. Henderson, J. P., Byun, J., Mueller, D. M., and Heinecke, J. W. (2001) The eosinophil peroxidase-hydrogen peroxide-bromide system of human eosinophils generates 5-bromouracil, a mutagenic thymine analogue. Biochemistry 40, 2052-2059.
6. Jiang, Q., Blount, B. C., and Ames, B. N. (2003) 5-Chlorouracil, a marker of DNA damage from hypochlorous acid during inflammation. J. Biol. Chem. 278, 32834-32840.
7. Ivarie, R. (1987) Thymine methyls and DNA-protein interactions. Nucleic Acids Res. 15, 9975-9983.
8. McClelland, M. (1981) The effect of sequence specific DNA methylation on restriction endonuclease cleavage. Nucleic Acids Res. 9, 5859-5866.
9. Rogstad, D. K., Liu, P., Burdzy, A., Lin, S. S., and Sowers, L. C. (2002) Endogenous DNA lesions can inhibit the binding of the AP-1 (c-Jun) transcription factor. Biochemistry 41, 8093-8102.
10. Valinluck, V., Tsai, H.-H., Rogstad, D. K., Burdzy, A., Bird, A., and Sowers, L. C. (2004) Oxidative damage to methyl-CpG sequences inhibits the binding of the methyl-CpG binding domain (MBD) of MeCP2. Nucleic Acids Res. 32, 4100-4108.
11. Bodnar, J. W., Zempsky, W., Warder, D., Bergson, C., and Ward, D. C. (1983) Effect of nucleotide analogues on the cleavage of DNA by the restriction enzymes AluI, DdeI, HinfI, RsaI, and TaqI. J. Biol. Chem. 258, 15206-15213.
12. Hoheisel, J. D., Craig, A. G., and Lehrach, H. (1990) Effect of 5-bromo- and 5-methyldeoxycytosine on duplex stability and discrimination of the NotI octadeoxynucleotide. Quantitative measurements using thin-layer chromatography. J. Biol. Chem. 265, 16656-16660.
13. Brennan, C. A., Van Cleve, M. D., and Gumport, R. I. (1986) The effects of base analogue substitutions on the methylation by the EcoRI modification methylase of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J. Biol. Chem. 261, 7279-7286.
14. Brennan, C. A., Van Cleve, M. D., and Gumport, R. I. (1986) The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J. Biol. Chem. 261, 7270-7278.
15. Valinluck, V., Liu, P., Kang, J. I., Jr., Burdzy, A., and Sowers, L. C. (2005) 5-halogenated pyrimidine lesions within a CpG sequence context mimic 5-methylcytosine by enhancing the binding of the methyl-CpG-binding domain of methyl-CpG-binding protein 2 (MeCP2). Nucleic Acids Res. 33, 3057-3064.
16. Liu, P., Burdzy, A., and Sowers, L. C. (2002) Substrate recognition by a family of uracil-DNA glycosylases: UNG, MUG and TDG. Chem. Res. Toxicol. 15, 1001-1009.
17. Ivanetich, K. M., and Santi, D. V. (1988) Thymidylate synthase and fluorouracil. Adv. Exp. Med. Biol. 244, 113-124.
18. Smith, S. S., Kaplan, B. E., Sowers, L. C., and Newman, E. M. (1992) Mechanism of human methyl-directed DNA methyltransferase and the fidelity of cytosine methylation. Proc. Natl. Acad. Sci. U.S.A. 89, 4744-4748.
19. Klimasauskas, S., Kumar, S., Roberts, R. J., and Cheng, X. (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
20. Greer, S., Schwade, J., and Marion, H. S. (1995) Five-chlorodeoxycytidine and biomodulators of its metabolism result in fifty to eighty percent cures of advanced EMT-6 tumors when used with fractionated radiation. Int. J. Radiat. Oncol. Biol. Phys. 32, 1059-1069.
21. Kang, J. I., Burdzy, A., Liu, P., and Sowers, L. C. (2004) Synthesis and Characterization of oligonucleotides containing 5-chlorocytosine. Chem. Res. Toxicol. 17, 1236-1244.
22. Sowers, L. C. (2000) 15N-enriched 5-fluorocytosine as a probe for examining unusual DNA structures. J. Biomol. Struct. Dyn. 17, 713-723.
23. Mann, M. B., and Smith, H. O. (1977) Specificity of Hpa II and Hae III DNA methylases. Nucleic Acids Res. 4, 4211-4221.
24. Waalwijk, C., and Flavell, R. A. (1978) MspI, an isoschizomer of HpaII which cleaves both unmethylated and methylated HpaII sites. Nucleic Acids Res. 5, 3231-3236.
25. Butkus, V., Petrauskiene, L., Maneliene, Z., Klimasauskas, S., Laucys, V., and Janulaitis, A. (1987) Cleavage of methylated CCCGGG sequences containing either N4-methylcytosine or 5-methylcytosine with MspI, HpaII, SmaI, XmaI and Cfr9I restriction endonucleases. Nucleic Acids Res. 15, 7091-7102.
26. Hardy, T. A., Baker, D. J., Newman, E. M., Sowers, L. C., Goodman, M. F., and Smith, S. S. (1987) Size of the directing moiety at carbon 5 of cytosine and the activity of human DNA (cytosine-5) methyltransferase. Biochem. Biophys. Res. Commun. 145, 146-152.
27. Doerfler, W. (2005) On the biological significance of DNA methylation. Biochemistry (Moscow) 70, 505-524.
28. Jones, P. A., and Takai, D. (2001) The role of DNA methylation in mammalian epigenetics. Science 293, 1068-1070.
29. Sober, H. A. (1970) Handbook of Biochemistry, p J3, The Chemical Rubber Co., Cleveland Ohio.
30. a values for 5-substituted uracils. J. Phys. Chem. A 105, 274-280.
31. Petruska, J., Sowers, L. C., and Goodman, M. F. (1986) Comparison of nucleotide interactions in water, proteins, and vacuum: Model of DNA polymerase fidelity. Proc. Natl. Acad. Sci. U.S.A. 83, 1559-1562.
32. Sowers, L. C., Shaw, B. R., and Sedwick, D. (1987) Base stacking and molecular polarizability: Effect of a methyl group in the 5-position of pyrimidines. Biochem. Biophys. Res. Commun. 148, 790-794.
33. Pingoud, A., Fuxreiter, M., Pingoud, V., and Wende, W. (2005) Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci. 62, 685-707.
34. Wilson, G. G., and Murray, N. E. (1991) Restriction and modification systems. Annu. Rev. Genet. 25, 585-627.
35. Chen, L., MacMillan, A. M., Chang, W., Ezaz-Nikpay, K., Lane, W. S., and Verdine, G. L. (1991) Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase. Biochemistry 30, 11018-11025.
36. Vilkaitis, G., Merkiene, E., Serva, S., Weinhold, E., and Klimasauskas, S. (2001) The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase. J. Biol. Chem. 276, 20924-20934.