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Volumn 6, Issue 3, 2009, Pages

Open-system thermodynamic analysis of DNA polymerase fidelity

Author keywords

[No Author keywords available]

Indexed keywords

CELL DNA; DNA POLYMERASE; EXONUCLEASE; DNA; DNA DIRECTED DNA POLYMERASE; NUCLEOTIDE;

EID: 68249140442     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/6/3/036011     Document Type: Article
Times cited : (42)

References (48)
  • 1
    • 0000359208 scopus 로고
    • Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity
    • Hopfield J J 1974 Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity Proc. Natl. Acad. Sci. USA 71 4135-9
    • (1974) Proc. Natl. Acad. Sci. USA , vol.71 , pp. 4135-4139
    • Hopfield, J.J.1
  • 2
    • 0016793283 scopus 로고
    • Kinetic amplification of enzyme discrimination
    • Ninio J 1975 Kinetic amplification of enzyme discrimination Biochime 57 587-95
    • (1975) Biochime , vol.57 , pp. 587-595
    • Ninio, J.1
  • 3
    • 0015499993 scopus 로고
    • Enzymatic synthesis of deoxyribonucleic acid: XXXVI. A proofreading function for the 3' to 5' exonuclease activity in deoxyribonucleic acid polymerases
    • Brutlag D and Kornberg A 1972 Enzymatic synthesis of deoxyribonucleic acid: XXXVI. A proofreading function for the 3' to 5' exonuclease activity in deoxyribonucleic acid polymerases J. Biol. Chem. 247 241-8
    • (1972) J. Biol. Chem. , vol.247 , pp. 241-248
    • Brutlag, D.1    Kornberg, A.2
  • 4
    • 8544278025 scopus 로고    scopus 로고
    • DNA polymerase fidelity: Kinetics, structure, and checkpoints
    • Joyce C M and Benkovic S J 2004 DNA polymerase fidelity: kinetics, structure, and checkpoints Biochemistry 43 14317-24
    • (2004) Biochemistry , vol.43 , pp. 14317-14324
    • Joyce, C.M.1    Benkovic, S.J.2
  • 5
    • 33747462891 scopus 로고    scopus 로고
    • A new paradigm for DNA polymerase specificifity
    • Tsai Y-C and Johnson K A 2006 A new paradigm for DNA polymerase specificifity Biochemistry 45 9675-87
    • (2006) Biochemistry , vol.45 , pp. 9675-9687
    • Tsai, Y.-C.1    Johnson, K.A.2
  • 6
    • 0141448966 scopus 로고    scopus 로고
    • Thermodynamic and extrathermodynamic requirements of enzyme catalysis
    • Wolfenden R 2003 Thermodynamic and extrathermodynamic requirements of enzyme catalysis Biophys. Chem. 105 559-72
    • (2003) Biophys. Chem. , vol.105 , pp. 559-572
    • Wolfenden, R.1
  • 7
    • 33748107406 scopus 로고    scopus 로고
    • Phosphorylation energy hypothesis: Open chemical systems and their biological functions
    • Qian H 2007 Phosphorylation energy hypothesis: open chemical systems and their biological functions Annu. Rev. Phys. Chem. 58 113-42
    • (2007) Annu. Rev. Phys. Chem. , vol.58 , pp. 113-142
    • Qian, H.1
  • 8
    • 33748096830 scopus 로고    scopus 로고
    • Open-system nonequilibrium steady-state: Statistical thermodynamics, fluctuations and chemical oscillations
    • Qian H 2006 Open-system nonequilibrium steady-state: statistical thermodynamics, fluctuations and chemical oscillations J. Phys. Chem. B 110 15063-74
    • (2006) J. Phys. Chem. B , vol.110 , pp. 15063-15074
    • Qian, H.1
  • 9
    • 0019160924 scopus 로고
    • Fidélité d'une reaction de polymerisation selon la proximité de l'équilibre
    • Herbomel P and Ninio J 1980 Fidélité d'une reaction de polymerisation selon la proximité de l'équilibre C. R. Acad. Sci. D 291 881-4
    • (1980) C. R. Acad. Sci. D , vol.291 , pp. 881-884
    • Herbomel, P.1    Ninio, J.2
  • 10
    • 0020032054 scopus 로고
    • On the relation between error rates on DNA replication and elementary chemical rate constants
    • Durup J 1982 On the relation between error rates on DNA replication and elementary chemical rate constants J. Theor. Biol. 94 607-32
    • (1982) J. Theor. Biol. , vol.94 , pp. 607-632
    • Durup, J.1
  • 11
    • 0018125962 scopus 로고
    • Enzymatic determinants of DNA polymerase accuracy: Theory of coliphage T4 polymerase mechanism
    • Galas D J and Branscomb E W 1978 Enzymatic determinants of DNA polymerase accuracy: theory of coliphage T4 polymerase mechanism J. Mol. Biol. 124 653-87
    • (1978) J. Mol. Biol. , vol.124 , pp. 653-687
    • Galas, D.J.1    Branscomb, E.W.2
  • 15
    • 0033613387 scopus 로고    scopus 로고
    • A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases
    • Yan J, Magnasco M O and Marko J F 1999 A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases Nature 401 932-5
    • (1999) Nature , vol.401 , pp. 932-935
    • Yan, J.1    Magnasco, M.O.2    Marko, J.F.3
  • 17
    • 0036109556 scopus 로고    scopus 로고
    • The role of proofreading in signal transduction specificity
    • Swain P S and Siggia E D 2002 The role of proofreading in signal transduction specificity Biophys. J. 82 2928-33
    • (2002) Biophys. J. , vol.82 , pp. 2928-2933
    • Swain, P.S.1    Siggia, E.D.2
  • 19
    • 46749083416 scopus 로고    scopus 로고
    • Cooperativity and specificity in enzyme kinetics: A single-molecule time-based perspective
    • Qian H 2008 Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective Biophys. J. 95 10-7
    • (2008) Biophys. J. , vol.95 , pp. 10-17
    • Qian, H.1
  • 20
    • 33748094844 scopus 로고    scopus 로고
    • Reducing intrinsic biochemical noise in cells and its thermodynamic limit
    • Qian H 2006 Reducing intrinsic biochemical noise in cells and its thermodynamic limit J. Mol. Biol. 362 387-92
    • (2006) J. Mol. Biol. , vol.362 , pp. 387-392
    • Qian, H.1
  • 21
    • 0019307935 scopus 로고
    • Implications of treadmilling for the stability and polarity of actin and tubulin polymers in vivo
    • Kirschner M W 1980 Implications of treadmilling for the stability and polarity of actin and tubulin polymers in vivo J. Cell. Biol. 86 330-4
    • (1980) J. Cell. Biol. , vol.86 , pp. 330-334
    • Kirschner, M.W.1
  • 22
    • 33645700220 scopus 로고    scopus 로고
    • Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen
    • Saffarian S, Qian H, Collier I E, Elson E L and Goldberg G 2006 Powering a burnt bridges Brownian ratchet: a model for an extracellular motor driven by proteolysis of collagen Phys. Rev. E 73 041909
    • (2006) Phys. Rev. e , vol.73 , pp. 041909
    • Saffarian, S.1    Qian, H.2    Collier, I.E.3    Elson, E.L.4    Goldberg, G.5
  • 25
    • 0344736713 scopus 로고    scopus 로고
    • The thermodynamics of template-directed DNA synthesis: Base insertion and extension enthalpies
    • Minetti C A S A et al 2003 The thermodynamics of template-directed DNA synthesis: base insertion and extension enthalpies Proc. Natl. Acad. Sci. USA 100 14719-24
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 14719-14724
    • Minetti, C.A.S.A.1
  • 26
    • 0030924437 scopus 로고    scopus 로고
    • Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replicationfidelit
    • Goodman M F 1997 Hydrogen bonding revisited: geometric selection as a principal determinant of DNA replicationfidelit Proc. Natl. Acad. Sci. USA 94 10493-95
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 10493-10495
    • Goodman, M.F.1
  • 27
    • 0015524054 scopus 로고
    • Biochemistry of deoxyribonucleic acid-defective amber mutants of bacteriophage T4: III. Nucleotide pools
    • Mathews C 1972 Biochemistry of deoxyribonucleic acid-defective amber mutants of bacteriophage T4: III. Nucleotide pools J. Biol. Chem. 247 7430-8
    • (1972) J. Biol. Chem. , vol.247 , pp. 7430-7438
    • Mathews, C.1
  • 30
    • 33846576261 scopus 로고    scopus 로고
    • Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae
    • Chabes A and Stillman B 2007 Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae Proc. Natl. Acad. Sci. USA 104 1183-8
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 1183-1188
    • Chabes, A.1    Stillman, B.2
  • 31
    • 0017730110 scopus 로고
    • Are further kinetic amplification schemes possible?
    • Ninio J 1977 Are further kinetic amplification schemes possible? Biochimie 59 759-60
    • (1977) Biochimie , vol.59 , pp. 759-760
    • Ninio, J.1
  • 32
    • 33744969828 scopus 로고    scopus 로고
    • Energy deregulation: Licensing tumors to grow
    • Garber K 2006 Energy deregulation: licensing tumors to grow Science 312 1158-9
    • (2006) Science , vol.312 , pp. 1158-1159
    • Garber, K.1
  • 33
    • 33745149291 scopus 로고    scopus 로고
    • P53 regulates mitochondrial respiration
    • Matoba S et al 2006 P53 regulates mitochondrial respiration Science 312 1650-3
    • (2006) Science , vol.312 , pp. 1650-1653
    • Matoba, S.1
  • 34
    • 24944546620 scopus 로고    scopus 로고
    • Genetic instability in cancer: Theory and experiment
    • Beckman R A and Loeb L A 2005 Genetic instability in cancer: theory and experiment Semin. Cancer Biol. 15 423-35
    • (2005) Semin. Cancer Biol. , vol.15 , pp. 423-435
    • Beckman, R.A.1    Loeb, L.A.2
  • 36
    • 33745246534 scopus 로고    scopus 로고
    • Intracellular nucleotides act as critical prosurvival factors by binding to cytochrome c and inhibiting apoptosome
    • Chandra D et al 2006 Intracellular nucleotides act as critical prosurvival factors by binding to cytochrome c and inhibiting apoptosome Cell 125 1333-46
    • (2006) Cell , vol.125 , pp. 1333-1346
    • Chandra, D.1
  • 37
    • 4243190170 scopus 로고    scopus 로고
    • Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes
    • Springer M, Wykoff D D, Miller N and O'Shea E K 2003 Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes PLoS Biol. 1 261-70
    • (2003) PLoS Biol. , vol.1 , pp. 8-270
    • Springer, M.1    Wykoff, D.D.2    Miller, N.3    O'Shea, E.K.4
  • 38
    • 0032760481 scopus 로고    scopus 로고
    • Progress of a half century in the study of the Luria Delbrück distribution
    • Zheng Q 1999 Progress of a half century in the study of the Luria Delbrück distribution Math. Biosci. 162 1-32
    • (1999) Math. Biosci. , vol.162 , pp. 1-32
    • Zheng, Q.1
  • 39
    • 50149110195 scopus 로고    scopus 로고
    • The nonequilibrium mechanism for ultrasensitivity in a biological switch: Sensing by Maxwell's demons
    • Tu Y 2008 The nonequilibrium mechanism for ultrasensitivity in a biological switch: sensing by Maxwell's demons Proc. Natl. Acad. Sci. USA 105 11737-41
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 11737-11741
    • Tu, Y.1
  • 40
    • 0023770718 scopus 로고
    • Kinetic mechanism whereby DNA polymerase i (Klenow) replicated DNA with high fidelity
    • Kuchta R D, Benkovic P and Benkovic S J 1988 Kinetic mechanism whereby DNA polymerase I (Klenow) replicated DNA with high fidelity Biochemistry 27 6716-25
    • (1988) Biochemistry , vol.27 , pp. 6716-6725
    • Kuchta, R.D.1    Benkovic, P.2    Benkovic, S.J.3
  • 41
    • 0031917762 scopus 로고    scopus 로고
    • DNA polymerase fidelity: From genetics toward a biochemical understanding
    • Goodman M F and Kuchnir F D 1998 DNA polymerase fidelity: from genetics toward a biochemical understanding Genetics 148 1475-82
    • (1998) Genetics , vol.148 , pp. 1475-1482
    • Goodman, M.F.1    Kuchnir, F.D.2
  • 42
    • 0019134996 scopus 로고
    • The energy relay: A proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis
    • Hopfield J J 1980 The energy relay: a proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis Proc. Natl. Acad. Sci. USA 77 5248-52
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 5248-5252
    • Hopfield, J.J.1
  • 43
    • 0026556058 scopus 로고
    • The elongation-termination decision in transcription
    • von Hippel P H and Yager T D 1992 The elongation-termination decision in transcription Science 255 809-12
    • (1992) Science , vol.255 , pp. 809-812
    • Von Hippel, P.H.1    Yager, T.D.2
  • 44
    • 34547864244 scopus 로고    scopus 로고
    • Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase
    • Luo G, Wang M, Konigsberg W H and Xie X S 2007 Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase Proc. Natl. Acad. Sci. USA 104 12610-5
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 12610-12615
    • Luo, G.1    Wang, M.2    Konigsberg, W.H.3    Xie, X.S.4
  • 46
    • 0030731335 scopus 로고    scopus 로고
    • A simple theory of motor protein kinetics and energetics
    • Qian H 1997 A simple theory of motor protein kinetics and energetics Biophys. Chem. 67 263-7
    • (1997) Biophys. Chem. , vol.67 , pp. 263-267
    • Qian, H.1
  • 47
    • 33746086718 scopus 로고    scopus 로고
    • Generalized Haldane equation and fluctuation theorem in the steady state cycle kinetics of single enzymes
    • Qian H and Xie X S 2006 Generalized Haldane equation and fluctuation theorem in the steady state cycle kinetics of single enzymes Phys. Rev. E 74 010902
    • (2006) Phys. Rev. e , vol.74 , pp. 010902
    • Qian, H.1    Xie, X.S.2


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