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. 1994 Mar 25;22(6):972–976. doi: 10.1093/nar/22.6.972

The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA.

J C Shen 1, W M Rideout 3rd 1, P A Jones 1
PMCID: PMC307917  PMID: 8152929

Abstract

The modified base, 5-methylcytosine, constitutes approximately 1% of human DNA, but sites containing 5-methylcytosine account for at least 30% of all germline and somatic point mutations. A genetic assay with a sensitivity of 1 in 10(7), based on reversion to neomycin resistance of a mutant pSV2-neo plasmid, was utilized to determine and compare the deamination rates of 5-methylcytosine and cytosine in double-stranded DNA for the first time. The rate constants for spontaneous hydrolytic deamination of 5-methylcytosine and cytosine in double-stranded DNA at 37 degrees C were 5.8 x 10(-13) s-1 and 2.6 x 10(-13) s-1, respectively. These rates are more than sufficient to explain the observed frequency of mutation at sites containing 5-methylcytosine and emphasize the importance of hydrolytic deamination as a major source of human mutations.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Breslauer K. J., Remeta D. P., Chou W. Y., Ferrante R., Curry J., Zaunczkowski D., Snyder J. G., Marky L. A. Enthalpy-entropy compensations in drug-DNA binding studies. Proc Natl Acad Sci U S A. 1987 Dec;84(24):8922–8926. doi: 10.1073/pnas.84.24.8922. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Brown T. C., Jiricny J. A specific mismatch repair event protects mammalian cells from loss of 5-methylcytosine. Cell. 1987 Sep 11;50(6):945–950. doi: 10.1016/0092-8674(87)90521-6. [DOI] [PubMed] [Google Scholar]
  3. Brown T. C., Jiricny J. Different base/base mispairs are corrected with different efficiencies and specificities in monkey kidney cells. Cell. 1988 Aug 26;54(5):705–711. doi: 10.1016/s0092-8674(88)80015-1. [DOI] [PubMed] [Google Scholar]
  4. Caradonna S. J., Cheng Y. C. Uracil DNA-glycosylase. Purification and properties of this enzyme isolated from blast cells of acute myelocytic leukemia patients. J Biol Chem. 1980 Mar 25;255(6):2293–2300. [PubMed] [Google Scholar]
  5. Cooper D. N., Youssoufian H. The CpG dinucleotide and human genetic disease. Hum Genet. 1988 Feb;78(2):151–155. doi: 10.1007/BF00278187. [DOI] [PubMed] [Google Scholar]
  6. Coulondre C., Miller J. H., Farabaugh P. J., Gilbert W. Molecular basis of base substitution hotspots in Escherichia coli. Nature. 1978 Aug 24;274(5673):775–780. doi: 10.1038/274775a0. [DOI] [PubMed] [Google Scholar]
  7. Crosby B., Prakash L., Davis H., Hinkle D. C. Purification and characterization of a uracil-DNA glycosylase from the yeast. Saccharomyces cerevisiae. Nucleic Acids Res. 1981 Nov 11;9(21):5797–5809. doi: 10.1093/nar/9.21.5797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Duncan B. K., Miller J. H. Mutagenic deamination of cytosine residues in DNA. Nature. 1980 Oct 9;287(5782):560–561. doi: 10.1038/287560a0. [DOI] [PubMed] [Google Scholar]
  9. Ehrlich M., Norris K. F., Wang R. Y., Kuo K. C., Gehrke C. W. DNA cytosine methylation and heat-induced deamination. Biosci Rep. 1986 Apr;6(4):387–393. doi: 10.1007/BF01116426. [DOI] [PubMed] [Google Scholar]
  10. Frederico L. A., Kunkel T. A., Shaw B. R. A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry. 1990 Mar 13;29(10):2532–2537. doi: 10.1021/bi00462a015. [DOI] [PubMed] [Google Scholar]
  11. Jones M., Wagner R., Radman M. Mismatch repair of deaminated 5-methyl-cytosine. J Mol Biol. 1987 Mar 5;194(1):155–159. doi: 10.1016/0022-2836(87)90724-8. [DOI] [PubMed] [Google Scholar]
  12. Jones P. A., Rideout W. M., 3rd, Shen J. C., Spruck C. H., Tsai Y. C. Methylation, mutation and cancer. Bioessays. 1992 Jan;14(1):33–36. doi: 10.1002/bies.950140107. [DOI] [PubMed] [Google Scholar]
  13. Koeberl D. D., Bottema C. D., Ketterling R. P., Bridge P. J., Lillicrap D. P., Sommer S. S. Mutations causing hemophilia B: direct estimate of the underlying rates of spontaneous germ-line transitions, transversions, and deletions in a human gene. Am J Hum Genet. 1990 Aug;47(2):202–217. [PMC free article] [PubMed] [Google Scholar]
  14. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lieb M. Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites. J Bacteriol. 1987 Nov;169(11):5241–5246. doi: 10.1128/jb.169.11.5241-5246.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lieb M. Specific mismatch correction in bacteriophage lambda crosses by very short patch repair. Mol Gen Genet. 1983;191(1):118–125. doi: 10.1007/BF00330898. [DOI] [PubMed] [Google Scholar]
  17. Lieb M. Spontaneous mutation at a 5-methylcytosine hotspot is prevented by very short patch (VSP) mismatch repair. Genetics. 1991 May;128(1):23–27. doi: 10.1093/genetics/128.1.23. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lindahl T. DNA glycosylases, endonucleases for apurinic/apyrimidinic sites, and base excision-repair. Prog Nucleic Acid Res Mol Biol. 1979;22:135–192. doi: 10.1016/s0079-6603(08)60800-4. [DOI] [PubMed] [Google Scholar]
  19. Lindahl T. DNA repair enzymes. Annu Rev Biochem. 1982;51:61–87. doi: 10.1146/annurev.bi.51.070182.000425. [DOI] [PubMed] [Google Scholar]
  20. Lindahl T. Instability and decay of the primary structure of DNA. Nature. 1993 Apr 22;362(6422):709–715. doi: 10.1038/362709a0. [DOI] [PubMed] [Google Scholar]
  21. Lindahl T., Ljungquist S., Siegert W., Nyberg B., Sperens B. DNA N-glycosidases: properties of uracil-DNA glycosidase from Escherichia coli. J Biol Chem. 1977 May 25;252(10):3286–3294. [PubMed] [Google Scholar]
  22. Lindahl T., Nyberg B. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry. 1974 Jul 30;13(16):3405–3410. doi: 10.1021/bi00713a035. [DOI] [PubMed] [Google Scholar]
  23. Morgan A. R., Chlebek J. Uracil-DNA glycosylase in insects. Drosophila and the locust. J Biol Chem. 1989 Jun 15;264(17):9911–9914. [PubMed] [Google Scholar]
  24. Pukkila P. J., Peterson J., Herman G., Modrich P., Meselson M. Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli. Genetics. 1983 Aug;104(4):571–582. doi: 10.1093/genetics/104.4.571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Radman M., Wagner R. Mismatch repair in Escherichia coli. Annu Rev Genet. 1986;20:523–538. doi: 10.1146/annurev.ge.20.120186.002515. [DOI] [PubMed] [Google Scholar]
  26. Rideout W. M., 3rd, Coetzee G. A., Olumi A. F., Jones P. A. 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes. Science. 1990 Sep 14;249(4974):1288–1290. doi: 10.1126/science.1697983. [DOI] [PubMed] [Google Scholar]
  27. Seal G., Arenaz P., Sirover M. A. Purification and properties of the human placental uracil DNA glycosylase. Biochim Biophys Acta. 1987 Aug 13;925(2):226–233. doi: 10.1016/0304-4165(87)90113-9. [DOI] [PubMed] [Google Scholar]
  28. Searle M. S., Williams D. H. On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res. 1993 May 11;21(9):2051–2056. doi: 10.1093/nar/21.9.2051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Shapiro R., Klein R. S. The deamination of cytidine and cytosine by acidic buffer solutions. Mutagenic implications. Biochemistry. 1966 Jul;5(7):2358–2362. doi: 10.1021/bi00871a026. [DOI] [PubMed] [Google Scholar]
  30. Shen J. C., Rideout W. M., 3rd, Jones P. A. High frequency mutagenesis by a DNA methyltransferase. Cell. 1992 Dec 24;71(7):1073–1080. doi: 10.1016/s0092-8674(05)80057-1. [DOI] [PubMed] [Google Scholar]
  31. Smith K. C. Spontaneous mutagenesis: experimental, genetic and other factors. Mutat Res. 1992 Aug;277(2):139–162. doi: 10.1016/0165-1110(92)90002-q. [DOI] [PubMed] [Google Scholar]
  32. Sommer S. S. Assessing the underlying pattern of human germline mutations: lessons from the factor IX gene. FASEB J. 1992 Jul;6(10):2767–2774. doi: 10.1096/fasebj.6.10.1634040. [DOI] [PubMed] [Google Scholar]
  33. Southern P. J., Berg P. Transformation of mammalian cells to antibiotic resistance with a bacterial gene under control of the SV40 early region promoter. J Mol Appl Genet. 1982;1(4):327–341. [PubMed] [Google Scholar]
  34. Sved J., Bird A. The expected equilibrium of the CpG dinucleotide in vertebrate genomes under a mutation model. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4692–4696. doi: 10.1073/pnas.87.12.4692. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Wiebauer K., Jiricny J. In vitro correction of G.T mispairs to G.C pairs in nuclear extracts from human cells. Nature. 1989 May 18;339(6221):234–236. doi: 10.1038/339234a0. [DOI] [PubMed] [Google Scholar]

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