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Volumn 29, Issue 2, 2005, Pages 101-110

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection

Author keywords

Biochemical engineering; Mathematical model; Molecular biology; Polymerase chain reaction

Indexed keywords

ANNEALING; BINDING ENERGY; BIOCHEMICAL ENGINEERING; CATALYSIS; ENZYME KINETICS; ENZYMES; MATHEMATICAL MODELS; MOLECULAR BIOLOGY; PARAMETER ESTIMATION; PROBABILITY; RATE CONSTANTS;

EID: 16344368485     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2005.02.003     Document Type: Article
Times cited : (8)

References (40)
  • 1
    • 2342453957 scopus 로고    scopus 로고
    • Telomerase, telomerase inhibition and cancer
    • A. Ahmed, and T.O. Tollefsbol Telomerase, telomerase inhibition and cancer J. Anti Aging Med. 6 2003 315 325
    • (2003) J. Anti Aging Med. , vol.6 , pp. 315-325
    • Ahmed, A.1    Tollefsbol, T.O.2
  • 2
    • 0019975354 scopus 로고
    • Effects of azidocytidine on DNA synthesis and deoxynucleotide pools of mouse fibroblast cell lines
    • L. Akerblom, E. Pontis, and P. Reichard Effects of azidocytidine on DNA synthesis and deoxynucleotide pools of mouse fibroblast cell lines J. Biol. Chem. 257 1982 6776 6782
    • (1982) J. Biol. Chem. , vol.257 , pp. 6776-6782
    • Akerblom, L.1    Pontis, E.2    Reichard, P.3
  • 3
    • 0000292524 scopus 로고
    • A note on the kinetics of enzyme action
    • GE. Briggs, and J.B.S. Haldane A note on the kinetics of enzyme action Biochem. J. 19 1925 338 339
    • (1925) Biochem. J. , vol.19 , pp. 338-339
    • Briggs, G.E.1    Haldane, J.B.S.2
  • 4
    • 0034671533 scopus 로고    scopus 로고
    • Ribonucleotide reductase a possible agent in deoxyribonucleotide pool asymmetries induced by hypoxia
    • K. Chimploy, M.L. Tassotto, and C.K. Mathews Ribonucleotide reductase a possible agent in deoxyribonucleotide pool asymmetries induced by hypoxia J. Biol. Chem. 275 2000 39267 39271
    • (2000) J. Biol. Chem. , vol.275 , pp. 39267-39271
    • Chimploy, K.1    Tassotto, M.L.2    Mathews, C.K.3
  • 6
    • 0020513510 scopus 로고
    • Rapid changes in deoxynucleoside triphosphate pools in mammalian cells treated with mutagens
    • S.K. Das, EP. Benditt, and L.A. Loeb Rapid changes in deoxynucleoside triphosphate pools in mammalian cells treated with mutagens Biochem. Biophys. Res. Commun. 114 1983 458 464
    • (1983) Biochem. Biophys. Res. Commun. , vol.114 , pp. 458-464
    • Das, S.K.1    Benditt, E.P.2    Loeb, L.A.3
  • 7
    • 0036894880 scopus 로고    scopus 로고
    • Structural basis for uracil recognition by archaeal family B DNA polymerises
    • M.J. Fogg, L.H. Pearl, and B.A. Connolly Structural basis for uracil recognition by archaeal family B DNA polymerises Nat. Struct. Biol. 9 2002 922 927
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 922-927
    • Fogg, M.J.1    Pearl, L.H.2    Connolly, B.A.3
  • 9
    • 0001486263 scopus 로고
    • Enzymatic synthesis of nucleic acid-like polynucleotides
    • M. Grundberg-Manago, PJ. Oritz, and S. Ochoa Enzymatic synthesis of nucleic acid-like polynucleotides Science 122 1955 907 910
    • (1955) Science , vol.122 , pp. 907-910
    • Grundberg-Manago, M.1    Oritz, P.J.2    Ochoa, S.3
  • 10
    • 0028832342 scopus 로고
    • Gemcitabine: A modulator of intracellular nucleotide and deoxynucleotide metabolism
    • V. Heinemann, L. Schulz, RD. Issels, and W. Plunkett Gemcitabine: a modulator of intracellular nucleotide and deoxynucleotide metabolism Semin. Oncol. 22 1995 11 18
    • (1995) Semin. Oncol. , vol.22 , pp. 11-18
    • Heinemann, V.1    Schulz, L.2    Issels, R.D.3    Plunkett, W.4
  • 11
    • 0039792280 scopus 로고    scopus 로고
    • Getting a grip: Polymerases and their substrate complexes
    • J. Jager, and J.D. Pata Getting a grip: polymerases and their substrate complexes Curr. Opin. Struct. Biol. 9 1999 21 28
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 21-28
    • Jager, J.1    Pata, J.D.2
  • 12
    • 0027074765 scopus 로고
    • Alterations in nucleotide pools in rats fed diets deficient in choline methionine and/or folic acid
    • S.J. James, D.R. Cross, and B.J. Miller Alterations in nucleotide pools in rats fed diets deficient in choline methionine and/or folic acid Carcinogenesis 13 1992 2471 2474
    • (1992) Carcinogenesis , vol.13 , pp. 2471-2474
    • James, S.J.1    Cross, D.R.2    Miller, B.J.3
  • 13
    • 0027220197 scopus 로고
    • Conformational coupling in DNA polymerase fidelity
    • K.A. Johnson Conformational coupling in DNA polymerase fidelity Annu. Rev. Biochem. 62 1993 685 713
    • (1993) Annu. Rev. Biochem. , vol.62 , pp. 685-713
    • Johnson, K.A.1
  • 14
    • 8544278025 scopus 로고    scopus 로고
    • DNA polymerase fidelity: Kinetics, structure and checkpoints
    • C.M. Joyce, and S.J. Benkovic DNA polymerase fidelity: kinetics, structure and checkpoints Biochem 43 2004 14317 14324
    • (2004) Biochem , vol.43 , pp. 14317-14324
    • Joyce, C.M.1    Benkovic, S.J.2
  • 15
    • 0031717603 scopus 로고    scopus 로고
    • Deoxyribonucleoside triphosphate pool imbalances in vivo are associated with an increased retroviral mutation rate
    • JG. Julias, and V.K. Pathak Deoxyribonucleoside triphosphate pool imbalances in vivo are associated with an increased retroviral mutation rate J. Virol. 72 1998 7941 7949
    • (1998) J. Virol. , vol.72 , pp. 7941-7949
    • Julias, J.G.1    Pathak, V.K.2
  • 16
    • 0027491514 scopus 로고
    • Decrease in deoxyribonucleotide triphosphate pools and induction of alkaline-labile sites in mouse bone marrow cells by multiple treatments with methotrexate
    • Y. Kasahara, Y. Nakai, D. Miura, H. Kanatani, K. Yagi, K. Hirabayashi, Y. Takahashi, and Y. Izawa Decrease in deoxyribonucleotide triphosphate pools and induction of alkaline-labile sites in mouse bone marrow cells by multiple treatments with methotrexate Mutat. Res. 319 1993 143 149
    • (1993) Mutat. Res. , vol.319 , pp. 143-149
    • Kasahara, Y.1    Nakai, Y.2    Miura, D.3    Kanatani, H.4    Yagi, K.5    Hirabayashi, K.6    Takahashi, Y.7    Izawa, Y.8
  • 17
    • 0032518524 scopus 로고    scopus 로고
    • Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    • J.R. Kiefer, C. Mao, J.C. Braman, and L.S. Beese Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal Nature 391 1998 304 347
    • (1998) Nature , vol.391 , pp. 304-347
    • Kiefer, J.R.1    Mao, C.2    Braman, J.C.3    Beese, L.S.4
  • 18
    • 2342419732 scopus 로고    scopus 로고
    • DNA replication fidelity
    • T.A. Kunkel DNA replication fidelity J. Biol. Chem. 279 2004 16895 16898
    • (2004) J. Biol. Chem. , vol.279 , pp. 16895-16898
    • Kunkel, T.A.1
  • 19
    • 0041816481 scopus 로고    scopus 로고
    • Discovery of DNA polymerase
    • I.R. Lehman Discovery of DNA polymerase J. Biol. Chem. 278 2003 34733 34738
    • (2003) J. Biol. Chem. , vol.278 , pp. 34733-34738
    • Lehman, I.R.1
  • 20
    • 0034864407 scopus 로고    scopus 로고
    • Structural studies of the Klentaq1 DNA polymerase
    • Y. Li, and G. Waksman Structural studies of the Klentaq1 DNA polymerase Curr. Org. Chem. 5 2001 871 883
    • (2001) Curr. Org. Chem. , vol.5 , pp. 871-883
    • Li, Y.1    Waksman, G.2
  • 21
    • 0016257644 scopus 로고
    • Heat-induced deamination of cytosine residues in deoxyribonucleic acid
    • T. Lindahl, and B. Nyberg Heat-induced deamination of cytosine residues in deoxyribonucleic acid Biochem 13 1974 3405 3410
    • (1974) Biochem , vol.13 , pp. 3405-3410
    • Lindahl, T.1    Nyberg, B.2
  • 22
    • 0037138464 scopus 로고    scopus 로고
    • Effects of biological DNA precursor pool asymmetry upon accuracy of DNA replication in vitro
    • S.A. Martomo, and C.K. Mathews Effects of biological DNA precursor pool asymmetry upon accuracy of DNA replication in vitro Mutat. Res. 499 2002 197 211
    • (2002) Mutat. Res. , vol.499 , pp. 197-211
    • Martomo, S.A.1    Mathews, C.K.2
  • 23
    • 0026863789 scopus 로고
    • DNA precursor asymmetries, replication fidelity, and variable genome evolution
    • C.K. Mathews, and J. Ji DNA precursor asymmetries, replication fidelity, and variable genome evolution Bioessays 14 1992 295 301
    • (1992) Bioessays , vol.14 , pp. 295-301
    • Mathews, C.K.1    Ji, J.2
  • 24
    • 0032860818 scopus 로고    scopus 로고
    • Uracil misincorporation, DNA strand breaks, and gene amplification are associated with tumorigenic cell transformation in folate deficient/repleted Chinese hamster ovary cells
    • S. Melnyk, M. Pogribna, B.J. Miller, A.G. Basnakian, I.P. Pogribny, and S.J. James Uracil misincorporation, DNA strand breaks, and gene amplification are associated with tumorigenic cell transformation in folate deficient/repleted Chinese hamster ovary cells Cancer Lett. 146 1999 35 44
    • (1999) Cancer Lett. , vol.146 , pp. 35-44
    • Melnyk, S.1    Pogribna, M.2    Miller, B.J.3    Basnakian, A.G.4    Pogribny, I.P.5    James, S.J.6
  • 25
    • 0000870544 scopus 로고
    • Die Kinetik der Invertinwirkung [Kinetics of Invertase Action]
    • L. Michaelis, and M.L. Menten Die Kinetik der Invertinwirkung [Kinetics of Invertase Action] Biochem. Z. 49 1913 333 369
    • (1913) Biochem. Z. , vol.49 , pp. 333-369
    • Michaelis, L.1    Menten, M.L.2
  • 26
    • 1442326735 scopus 로고    scopus 로고
    • DNA polymerases as targets of anticancer nucleosides
    • S. Miura, and S. Izuta DNA polymerases as targets of anticancer nucleosides Curr. Drug Targets 5 2004 191 195
    • (2004) Curr. Drug Targets , vol.5 , pp. 191-195
    • Miura, S.1    Izuta, S.2
  • 27
    • 0023294732 scopus 로고
    • Alternative to the steady-state method: Derivation of reaction rates from first-passage times and pathway probabilities
    • J. Ninio Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities Proc. Natl. Acad. Sci. U.S.A. 84 1987 663 667
    • (1987) Proc. Natl. Acad. Sci. U.S.A. , vol.84 , pp. 663-667
    • Ninio, J.1
  • 28
    • 0026033193 scopus 로고
    • Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant
    • S.S. Patel, I. Wong, and K.A. Johnson Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant Biochem 30 1991 511 525
    • (1991) Biochem , vol.30 , pp. 511-525
    • Patel, S.S.1    Wong, I.2    Johnson, K.A.3
  • 29
    • 0035179561 scopus 로고    scopus 로고
    • Mutant mitochondrial thymidine kinase in mitochondrial DNA depletion myopathy
    • A. Saada, A. Shaag, H. Mandel, Y. Nevo, S. Eriksson, and O. Elpeleg Mutant mitochondrial thymidine kinase in mitochondrial DNA depletion myopathy Nat. Genet. 29 2001 342 344
    • (2001) Nat. Genet. , vol.29 , pp. 342-344
    • Saada, A.1    Shaag, A.2    Mandel, H.3    Nevo, Y.4    Eriksson, S.5    Elpeleg, O.6
  • 30
    • 0022372670 scopus 로고
    • Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia
    • R.K. Saiki, S. Scharf, F. Faloona, K.B. Mullis, G.T. Horn, H.A. Erlich, and N. Arnheim Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia Science 1985 230
    • (1985) Science , pp. 230
    • Saiki, R.K.1    Scharf, S.2    Faloona, F.3    Mullis, K.B.4    Horn, G.T.5    Erlich, H.A.6    Arnheim, N.7
  • 32
    • 0018893023 scopus 로고
    • DNA sequence analysis by primed synthesis
    • A.J. Smith DNA sequence analysis by primed synthesis Methods Enzymol. 65 1980 560 580
    • (1980) Methods Enzymol. , vol.65 , pp. 560-580
    • Smith, A.J.1
  • 33
    • 0242582958 scopus 로고    scopus 로고
    • Deoxyribonucleotide pool imbalance stimulates deletions in HeLa cell mitochondrial DNA
    • S. Song, L.J. Wheeler, and C.K. Mathews Deoxyribonucleotide pool imbalance stimulates deletions in HeLa cell mitochondrial DNA J. Biol. Chem. 278 2003 43893 43896
    • (2003) J. Biol. Chem. , vol.278 , pp. 43893-43896
    • Song, S.1    Wheeler, L.J.2    Mathews, C.K.3
  • 34
    • 0021031204 scopus 로고
    • UV-induced imbalance of the deoxyribonucleoside triphosphate pool in E. coli
    • K. Suzuki, M. Miyaki, T. Ono, H. Mori, H. Moriya, and T. Kato UV-induced imbalance of the deoxyribonucleoside triphosphate pool in E. coli Mutat. Res. 122 1983 293 298
    • (1983) Mutat. Res. , vol.122 , pp. 293-298
    • Suzuki, K.1    Miyaki, M.2    Ono, T.3    Mori, H.4    Moriya, H.5    Kato, T.6
  • 35
    • 0035098779 scopus 로고    scopus 로고
    • Hyperthermophilic enzymes: Sources, uses and molecular mechanisms for thermostability
    • C. Vieille, and G.J. Zeikus Hyperthermophilic enzymes: sources, uses and molecular mechanisms for thermostability Microbiol. Mol. Biol. Rev. 65 2001 1 43
    • (2001) Microbiol. Mol. Biol. Rev. , vol.65 , pp. 1-43
    • Vieille, C.1    Zeikus, G.J.2
  • 36
    • 0037470065 scopus 로고    scopus 로고
    • Kinetic properties of mutant human thymidine kinase 2 suggest a mechanism for mitochondrial DNA depletion myopathy
    • L. Wang, A. Saada, and S. Eriksson Kinetic properties of mutant human thymidine kinase 2 suggest a mechanism for mitochondrial DNA depletion myopathy J. Biol. Chem. 278 2003 6963 6968
    • (2003) J. Biol. Chem. , vol.278 , pp. 6963-6968
    • Wang, L.1    Saada, A.2    Eriksson, S.3
  • 37
    • 0024258165 scopus 로고
    • Detection of deoxyribonucleoside-triphosphate imbalance death-induced DNA double strand breakage in FM3A cells by orthogonal-field-alternation gel electrophoresis (OFAGE)
    • Y. Wataya, T. Hazawa, K. Watanabe, Y. Hirota, and A. Yoshioka-Hiramoto Detection of deoxyribonucleoside-triphosphate imbalance death-induced DNA double strand breakage in FM3A cells by orthogonal-field-alternation gel electrophoresis (OFAGE) Nucl. Acids Symp. Ser. 1988 53 55
    • (1988) Nucl. Acids Symp. Ser. , pp. 53-55
    • Wataya, Y.1    Hazawa, T.2    Watanabe, K.3    Hirota, Y.4    Yoshioka-Hiramoto, A.5
  • 38
    • 3142571337 scopus 로고    scopus 로고
    • Principles of rapid polymerase chain reactions: Mathematical modeling and experimental verification
    • S.E. Whitney, S. Alugupally, R.M. Nelson, and H.J. Viljoen Principles of rapid polymerase chain reactions: mathematical modeling and experimental verification Comp. Biol. Chem. 28 2004 195 209
    • (2004) Comp. Biol. Chem. , vol.28 , pp. 195-209
    • Whitney, S.E.1    Alugupally, S.2    Nelson, R.M.3    Viljoen, H.J.4
  • 39
    • 0026683367 scopus 로고
    • Imbalance of deoxyribonucleoside triphosphates and DNA double-strand breaks in mouse mammary tumor FM3A cells treated in vitro with an antineoplastic tropolone derivative
    • M. Yamato, Y. Hirota, S. Yoshida, S. Tanaka, T. Morita, J. Sakai, K. Hashigaki, H. Hayatsu, and Y. Wataya Imbalance of deoxyribonucleoside triphosphates and DNA double-strand breaks in mouse mammary tumor FM3A cells treated in vitro with an antineoplastic tropolone derivative Jpn. J. Cancer Res. 83 1992 661 668
    • (1992) Jpn. J. Cancer Res. , vol.83 , pp. 661-668
    • Yamato, M.1    Hirota, Y.2    Yoshida, S.3    Tanaka, S.4    Morita, T.5    Sakai, J.6    Hashigaki, K.7    Hayatsu, H.8    Wataya, Y.9
  • 40
    • 0023655202 scopus 로고
    • Deoxyribonucleoside triphosphate imbalance. 5-Fluorodeoxyuridine-induced DNA double strand breaks in mouse FM3A cells and the mechanism of cell death
    • A. Yoshioka, S. Tanaka, O. Hiraoka, Y. Koyama, Y. Hirota, D. Ayusawa, T. Seno, C. Garrett, and Y. Wataya Deoxyribonucleoside triphosphate imbalance. 5-Fluorodeoxyuridine-induced DNA double strand breaks in mouse FM3A cells and the mechanism of cell death J. Biol. Chem. 262 1987 8235 8241
    • (1987) J. Biol. Chem. , vol.262 , pp. 8235-8241
    • Yoshioka, A.1    Tanaka, S.2    Hiraoka, O.3    Koyama, Y.4    Hirota, Y.5    Ayusawa, D.6    Seno, T.7    Garrett, C.8    Wataya, Y.9


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