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Volumn 38, Issue 21, 2010, Pages

A one-step method for quantitative determination of uracil in DNA by real-time PCR

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; THYMIDINE PHOSPHATE; URACIL;

EID: 84855639293     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq815     Document Type: Article
Times cited : (35)

References (48)
  • 1
    • 34250188803 scopus 로고    scopus 로고
    • Genomic patterns of DNA methylation: Targets and function of an epigenetic mark
    • Weber, M. and Schubeler, D. (2007) Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr. Opin. Cell. Biol., 19, 273-280.
    • (2007) Curr. Opin. Cell. Biol. , vol.19 , pp. 273-280
    • Weber, M.1    Schubeler, D.2
  • 4
    • 61849128423 scopus 로고    scopus 로고
    • Keeping uracil out of DNA: Physiological role, structure and catalytic mechanism of dUTPases
    • Vertessy, B. G. and Toth, J. (2009) Keeping uracil out of DNA: physiological role, structure and catalytic mechanism of dUTPases. Acc. Chem. Res., 42, 97-106.
    • (2009) Acc. Chem. Res. , vol.42 , pp. 97-106
    • Vertessy, B.G.1    Toth, J.2
  • 5
    • 19144373027 scopus 로고    scopus 로고
    • The problem with pyrimidines
    • Pearl, L. H. and Savva, R. (1996) The problem with pyrimidines. Nat. Struct. Biol., 3, 485-487.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 485-487
    • Pearl, L.H.1    Savva, R.2
  • 6
    • 0027278557 scopus 로고
    • Instability and decay of the primary structure of DNA
    • Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature, 362, 709-715.
    • (1993) Nature , vol.362 , pp. 709-715
    • Lindahl, T.1
  • 7
    • 0036801346 scopus 로고    scopus 로고
    • Repair of deaminated bases in DNA
    • Kow, Y. W. (2002) Repair of deaminated bases in DNA. Free Radic. Biol. Med., 33, 886-893.
    • (2002) Free Radic. Biol. Med. , vol.33 , pp. 886-893
    • Kow, Y.W.1
  • 8
    • 42649123314 scopus 로고    scopus 로고
    • Mechanism and regulation of class switch recombination
    • Stavnezer, J., Guikema, J. E. and Schrader, C. E. (2008) Mechanism and regulation of class switch recombination. Annu. Rev. Immunol., 26, 261-292.
    • (2008) Annu. Rev. Immunol. , vol.26 , pp. 261-292
    • Stavnezer, J.1    Guikema, J.E.2    Schrader, C.E.3
  • 9
    • 0023949768 scopus 로고
    • Purification and characterization of porcine liver DNA polymerase gamma: Utilization of dUTP and dTTP during in vitro DNA synthesis
    • Mosbaugh, D. W. (1988) Purification and characterization of porcine liver DNA polymerase gamma: utilization of dUTP and dTTP during in vitro DNA synthesis. Nucleic Acids Res., 16, 5645-5659.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 5645-5659
    • Mosbaugh, D.W.1
  • 10
    • 33750935665 scopus 로고    scopus 로고
    • Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance
    • Lari, S. U., Chen, C. Y., Vertessy, B. G., Morre, J. and Bennett, S. E. (2006) Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance. DNA Repair, 5, 1407-1420.
    • (2006) DNA Repair , vol.5 , pp. 1407-1420
    • Lari, S.U.1    Chen, C.Y.2    Vertessy, B.G.3    Morre, J.4    Bennett, S.E.5
  • 11
    • 50649108365 scopus 로고    scopus 로고
    • Base excision repair and its role in maintaining genome stability
    • Baute, J. and Depicker, A. (2008) Base excision repair and its role in maintaining genome stability. Crit. Rev. Biochem. Mol. Biol., 43, 239-276.
    • (2008) Crit. Rev. Biochem. Mol. Biol. , vol.43 , pp. 239-276
    • Baute, J.1    Depicker, A.2
  • 12
    • 0030035663 scopus 로고    scopus 로고
    • Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase
    • Kavli, B., Slupphaug, G., Mol, C. D., Arvai, A. S., Peterson, S. B., Tainer, J. A. and Krokan, H. E. (1996) Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBO J., 15, 3442-3447.
    • (1996) EMBO J. , vol.15 , pp. 3442-3447
    • Kavli, B.1    Slupphaug, G.2    Mol, C.D.3    Arvai, A.S.4    Peterson, S.B.5    Tainer, J.A.6    Krokan, H.E.7
  • 13
    • 0036894880 scopus 로고    scopus 로고
    • Structural basis for uracil recognition by archaeal family B DNA polymerases
    • Fogg, M. J., Pearl, L. H. and Connolly, B. A. (2002) Structural basis for uracil recognition by archaeal family B DNA polymerases. Nat. Struct. Biol., 9, 922-927.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 922-927
    • Fogg, M.J.1    Pearl, L.H.2    Connolly, B.A.3
  • 14
    • 34548426097 scopus 로고    scopus 로고
    • Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases
    • Gill, S., O'Neill, R., Lewis, R. J. and Connolly, B. A. (2007) Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. J. Mol. Biol., 372, 855-863.
    • (2007) J. Mol. Biol. , vol.372 , pp. 855-863
    • Gill, S.1    O'Neill, R.2    Lewis, R.J.3    Connolly, B.A.4
  • 16
    • 1542358786 scopus 로고    scopus 로고
    • Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea
    • Shuttleworth, G., Fogg, M. J., Kurpiewski, M. R., Jen-Jacobson, L. and Connolly, B. A. (2004) Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea. J. Mol. Biol., 337, 621-634.
    • (2004) J. Mol. Biol. , vol.337 , pp. 621-634
    • Shuttleworth, G.1    Fogg, M.J.2    Kurpiewski, M.R.3    Jen-Jacobson, L.4    Connolly, B.A.5
  • 18
    • 0035148615 scopus 로고    scopus 로고
    • Apoptosis of haematopoietic cells upon thymidylate synthase inhibition is independent of p53 accumulation and CD95-CD95 ligand interaction
    • Munoz-Pinedo, C., Oliver, F. J. and Lopez-Rivas, A. (2001) Apoptosis of haematopoietic cells upon thymidylate synthase inhibition is independent of p53 accumulation and CD95-CD95 ligand interaction. Biochem. J., 353, 101-108.
    • (2001) Biochem. J. , vol.353 , pp. 101-108
    • Munoz-Pinedo, C.1    Oliver, F.J.2    Lopez-Rivas, A.3
  • 19
    • 3142540614 scopus 로고    scopus 로고
    • Thymidylate synthase inhibition triggers glucose-dependent apoptosis in p53-negative leukemic cells
    • Munoz-Pinedo, C., Robledo, G. and Lopez-Rivas, A. (2004) Thymidylate synthase inhibition triggers glucose-dependent apoptosis in p53-negative leukemic cells. FEBS Lett., 570, 205-210.
    • (2004) FEBS Lett. , vol.570 , pp. 205-210
    • Munoz-Pinedo, C.1    Robledo, G.2    Lopez-Rivas, A.3
  • 20
    • 2942648695 scopus 로고    scopus 로고
    • Four decades of continuing innovation with fluorouracil: Current and future approaches to fluorouracil chemoradiation therapy
    • Rich, T. A., Shepard, R. C. and Mosley, S. T. (2004) Four decades of continuing innovation with fluorouracil: current and future approaches to fluorouracil chemoradiation therapy. J. Clin. Oncol., 22, 2214-2232.
    • (2004) J. Clin. Oncol. , vol.22 , pp. 2214-2232
    • Rich, T.A.1    Shepard, R.C.2    Mosley, S.T.3
  • 21
    • 0034114654 scopus 로고    scopus 로고
    • Downstream molecular determinants of response to 5-fluorouracil and antifolate thymidylate synthase inhibitors
    • Van Triest, B., Pinedo, H. M., Giaccone, G. and Peters, G. J. (2000) Downstream molecular determinants of response to 5-fluorouracil and antifolate thymidylate synthase inhibitors. Ann. Oncol., 11, 385-391.
    • (2000) Ann. Oncol. , vol.11 , pp. 385-391
    • Van Triest, B.1    Pinedo, H.M.2    Giaccone, G.3    Peters, G.J.4
  • 22
    • 0030032030 scopus 로고    scopus 로고
    • Methotrexate: An effective agent for treating cancer and building careers
    • Schilsky, R. L. (1996) Methotrexate: an effective agent for treating cancer and building careers. The polyglutamate era. Stem Cells, 14, 29-32.
    • (1996) The Polyglutamate Era. Stem Cells , vol.14 , pp. 29-32
    • Schilsky, R.L.1
  • 23
    • 26944498660 scopus 로고    scopus 로고
    • Determination of apoptosis, uracil incorporation, DNA strand breaks, and sister chromatid exchanges under conditions of thymidylate deprivation in a model of BER deficiency
    • Li, L., Connor, E. E., Berger, S. H. and Wyatt, M. D. (2005) Determination of apoptosis, uracil incorporation, DNA strand breaks, and sister chromatid exchanges under conditions of thymidylate deprivation in a model of BER deficiency. Biochem. Pharmacol., 70, 1458-1468.
    • (2005) Biochem. Pharmacol. , vol.70 , pp. 1458-1468
    • Li, L.1    Connor, E.E.2    Berger, S.H.3    Wyatt, M.D.4
  • 24
    • 29244485920 scopus 로고    scopus 로고
    • Yersiniophage phiR1-37 is a tailed bacteriophage having a 270kb DNA genome with thymidine replaced by deoxyuridine
    • Kiljunen, S., Hakala, K., Pinta, E., Huttunen, S., Pluta, P., Gador, A., Lonnberg, H. and Skurnik, M. (2005) Yersiniophage phiR1-37 is a tailed bacteriophage having a 270kb DNA genome with thymidine replaced by deoxyuridine. Microbiology, 151, 4093-4102.
    • (2005) Microbiology , vol.151 , pp. 4093-4102
    • Kiljunen, S.1    Hakala, K.2    Pinta, E.3    Huttunen, S.4    Pluta, P.5    Gador, A.6    Lonnberg, H.7    Skurnik, M.8
  • 25
    • 0028229675 scopus 로고
    • Analysis of uracil in DNA by gas chromatography-mass spectrometry
    • Blount, B. C. and Ames, B. N. (1994) Analysis of uracil in DNA by gas chromatography-mass spectrometry. Anal. Biochem., 219, 195-200.
    • (1994) Anal. Biochem. , vol.219 , pp. 195-200
    • Blount, B.C.1    Ames, B.N.2
  • 27
    • 37549072672 scopus 로고    scopus 로고
    • Uracil incorporation into genomic DNA does not predict toxicity caused by chemotherapeutic inhibition of thymidylate synthase
    • Luo, Y., Walla, M. and Wyatt, M. D. (2008) Uracil incorporation into genomic DNA does not predict toxicity caused by chemotherapeutic inhibition of thymidylate synthase. DNA Repair, 7, 162-169.
    • (2008) DNA Repair , vol.7 , pp. 162-169
    • Luo, Y.1    Walla, M.2    Wyatt, M.D.3
  • 28
    • 0036139822 scopus 로고    scopus 로고
    • Uracil in human DNA from subjects with normal and impaired folate status as determined by high-performance liquid chromatography-tandem mass spectrometry
    • Ren, J., Ulvik, A., Refsum, H. and Ueland, P. M. (2002) Uracil in human DNA from subjects with normal and impaired folate status as determined by high-performance liquid chromatography-tandem mass spectrometry. Anal. Chem., 74, 295-299.
    • (2002) Anal. Chem. , vol.74 , pp. 295-299
    • Ren, J.1    Ulvik, A.2    Refsum, H.3    Ueland, P.M.4
  • 29
    • 0021843514 scopus 로고
    • A new approach to the study of the base-excision repair pathway using methoxyamine
    • Liuzzi, M. and Talpaert-Borle, M. (1985) A new approach to the study of the base-excision repair pathway using methoxyamine. J. Biol. Chem., 260, 5252-5258.
    • (1985) J. Biol. Chem. , vol.260 , pp. 5252-5258
    • Liuzzi, M.1    Talpaert-Borle, M.2
  • 30
    • 0026754035 scopus 로고
    • A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion
    • Kubo, K., Ide, H., Wallace, S. S. and Kow, Y. W. (1992) A novel, sensitive, and specific assay for abasic sites, the most commonly produced DNA lesion. Biochemistry, 31, 3703-3708.
    • (1992) Biochemistry , vol.31 , pp. 3703-3708
    • Kubo, K.1    Ide, H.2    Wallace, S.S.3    Kow, Y.W.4
  • 31
    • 0034681176 scopus 로고    scopus 로고
    • A method for detecting abasic sites in living cells: Age-dependent changes in base excision repair
    • Atamna, H., Cheung, I. and Ames, B. N. (2000) A method for detecting abasic sites in living cells: age-dependent changes in base excision repair. Proc. Natl Acad. Sci. USA, 97, 686-691.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 686-691
    • Atamna, H.1    Cheung, I.2    Ames, B.N.3
  • 32
    • 0031410086 scopus 로고    scopus 로고
    • Uracil misincorporation in human DNA detected using single cell gel electrophoresis
    • Duthie, S. J. and McMillan, P. (1997) Uracil misincorporation in human DNA detected using single cell gel electrophoresis. Carcinogenesis, 18, 1709-1714.
    • (1997) Carcinogenesis , vol.18 , pp. 1709-1714
    • Duthie, S.J.1    McMillan, P.2
  • 33
    • 27844591343 scopus 로고    scopus 로고
    • Monoclonal B-cell hyperplasia and leukocyte imbalance precede development of B-cell malignancies in uracil-DNA glycosylase deficient mice
    • Andersen, S., Ericsson, M., Dai, H. Y., Pena-Diaz, J., Slupphaug, G., Nilsen, H., Aarset, H. and Krokan, H. E. (2005) Monoclonal B-cell hyperplasia and leukocyte imbalance precede development of B-cell malignancies in uracil-DNA glycosylase deficient mice. DNA Repair, 4, 1432-1441.
    • (2005) DNA Repair , vol.4 , pp. 1432-1441
    • Andersen, S.1    Ericsson, M.2    Dai, H.Y.3    Pena-Diaz, J.4    Slupphaug, G.5    Nilsen, H.6    Aarset, H.7    Krokan, H.E.8
  • 34
    • 16244423009 scopus 로고    scopus 로고
    • Incorporation of dUMP into DNA is a major source of spontaneous DNA damage, while excision of uracil is not required for cytotoxicity of fluoropyrimidines in mouse embryonic fibroblasts
    • Andersen, S., Heine, T., Sneve, R., Konig, I., Krokan, H. E., Epe, B. and Nilsen, H. (2005) Incorporation of dUMP into DNA is a major source of spontaneous DNA damage, while excision of uracil is not required for cytotoxicity of fluoropyrimidines in mouse embryonic fibroblasts. Carcinogenesis, 26, 547-555.
    • (2005) Carcinogenesis , vol.26 , pp. 547-555
    • Andersen, S.1    Heine, T.2    Sneve, R.3    Konig, I.4    Krokan, H.E.5    Epe, B.6    Nilsen, H.7
  • 36
    • 4544356659 scopus 로고    scopus 로고
    • Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method
    • Sikorsky, J. A., Primerano, D. A., Fenger, T. W. and Denvir, J. (2004) Effect of DNA damage on PCR amplification efficiency with the relative threshold cycle method. Biochem. Biophys. Res. Commun., 323, 823-830.
    • (2004) Biochem. Biophys. Res. Commun. , vol.323 , pp. 823-830
    • Sikorsky, J.A.1    Primerano, D.A.2    Fenger, T.W.3    Denvir, J.4
  • 37
  • 38
    • 34047130220 scopus 로고    scopus 로고
    • DNA supercoiling suppresses real-time PCR: A new approach to the quantification of mitochondrial DNA damage and repair
    • Chen, J., Kadlubar, F. F. and Chen, J. Z. (2007) DNA supercoiling suppresses real-time PCR: a new approach to the quantification of mitochondrial DNA damage and repair. Nucleic Acids Res., 35, 1377-1388.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1377-1388
    • Chen, J.1    Kadlubar, F.F.2    Chen, J.Z.3
  • 39
    • 77951186338 scopus 로고    scopus 로고
    • Analysis of differential DNA damage in the mitochondrial genome employing a semi-long run real-time PCR approach
    • Rothfuss, O., Gasser, T. and Patenge, N. Analysis of differential DNA damage in the mitochondrial genome employing a semi-long run real-time PCR approach. Nucleic Acids Res., 38, e24.
    • Nucleic Acids Res. , vol.38
    • Rothfuss, O.1    Gasser, T.2    Patenge, N.3
  • 40
    • 77952236020 scopus 로고    scopus 로고
    • QPCR: A tool for analysis of mitochondrial and nuclear DNA damage in ecotoxicology
    • Meyer, J. N. QPCR: a tool for analysis of mitochondrial and nuclear DNA damage in ecotoxicology. Ecotoxicology, 19, 804-811.
    • Ecotoxicology , vol.19 , pp. 804-811
    • Meyer, J.N.1
  • 41
    • 34247884259 scopus 로고    scopus 로고
    • Monitoring repair of DNA damage in cell lines and human peripheral blood mononuclear cells
    • Lee, H. W., Lee, H. J., Hong, C. M., Baker, D. J., Bhatia, R. and O'Connor, T. R. (2007) Monitoring repair of DNA damage in cell lines and human peripheral blood mononuclear cells. Anal. Biochem., 365, 246-259.
    • (2007) Anal. Biochem. , vol.365 , pp. 246-259
    • Lee, H.W.1    Lee, H.J.2    Hong, C.M.3    Baker, D.J.4    Bhatia, R.5    O'Connor, T.R.6
  • 42
    • 16544382188 scopus 로고    scopus 로고
    • MethylQuant: A sensitive method for quantifying methylation of specific cytosines within the genome
    • Thomassin, H., Kress, C. and Grange, T. (2004) MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome. Nucleic Acids Res., 32, e168.
    • (2004) Nucleic Acids Res. , vol.32
    • Thomassin, H.1    Kress, C.2    Grange, T.3
  • 43
    • 0029929717 scopus 로고    scopus 로고
    • Archaebacterial DNA polymerases tightly bind uracil-containing DNA
    • Lasken, R. S., Schuster, D. M. and Rashtchian, A. (1996) Archaebacterial DNA polymerases tightly bind uracil-containing DNA. J. Biol. Chem., 271, 17692-17696.
    • (1996) J. Biol. Chem. , vol.271 , pp. 17692-17696
    • Lasken, R.S.1    Schuster, D.M.2    Rashtchian, A.3
  • 44
    • 4444337502 scopus 로고    scopus 로고
    • Mathematics of quantitative kinetic PCR and the application of standard curves
    • Rutledge, R. G. and Cote, C. (2003) Mathematics of quantitative kinetic PCR and the application of standard curves. Nucleic Acids Res., 31, e93.
    • (2003) Nucleic Acids Res. , vol.31
    • Rutledge, R.G.1    Cote, C.2
  • 45
    • 17344392308 scopus 로고    scopus 로고
    • A new mathematical model for relative quantification in real-time RT-PCR
    • Pfaffl, M. W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res., 29, e45.
    • (2001) Nucleic Acids Res. , vol.29
    • Pfaffl, M.W.1
  • 47
    • 17644373059 scopus 로고    scopus 로고
    • Variance in the expression of 5-Fluorouracil pathway genes in colorectal cancer
    • Kidd, E. A., Yu, J., Li, X., Shannon, W. D., Watson, M. A. and McLeod, H. L. (2005) Variance in the expression of 5-Fluorouracil pathway genes in colorectal cancer. Clin. Cancer Res., 11, 2612-2619.
    • (2005) Clin. Cancer Res. , vol.11 , pp. 2612-2619
    • Kidd, E.A.1    Yu, J.2    Li, X.3    Shannon, W.D.4    Watson, M.A.5    McLeod, H.L.6
  • 48
    • 67649559461 scopus 로고    scopus 로고
    • DUTP incorporation into genomic DNA is linked to transcription in yeast
    • Kim, N. and Jinks-Robertson, S. (2009) dUTP incorporation into genomic DNA is linked to transcription in yeast. Nature, 459, 1150-1153.
    • (2009) Nature , vol.459 , pp. 1150-1153
    • Kim, N.1    Jinks-Robertson, S.2


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