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Volumn 53, Issue 17, 2014, Pages 2804-2814

Recent insight into the kinetic mechanisms and conformational dynamics of Y-family DNA polymerases

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; KINETICS; POLYMERS; REPAIR; SUBSTRATES;

EID: 84899790966     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi5000405     Document Type: Article
Times cited : (35)

References (137)
  • 2
    • 0033581011 scopus 로고    scopus 로고
    • DNA polymerases: Structural diversity and common mechanisms
    • Steitz, T. A. (1999) DNA polymerases: Structural diversity and common mechanisms J. Biol. Chem. 274, 17395-17398
    • (1999) J. Biol. Chem. , vol.274 , pp. 17395-17398
    • Steitz, T.A.1
  • 3
    • 0032518374 scopus 로고    scopus 로고
    • A mechanism for all polymerases
    • Steitz, T. A. (1998) A mechanism for all polymerases Nature 391, 231-232
    • (1998) Nature , vol.391 , pp. 231-232
    • Steitz, T.A.1
  • 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, 14317-14324
    • (2004) Biochemistry , vol.43 , pp. 14317-14324
    • Joyce, C.M.1    Benkovic, S.J.2
  • 5
    • 0032535528 scopus 로고    scopus 로고
    • Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation
    • Li, Y., Korolev, S., and Waksman, G. (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation EMBO J. 17, 7514-7525
    • (1998) EMBO J. , vol.17 , pp. 7514-7525
    • Li, Y.1    Korolev, S.2    Waksman, G.3
  • 6
    • 0030930760 scopus 로고    scopus 로고
    • Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism
    • Sawaya, M. R., Prasad, R., Wilson, S. H., Kraut, J., and Pelletier, H. (1997) Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism Biochemistry 36, 11205-11215
    • (1997) Biochemistry , vol.36 , pp. 11205-11215
    • Sawaya, M.R.1    Prasad, R.2    Wilson, S.H.3    Kraut, J.4    Pelletier, H.5
  • 7
    • 0027231782 scopus 로고
    • Structure of DNA polymerase i Klenow fragment bound to duplex DNA
    • Beese, L. S., Derbyshire, V., and Steitz, T. A. (1993) Structure of DNA polymerase I Klenow fragment bound to duplex DNA Science 260, 352-355
    • (1993) Science , vol.260 , pp. 352-355
    • Beese, L.S.1    Derbyshire, V.2    Steitz, T.A.3
  • 8
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution
    • Doublie, S., Tabor, S., Long, A. M., Richardson, C. C., and Ellenberger, T. (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution Nature 391, 251-258
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublie, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 9
    • 0035812849 scopus 로고    scopus 로고
    • Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication
    • Ling, H., Boudsocq, F., Woodgate, R., and Yang, W. (2001) Crystal structure of a Y-family DNA polymerase in action: A mechanism for error-prone and lesion-bypass replication Cell 107, 91-102
    • (2001) Cell , vol.107 , pp. 91-102
    • Ling, H.1    Boudsocq, F.2    Woodgate, R.3    Yang, W.4
  • 10
    • 0037205001 scopus 로고    scopus 로고
    • Specialized DNA polymerases, cellular survival, and the genesis of mutations
    • Friedberg, E. C., Wagner, R., and Radman, M. (2002) Specialized DNA polymerases, cellular survival, and the genesis of mutations Science 296, 1627-1630
    • (2002) Science , vol.296 , pp. 1627-1630
    • Friedberg, E.C.1    Wagner, R.2    Radman, M.3
  • 12
    • 0034720285 scopus 로고    scopus 로고
    • Low fidelity DNA synthesis by human DNA polymerase-π
    • Matsuda, T., Bebenek, K., Masutani, C., Hanaoka, F., and Kunkel, T. A. (2000) Low fidelity DNA synthesis by human DNA polymerase-π Nature 404, 1011-1013
    • (2000) Nature , vol.404 , pp. 1011-1013
    • Matsuda, T.1    Bebenek, K.2    Masutani, C.3    Hanaoka, F.4    Kunkel, T.A.5
  • 15
    • 0034738983 scopus 로고    scopus 로고
    • Eukaryotic polymerases and act sequentially to bypass DNA lesions
    • Johnson, R. E., Washington, M. T., Haracska, L., Prakash, S., and Prakash, L. (2000) Eukaryotic polymerases and act sequentially to bypass DNA lesions Nature 406, 1015-1019
    • (2000) Nature , vol.406 , pp. 1015-1019
    • Johnson, R.E.1    Washington, M.T.2    Haracska, L.3    Prakash, S.4    Prakash, L.5
  • 16
    • 0034327552 scopus 로고    scopus 로고
    • Human DNA polymerase synthesizes DNA with extraordinarily low fidelity
    • Zhang, Y., Yuan, F., Xin, H., Wu, X., Rajpal, D. K., Yang, D., and Wang, Z. (2000) Human DNA polymerase synthesizes DNA with extraordinarily low fidelity Nucleic Acids Res. 28, 4147-4156
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4147-4156
    • Zhang, Y.1    Yuan, F.2    Xin, H.3    Wu, X.4    Rajpal, D.K.5    Yang, D.6    Wang, Z.7
  • 17
    • 0035850235 scopus 로고    scopus 로고
    • Translesion synthesis by the UmuC family of DNA polymerases
    • Wang, Z. (2001) Translesion synthesis by the UmuC family of DNA polymerases Mutat. Res. 486, 59-70
    • (2001) Mutat. Res. , vol.486 , pp. 59-70
    • Wang, Z.1
  • 18
    • 2542571187 scopus 로고    scopus 로고
    • Pre-Steady-State Kinetic Studies of the Fidelity and Mechanism of Polymerization Catalyzed by Truncated Human DNA Polymerase λ
    • Fiala, K. A., Abdel-Gawad, W., and Suo, Z. (2004) Pre-Steady-State Kinetic Studies of the Fidelity and Mechanism of Polymerization Catalyzed by Truncated Human DNA Polymerase λ Biochemistry 43, 6751-6762
    • (2004) Biochemistry , vol.43 , pp. 6751-6762
    • Fiala, K.A.1    Abdel-Gawad, W.2    Suo, Z.3
  • 19
    • 1242307762 scopus 로고    scopus 로고
    • Mechanism of DNA Polymerization Catalyzed by Sulfolobus solfataricus P2 DNA Polymerase IV
    • Fiala, K. A. and Suo, Z. (2004) Mechanism of DNA Polymerization Catalyzed by Sulfolobus solfataricus P2 DNA Polymerase IV Biochemistry 43, 2116-2125
    • (2004) Biochemistry , vol.43 , pp. 2116-2125
    • Fiala, K.A.1    Suo, Z.2
  • 20
    • 78650647927 scopus 로고    scopus 로고
    • Pre-steady-state kinetic analysis of the incorporation of anti-HIV nucleotide analogs catalyzed by human X- and Y-family DNA polymerases
    • Brown, J. A., Pack, L. R., Fowler, J. D., and Suo, Z. (2011) Pre-steady-state kinetic analysis of the incorporation of anti-HIV nucleotide analogs catalyzed by human X- and Y-family DNA polymerases Antimicrob. Agents Chemother. 55, 276-283
    • (2011) Antimicrob. Agents Chemother. , vol.55 , pp. 276-283
    • Brown, J.A.1    Pack, L.R.2    Fowler, J.D.3    Suo, Z.4
  • 21
    • 84862910201 scopus 로고    scopus 로고
    • Presteady state kinetic investigation of the incorporation of anti-hepatitis B nucleotide analogues catalyzed by noncanonical human DNA polymerases
    • Brown, J. A., Pack, L. R., Fowler, J. D., and Suo, Z. (2012) Presteady state kinetic investigation of the incorporation of anti-hepatitis B nucleotide analogues catalyzed by noncanonical human DNA polymerases Chem. Res. Toxicol. 25, 225-233
    • (2012) Chem. Res. Toxicol. , vol.25 , pp. 225-233
    • Brown, J.A.1    Pack, L.R.2    Fowler, J.D.3    Suo, Z.4
  • 22
    • 0034762679 scopus 로고    scopus 로고
    • Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus
    • Silvian, L. F., Toth, E. A., Pham, P., Goodman, M. F., and Ellenberger, T. (2001) Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus Nat. Struct. Biol. 8, 984-989
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 984-989
    • Silvian, L.F.1    Toth, E.A.2    Pham, P.3    Goodman, M.F.4    Ellenberger, T.5
  • 23
    • 3543028588 scopus 로고    scopus 로고
    • Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication
    • Boudsocq, F., Kokoska, R. J., Plosky, B. S., Vaisman, A., Ling, H., Kunkel, T. A., Yang, W., and Woodgate, R. (2004) Investigating the role of the little finger domain of Y-family DNA polymerases in low fidelity synthesis and translesion replication J. Biol. Chem. 279, 32932-32940
    • (2004) J. Biol. Chem. , vol.279 , pp. 32932-32940
    • Boudsocq, F.1    Kokoska, R.J.2    Plosky, B.S.3    Vaisman, A.4    Ling, H.5    Kunkel, T.A.6    Yang, W.7    Woodgate, R.8
  • 24
    • 0034847259 scopus 로고    scopus 로고
    • Structure of the catalytic core of S cerevisiae DNA polymerase π: Implications for translesion DNA synthesis
    • Trincao, J., Johnson, R. E., Escalante, C. R., Prakash, S., Prakash, L., and Aggarwal, A. K. (2001) Structure of the catalytic core of S. cerevisiae DNA polymerase π: Implications for translesion DNA synthesis Mol. Cell 8, 417-426
    • (2001) Mol. Cell , vol.8 , pp. 417-426
    • Trincao, J.1    Johnson, R.E.2    Escalante, C.R.3    Prakash, S.4    Prakash, L.5    Aggarwal, A.K.6
  • 25
    • 84872158843 scopus 로고    scopus 로고
    • Y-family polymerase conformation is a major determinant of fidelity and translesion specificity
    • Wilson, R. C., Jackson, M. A., and Pata, J. D. (2013) Y-family polymerase conformation is a major determinant of fidelity and translesion specificity Structure 21, 20-31
    • (2013) Structure , vol.21 , pp. 20-31
    • Wilson, R.C.1    Jackson, M.A.2    Pata, J.D.3
  • 28
    • 84899827339 scopus 로고    scopus 로고
    • A summary of Y-family DNA polymerases and a case study of human DNA pol π
    • Yang, W. (2014) A summary of Y-family DNA polymerases and a case study of human DNA pol π Biochemistry 53, DOI: 10.1021/bi500019s
    • (2014) Biochemistry , vol.53
    • Yang, W.1
  • 31
    • 0000918686 scopus 로고    scopus 로고
    • The dinB gene encodes a novel E coli DNA polymerase, DNA Pol IV, involved in mutagenesis
    • Wagner, J., Gruz, P., Kim, S. R., Yamada, M., Matsui, K., Fuchs, R. P., and Nohmi, T. (1999) The dinB gene encodes a novel E. coli DNA polymerase, DNA Pol IV, involved in mutagenesis Mol. Cell 4, 281-286
    • (1999) Mol. Cell , vol.4 , pp. 281-286
    • Wagner, J.1    Gruz, P.2    Kim, S.R.3    Yamada, M.4    Matsui, K.5    Fuchs, R.P.6    Nohmi, T.7
  • 33
    • 0035890599 scopus 로고    scopus 로고
    • Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): An archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic pol π
    • Boudsocq, F., Iwai, S., Hanaoka, F., and Woodgate, R. (2001) Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): An archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic pol π Nucleic Acids Res. 29, 4607-4616
    • (2001) Nucleic Acids Res. , vol.29 , pp. 4607-4616
    • Boudsocq, F.1    Iwai, S.2    Hanaoka, F.3    Woodgate, R.4
  • 34
    • 1242285442 scopus 로고    scopus 로고
    • Pre-Steady-State Kinetic Studies of the Fidelity of Sulfolobus solfataricus P2 DNA Polymerase IV
    • Fiala, K. A. and Suo, Z. (2004) Pre-Steady-State Kinetic Studies of the Fidelity of Sulfolobus solfataricus P2 DNA Polymerase IV Biochemistry 43, 2106-2115
    • (2004) Biochemistry , vol.43 , pp. 2106-2115
    • Fiala, K.A.1    Suo, Z.2
  • 36
    • 35648951199 scopus 로고    scopus 로고
    • What a difference a decade makes: Insights into translesion DNA synthesis
    • Yang, W. and Woodgate, R. (2007) What a difference a decade makes: Insights into translesion DNA synthesis Proc. Natl. Acad. Sci. U.S.A. 104, 15591-15598
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 15591-15598
    • Yang, W.1    Woodgate, R.2
  • 37
    • 77949570579 scopus 로고    scopus 로고
    • Structural diversity of the Y-family DNA polymerases
    • Pata, J. D. (2010) Structural diversity of the Y-family DNA polymerases Biochim. Biophys. Acta 1804, 1124-1135
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 1124-1135
    • Pata, J.D.1
  • 38
    • 84857411787 scopus 로고    scopus 로고
    • Y-family DNA polymerases and their role in tolerance of cellular DNA damage
    • Sale, J. E., Lehmann, A. R., and Woodgate, R. (2012) Y-family DNA polymerases and their role in tolerance of cellular DNA damage Nat. Rev. Mol. Cell Biol. 13, 141-152
    • (2012) Nat. Rev. Mol. Cell Biol. , vol.13 , pp. 141-152
    • Sale, J.E.1    Lehmann, A.R.2    Woodgate, R.3
  • 39
    • 60349088938 scopus 로고    scopus 로고
    • Crystal structure analysis of DNA lesion repair and tolerance mechanisms
    • Schneider, S., Schorr, S., and Carell, T. (2009) Crystal structure analysis of DNA lesion repair and tolerance mechanisms Curr. Opin. Struct. Biol. 19, 87-95
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 87-95
    • Schneider, S.1    Schorr, S.2    Carell, T.3
  • 40
    • 0026033193 scopus 로고
    • Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant
    • Patel, S. S., Wong, I., and Johnson, K. A. (1991) Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant Biochemistry 30, 511-525
    • (1991) Biochemistry , vol.30 , pp. 511-525
    • Patel, S.S.1    Wong, I.2    Johnson, K.A.3
  • 41
    • 0026026192 scopus 로고
    • An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics
    • Wong, I., Patel, S. S., and Johnson, K. A. (1991) An induced-fit kinetic mechanism for DNA replication fidelity: Direct measurement by single-turnover kinetics Biochemistry 30, 526-537
    • (1991) Biochemistry , vol.30 , pp. 526-537
    • Wong, I.1    Patel, S.S.2    Johnson, K.A.3
  • 42
    • 0025963376 scopus 로고
    • Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction
    • Donlin, M. J., Patel, S. S., and Johnson, K. A. (1991) Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction Biochemistry 30, 538-546
    • (1991) Biochemistry , vol.30 , pp. 538-546
    • Donlin, M.J.1    Patel, S.S.2    Johnson, K.A.3
  • 43
    • 0027092323 scopus 로고
    • Mechanism and fidelity of HIV reverse transcriptase
    • Kati, W. M., Johnson, K. A., Jerva, L. F., and Anderson, K. S. (1992) Mechanism and fidelity of HIV reverse transcriptase J. Biol. Chem. 267, 25988-25997
    • (1992) J. Biol. Chem. , vol.267 , pp. 25988-25997
    • Kati, W.M.1    Johnson, K.A.2    Jerva, L.F.3    Anderson, K.S.4
  • 44
    • 0035851098 scopus 로고    scopus 로고
    • Exonuclease proofreading by human mitochondrial DNA polymerase
    • Johnson, A. A. and Johnson, K. A. (2001) Exonuclease proofreading by human mitochondrial DNA polymerase J. Biol. Chem. 276, 38097-38107
    • (2001) J. Biol. Chem. , vol.276 , pp. 38097-38107
    • Johnson, A.A.1    Johnson, K.A.2
  • 45
    • 0031053276 scopus 로고    scopus 로고
    • DNA polymerase β: Structure-fidelity relationship from pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant
    • Ahn, J., Werneburg, B. G., and Tsai, M. D. (1997) DNA polymerase β: Structure-fidelity relationship from pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant Biochemistry 36, 1100-1107
    • (1997) Biochemistry , vol.36 , pp. 1100-1107
    • Ahn, J.1    Werneburg, B.G.2    Tsai, M.D.3
  • 46
    • 0026785756 scopus 로고
    • Minimal kinetic mechanism for misincorporation by DNA polymerase i (Klenow fragment)
    • Eger, B. T. and Benkovic, S. J. (1992) Minimal kinetic mechanism for misincorporation by DNA polymerase I (Klenow fragment) Biochemistry 31, 9227-9236
    • (1992) Biochemistry , vol.31 , pp. 9227-9236
    • Eger, B.T.1    Benkovic, S.J.2
  • 47
    • 0029085240 scopus 로고
    • The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase i and bacteriophage T4 DNA polymerase
    • Frey, M. W., Sowers, L. C., Millar, D. P., and Benkovic, S. J. (1995) The nucleotide analog 2-aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase Biochemistry 34, 9185-9192
    • (1995) Biochemistry , vol.34 , pp. 9185-9192
    • Frey, M.W.1    Sowers, L.C.2    Millar, D.P.3    Benkovic, S.J.4
  • 48
    • 0025799903 scopus 로고
    • Kinetic mechanism of DNA polymerase i (Klenow fragment): Identification of a second conformational change and evaluation of the internal equilibrium constant
    • Dahlberg, M. E. and Benkovic, S. J. (1991) Kinetic mechanism of DNA polymerase I (Klenow fragment): Identification of a second conformational change and evaluation of the internal equilibrium constant Biochemistry 30, 4835-4843
    • (1991) Biochemistry , vol.30 , pp. 4835-4843
    • Dahlberg, M.E.1    Benkovic, S.J.2
  • 49
    • 0026464542 scopus 로고
    • Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4
    • Capson, T. L., Peliska, J. A., Kaboord, B. F., Frey, M. W., Lively, C., Dahlberg, M., and Benkovic, S. J. (1992) Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4 Biochemistry 31, 10984-10994
    • (1992) Biochemistry , vol.31 , pp. 10984-10994
    • Capson, T.L.1    Peliska, J.A.2    Kaboord, B.F.3    Frey, M.W.4    Lively, C.5    Dahlberg, M.6    Benkovic, S.J.7
  • 50
    • 0027365750 scopus 로고
    • Kinetic mechanism of the DNA-dependent DNA polymerase activity of human immunodeficiency virus reverse transcriptase
    • Hsieh, J. C., Zinnen, S., and Modrich, P. (1993) Kinetic mechanism of the DNA-dependent DNA polymerase activity of human immunodeficiency virus reverse transcriptase J. Biol. Chem. 268, 24607-24613
    • (1993) J. Biol. Chem. , vol.268 , pp. 24607-24613
    • Hsieh, J.C.1    Zinnen, S.2    Modrich, P.3
  • 51
    • 0035966270 scopus 로고    scopus 로고
    • Yeast DNA polymerase π utilizes an induced-fit mechanism of nucleotide incorporation
    • Washington, M. T., Prakash, L., and Prakash, S. (2001) Yeast DNA polymerase π utilizes an induced-fit mechanism of nucleotide incorporation Cell 107, 917-927
    • (2001) Cell , vol.107 , pp. 917-927
    • Washington, M.T.1    Prakash, L.2    Prakash, S.3
  • 52
    • 0035793560 scopus 로고    scopus 로고
    • DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase β. Implication for the identity of the rate-limiting conformational change
    • Vande Berg, B. J., Beard, W. A., and Wilson, S. H. (2001) DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase β. Implication for the identity of the rate-limiting conformational change J. Biol. Chem. 276, 3408-3416
    • (2001) J. Biol. Chem. , vol.276 , pp. 3408-3416
    • Vande Berg, B.J.1    Beard, W.A.2    Wilson, S.H.3
  • 54
    • 0028085880 scopus 로고
    • Isolation, characterization, and kinetic properties of truncated forms of T4 DNA polymerase that exhibit 3′-5′ exonuclease activity
    • Lin, T. C., Karam, G., and Konigsberg, W. H. (1994) Isolation, characterization, and kinetic properties of truncated forms of T4 DNA polymerase that exhibit 3′-5′ exonuclease activity J. Biol. Chem. 269, 19286-19294
    • (1994) J. Biol. Chem. , vol.269 , pp. 19286-19294
    • Lin, T.C.1    Karam, G.2    Konigsberg, W.H.3
  • 55
    • 0030897244 scopus 로고    scopus 로고
    • DNA polymerase β: Analysis of the contributions of tyrosine-271 and asparagine-279 to substrate specificity and fidelity of DNA replication by pre-steady-state kinetics
    • Kraynov, V. S., Werneburg, B. G., Zhong, X., Lee, H., Ahn, J., and Tsai, M. D. (1997) DNA polymerase β: Analysis of the contributions of tyrosine-271 and asparagine-279 to substrate specificity and fidelity of DNA replication by pre-steady-state kinetics Biochem. J. 323 (Part 1) 103-111
    • (1997) Biochem. J. , vol.323 , Issue.PART 1 , pp. 103-111
    • Kraynov, V.S.1    Werneburg, B.G.2    Zhong, X.3    Lee, H.4    Ahn, J.5    Tsai, M.D.6
  • 56
    • 0030010766 scopus 로고    scopus 로고
    • DNA polymerase β: Pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity
    • Werneburg, B. G., Ahn, J., Zhong, X., Hondal, R. J., Kraynov, V. S., and Tsai, M. D. (1996) DNA polymerase β: Pre-steady-state kinetic analysis and roles of arginine-283 in catalysis and fidelity Biochemistry 35, 7041-7050
    • (1996) Biochemistry , vol.35 , pp. 7041-7050
    • Werneburg, B.G.1    Ahn, J.2    Zhong, X.3    Hondal, R.J.4    Kraynov, V.S.5    Tsai, M.D.6
  • 57
    • 0030760966 scopus 로고    scopus 로고
    • DNA polymerase β: Multiple conformational changes in the mechanism of catalysis
    • Zhong, X., Patel, S. S., Werneburg, B. G., and Tsai, M. D. (1997) DNA polymerase β: Multiple conformational changes in the mechanism of catalysis Biochemistry 36, 11891-11900
    • (1997) Biochemistry , vol.36 , pp. 11891-11900
    • Zhong, X.1    Patel, S.S.2    Werneburg, B.G.3    Tsai, M.D.4
  • 58
    • 0040978680 scopus 로고    scopus 로고
    • Refined model for primer/template binding by HIV-1 reverse transcriptase: Pre-steady-state kinetic analyses of primer/template binding and nucleotide incorporation events distinguish between different binding modes depending on the nature of the nucleic acid substrate
    • Wohrl, B. M., Krebs, R., Goody, R. S., and Restle, T. (1999) Refined model for primer/template binding by HIV-1 reverse transcriptase: Pre-steady-state kinetic analyses of primer/template binding and nucleotide incorporation events distinguish between different binding modes depending on the nature of the nucleic acid substrate J. Mol. Biol. 292, 333-344
    • (1999) J. Mol. Biol. , vol.292 , pp. 333-344
    • Wohrl, B.M.1    Krebs, R.2    Goody, R.S.3    Restle, T.4
  • 59
    • 0037125947 scopus 로고    scopus 로고
    • Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase β
    • Dunlap, C. A. and Tsai, M. D. (2002) Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase β Biochemistry 41, 11226-11235
    • (2002) Biochemistry , vol.41 , pp. 11226-11235
    • Dunlap, C.A.1    Tsai, M.D.2
  • 61
    • 23044492225 scopus 로고    scopus 로고
    • Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases
    • Rothwell, P. J., Mitaksov, V., and Waksman, G. (2005) Motions of the fingers subdomain of klentaq1 are fast and not rate limiting: Implications for the molecular basis of fidelity in DNA polymerases Mol. Cell 19, 345-355
    • (2005) Mol. Cell , vol.19 , pp. 345-355
    • Rothwell, P.J.1    Mitaksov, V.2    Waksman, G.3
  • 63
    • 0037183526 scopus 로고    scopus 로고
    • A reexamination of the nucleotide incorporation fidelity of DNA polymerases
    • Showalter, A. K. and Tsai, M. D. (2002) A reexamination of the nucleotide incorporation fidelity of DNA polymerases Biochemistry 41, 10571-10576
    • (2002) Biochemistry , vol.41 , pp. 10571-10576
    • Showalter, A.K.1    Tsai, M.D.2
  • 64
    • 55549109430 scopus 로고    scopus 로고
    • Role of induced fit in enzyme specificity: A molecular forward/reverse switch
    • Johnson, K. A. (2008) Role of induced fit in enzyme specificity: A molecular forward/reverse switch J. Biol. Chem. 283, 26297-26301
    • (2008) J. Biol. Chem. , vol.283 , pp. 26297-26301
    • Johnson, K.A.1
  • 65
    • 0023770718 scopus 로고
    • Kinetic mechanism whereby DNA polymerase i (Klenow) replicates DNA with high fidelity
    • Kuchta, R. D., Benkovic, P., and Benkovic, S. J. (1988) Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity Biochemistry 27, 6716-6725
    • (1988) Biochemistry , vol.27 , pp. 6716-6725
    • Kuchta, R.D.1    Benkovic, P.2    Benkovic, S.J.3
  • 66
    • 0242663959 scopus 로고    scopus 로고
    • The mechanism of nucleotide incorporation by human DNA polymerase π differs from that of the yeast enzyme
    • Washington, M. T., Johnson, R. E., Prakash, L., and Prakash, S. (2003) The mechanism of nucleotide incorporation by human DNA polymerase π differs from that of the yeast enzyme Mol. Cell. Biol. 23, 8316-8322
    • (2003) Mol. Cell. Biol. , vol.23 , pp. 8316-8322
    • Washington, M.T.1    Johnson, R.E.2    Prakash, L.3    Prakash, S.4
  • 67
    • 84858063899 scopus 로고    scopus 로고
    • Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase π
    • Brown, J. A., Zhang, L., Sherrer, S. M., Taylor, J. S., Burgers, P. M., and Suo, Z. (2010) Pre-Steady-State Kinetic Analysis of Truncated and Full-Length Saccharomyces cerevisiae DNA Polymerase π J. Nucleic Acids 2010, 871939
    • (2010) J. Nucleic Acids , vol.2010 , pp. 871939
    • Brown, J.A.1    Zhang, L.2    Sherrer, S.M.3    Taylor, J.S.4    Burgers, P.M.5    Suo, Z.6
  • 68
    • 48649102536 scopus 로고    scopus 로고
    • Formation of purine-purine mispairs by Sulfolobus solfataricus DNA polymerase IV
    • DeCarlo, L., Gowda, A. S., Suo, Z., and Spratt, T. E. (2008) Formation of purine-purine mispairs by Sulfolobus solfataricus DNA polymerase IV Biochemistry 47, 8157-8164
    • (2008) Biochemistry , vol.47 , pp. 8157-8164
    • Decarlo, L.1    Gowda, A.S.2    Suo, Z.3    Spratt, T.E.4
  • 69
    • 79956104089 scopus 로고    scopus 로고
    • The Y-family DNA polymerase Dpo4 uses a template slippage mechanism to create single-base deletions
    • Wu, Y., Wilson, R. C., and Pata, J. D. (2011) The Y-family DNA polymerase Dpo4 uses a template slippage mechanism to create single-base deletions J. Bacteriol. 193, 2630-2636
    • (2011) J. Bacteriol. , vol.193 , pp. 2630-2636
    • Wu, Y.1    Wilson, R.C.2    Pata, J.D.3
  • 70
    • 84877247843 scopus 로고    scopus 로고
    • Human polymerase uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions
    • Mukherjee, P., Lahiri, I., and Pata, J. D. (2013) Human polymerase uses a template-slippage deletion mechanism, but can realign the slipped strands to favour base substitution mutations over deletions Nucleic Acids Res. 41, 5024-5035
    • (2013) Nucleic Acids Res. , vol.41 , pp. 5024-5035
    • Mukherjee, P.1    Lahiri, I.2    Pata, J.D.3
  • 71
    • 33845638804 scopus 로고    scopus 로고
    • Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase
    • Fiala, K. A., Brown, J. A., Ling, H., Kshetry, A. K., Zhang, J., Taylor, J. S., Yang, W., and Suo, Z. (2007) Mechanism of Template-independent Nucleotide Incorporation Catalyzed by a Template-dependent DNA Polymerase J. Mol. Biol. 365, 590-602
    • (2007) J. Mol. Biol. , vol.365 , pp. 590-602
    • Fiala, K.A.1    Brown, J.A.2    Ling, H.3    Kshetry, A.K.4    Zhang, J.5    Taylor, J.S.6    Yang, W.7    Suo, Z.8
  • 72
    • 0347986655 scopus 로고    scopus 로고
    • Human DNA polymerase utilizes different nucleotide incorporation mechanisms dependent upon the template base
    • Washington, M. T., Johnson, R. E., Prakash, L., and Prakash, S. (2004) Human DNA polymerase utilizes different nucleotide incorporation mechanisms dependent upon the template base Mol. Cell. Biol. 24, 936-943
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 936-943
    • Washington, M.T.1    Johnson, R.E.2    Prakash, L.3    Prakash, S.4
  • 73
    • 0033830464 scopus 로고    scopus 로고
    • Preferential incorporation of G opposite template T by the low-fidelity human DNA polymerase
    • Zhang, Y., Yuan, F., Wu, X., and Wang, Z. (2000) Preferential incorporation of G opposite template T by the low-fidelity human DNA polymerase Mol. Cell. Biol. 20, 7099-7108
    • (2000) Mol. Cell. Biol. , vol.20 , pp. 7099-7108
    • Zhang, Y.1    Yuan, F.2    Wu, X.3    Wang, Z.4
  • 74
    • 0034214838 scopus 로고    scopus 로고
    • Pol, a remarkably error-prone human DNA polymerase
    • Tissier, A., McDonald, J. P., Frank, E. G., and Woodgate, R. (2000) pol, a remarkably error-prone human DNA polymerase Genes Dev. 14, 1642-1650
    • (2000) Genes Dev. , vol.14 , pp. 1642-1650
    • Tissier, A.1    McDonald, J.P.2    Frank, E.G.3    Woodgate, R.4
  • 76
    • 33646492746 scopus 로고    scopus 로고
    • An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase- active site
    • Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S., and Aggarwal, A. K. (2006) An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase- active site Structure 14, 749-755
    • (2006) Structure , vol.14 , pp. 749-755
    • Nair, D.T.1    Johnson, R.E.2    Prakash, L.3    Prakash, S.4    Aggarwal, A.K.5
  • 77
    • 67349236998 scopus 로고    scopus 로고
    • Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase
    • Kirouac, K. N. and Ling, H. (2009) Structural basis of error-prone replication and stalling at a thymine base by human DNA polymerase EMBO J. 28, 1644-1654
    • (2009) EMBO J. , vol.28 , pp. 1644-1654
    • Kirouac, K.N.1    Ling, H.2
  • 78
    • 65549112632 scopus 로고    scopus 로고
    • Kinetic analysis of base-pairing preference for nucleotide incorporation opposite template pyrimidines by human DNA polymerase
    • Choi, J. Y., Lim, S., Eoff, R. L., and Guengerich, F. P. (2009) Kinetic analysis of base-pairing preference for nucleotide incorporation opposite template pyrimidines by human DNA polymerase J. Mol. Biol. 389, 264-274
    • (2009) J. Mol. Biol. , vol.389 , pp. 264-274
    • Choi, J.Y.1    Lim, S.2    Eoff, R.L.3    Guengerich, F.P.4
  • 79
    • 25844440534 scopus 로고    scopus 로고
    • Rev1 employs a novel mechanism of DNA synthesis using a protein template
    • Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S., and Aggarwal, A. K. (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template Science 309, 2219-2222
    • (2005) Science , vol.309 , pp. 2219-2222
    • Nair, D.T.1    Johnson, R.E.2    Prakash, L.3    Prakash, S.4    Aggarwal, A.K.5
  • 80
    • 36348982676 scopus 로고    scopus 로고
    • Pre-steady-state kinetic studies of protein-template-directed nucleotide incorporation by the yeast Rev1 protein
    • Howell, C. A., Prakash, S., and Washington, M. T. (2007) Pre-steady-state kinetic studies of protein-template-directed nucleotide incorporation by the yeast Rev1 protein Biochemistry 46, 13451-13459
    • (2007) Biochemistry , vol.46 , pp. 13451-13459
    • Howell, C.A.1    Prakash, S.2    Washington, M.T.3
  • 81
    • 77954185481 scopus 로고    scopus 로고
    • Kinetic basis of nucleotide selection employed by a protein template-dependent DNA polymerase
    • Brown, J. A., Fowler, J. D., and Suo, Z. (2010) Kinetic basis of nucleotide selection employed by a protein template-dependent DNA polymerase Biochemistry 49, 5504-5510
    • (2010) Biochemistry , vol.49 , pp. 5504-5510
    • Brown, J.A.1    Fowler, J.D.2    Suo, Z.3
  • 82
    • 0142123120 scopus 로고    scopus 로고
    • Mechanism of nucleotide incorporation opposite a thymine-thymine dimer by yeast DNA polymerase
    • Washington, M. T., Prakash, L., and Prakash, S. (2003) Mechanism of nucleotide incorporation opposite a thymine-thymine dimer by yeast DNA polymerase π Proc. Natl. Acad. Sci. U.S.A. 100, 12093-12098
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 12093-12098
    • Washington, M.T.1    Prakash, L.2    Prakash, S.3
  • 83
    • 14844364365 scopus 로고    scopus 로고
    • Mechanism of efficient and accurate nucleotide incorporation opposite 7,8-dihydro-8-oxoguanine by Saccharomyces cerevisiae DNA polymerase π
    • Carlson, K. D. and Washington, M. T. (2005) Mechanism of efficient and accurate nucleotide incorporation opposite 7,8-dihydro-8-oxoguanine by Saccharomyces cerevisiae DNA polymerase π Mol. Cell. Biol. 25, 2169-2176
    • (2005) Mol. Cell. Biol. , vol.25 , pp. 2169-2176
    • Carlson, K.D.1    Washington, M.T.2
  • 84
    • 63649090634 scopus 로고    scopus 로고
    • Versatility of Y-family Sulfolobus solfataricus DNA polymerase Dpo4 in translesion synthesis past bulky N2-alkylguanine adducts
    • Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2009) Versatility of Y-family Sulfolobus solfataricus DNA polymerase Dpo4 in translesion synthesis past bulky N2-alkylguanine adducts J. Biol. Chem. 284, 3563-3576
    • (2009) J. Biol. Chem. , vol.284 , pp. 3563-3576
    • Zhang, H.1    Eoff, R.L.2    Kozekov, I.D.3    Rizzo, C.J.4    Egli, M.5    Guengerich, F.P.6
  • 85
    • 47249163382 scopus 로고    scopus 로고
    • Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase
    • Brown, J. A., Newmister, S. A., Fiala, K. A., and Suo, Z. (2008) Mechanism of double-base lesion bypass catalyzed by a Y-family DNA polymerase Nucleic Acids Res. 36, 3867-3878
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3867-3878
    • Brown, J.A.1    Newmister, S.A.2    Fiala, K.A.3    Suo, Z.4
  • 86
    • 40149083124 scopus 로고    scopus 로고
    • Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: A 5′-slippage mechanism
    • Xu, P., Oum, L., Geacintov, N. E., and Broyde, S. (2008) Nucleotide selectivity opposite a benzo[a]pyrene-derived N2-dG adduct in a Y-family DNA polymerase: A 5′-slippage mechanism Biochemistry 47, 2701-2709
    • (2008) Biochemistry , vol.47 , pp. 2701-2709
    • Xu, P.1    Oum, L.2    Geacintov, N.E.3    Broyde, S.4
  • 87
    • 33644866040 scopus 로고    scopus 로고
    • Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4
    • Zang, H., Irimia, A., Choi, J. Y., Angel, K. C., Loukachevitch, L. V., Egli, M., and Guengerich, F. P. (2006) Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4 J. Biol. Chem. 281, 2358-2372
    • (2006) J. Biol. Chem. , vol.281 , pp. 2358-2372
    • Zang, H.1    Irimia, A.2    Choi, J.Y.3    Angel, K.C.4    Loukachevitch, L.V.5    Egli, M.6    Guengerich, F.P.7
  • 88
    • 84860189814 scopus 로고    scopus 로고
    • Kinetic Basis for the Differing Response to an Oxidative Lesion by a Replicative and a Lesion Bypass DNA Polymerase from Solfolobus solfataricus
    • Maxwell, B. A. and Suo, Z. (2012) Kinetic Basis for the Differing Response to an Oxidative Lesion by a Replicative and a Lesion Bypass DNA Polymerase from Solfolobus solfataricus Biochemistry 51, 3485-3496
    • (2012) Biochemistry , vol.51 , pp. 3485-3496
    • Maxwell, B.A.1    Suo, Z.2
  • 89
    • 33847713782 scopus 로고    scopus 로고
    • Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred
    • Eoff, R. L., Irimia, A., Egli, M., and Guengerich, F. P. (2007) Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred J. Biol. Chem. 282, 1456-1467
    • (2007) J. Biol. Chem. , vol.282 , pp. 1456-1467
    • Eoff, R.L.1    Irimia, A.2    Egli, M.3    Guengerich, F.P.4
  • 90
    • 34247181139 scopus 로고    scopus 로고
    • Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase
    • Fiala, K. A., Hypes, C. D., and Suo, Z. (2007) Mechanism of abasic lesion bypass catalyzed by a Y-family DNA polymerase J. Biol. Chem. 282, 8188-8198
    • (2007) J. Biol. Chem. , vol.282 , pp. 8188-8198
    • Fiala, K.A.1    Hypes, C.D.2    Suo, Z.3
  • 92
    • 77957080930 scopus 로고    scopus 로고
    • In vitro bypass of the major malondialdehyde- and base propenal-derived DNA adduct by human Y-family DNA polymerases, and Rev1
    • Maddukuri, L., Eoff, R. L., Choi, J. Y., Rizzo, C. J., Guengerich, F. P., and Marnett, L. J. (2010) In vitro bypass of the major malondialdehyde- and base propenal-derived DNA adduct by human Y-family DNA polymerases, and Rev1 Biochemistry 49, 8415-8424
    • (2010) Biochemistry , vol.49 , pp. 8415-8424
    • Maddukuri, L.1    Eoff, R.L.2    Choi, J.Y.3    Rizzo, C.J.4    Guengerich, F.P.5    Marnett, L.J.6
  • 93
    • 78049421745 scopus 로고    scopus 로고
    • Translesion synthesis across abasic lesions by human B-family and Y-family DNA polymerases α, and REV1
    • Choi, J. Y., Lim, S., Kim, E. J., Jo, A., and Guengerich, F. P. (2010) Translesion synthesis across abasic lesions by human B-family and Y-family DNA polymerases α, and REV1 J. Mol. Biol. 404, 34-44
    • (2010) J. Mol. Biol. , vol.404 , pp. 34-44
    • Choi, J.Y.1    Lim, S.2    Kim, E.J.3    Jo, A.4    Guengerich, F.P.5
  • 94
    • 78650637385 scopus 로고    scopus 로고
    • Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases
    • Sherrer, S. M., Fiala, K. A., Fowler, J. D., Newmister, S. A., Pryor, J. M., and Suo, Z. (2011) Quantitative analysis of the efficiency and mutagenic spectra of abasic lesion bypass catalyzed by human Y-family DNA polymerases Nucleic Acids Res. 39, 609-622
    • (2011) Nucleic Acids Res. , vol.39 , pp. 609-622
    • Sherrer, S.M.1    Fiala, K.A.2    Fowler, J.D.3    Newmister, S.A.4    Pryor, J.M.5    Suo, Z.6
  • 95
    • 41849102779 scopus 로고    scopus 로고
    • Mechanistic consequences of temperature on DNA polymerization catalyzed by a Y-family DNA polymerase
    • Fiala, K. A., Sherrer, S. M., Brown, J. A., and Suo, Z. (2008) Mechanistic consequences of temperature on DNA polymerization catalyzed by a Y-family DNA polymerase Nucleic Acids Res. 36, 1990-2001
    • (2008) Nucleic Acids Res. , vol.36 , pp. 1990-2001
    • Fiala, K.A.1    Sherrer, S.M.2    Brown, J.A.3    Suo, Z.4
  • 97
    • 84899817319 scopus 로고    scopus 로고
    • Mechanistic Investigation of the Bypass of a Bulky Aromatic DNA Adduct Catalyzed by a Y-family DNA Polymerase
    • in press
    • Gadkari, V. V., Tokarsky, E. J., Malik, C. K., Basu, A. K., and Suo, Z. (2014) Mechanistic Investigation of the Bypass of a Bulky Aromatic DNA Adduct Catalyzed by a Y-family DNA Polymerase, Chem. Res. Toxicol., in press.
    • (2014) Chem. Res. Toxicol.
    • Gadkari, V.V.1    Tokarsky, E.J.2    Malik, C.K.3    Basu, A.K.4    Suo, Z.5
  • 98
    • 65249138294 scopus 로고    scopus 로고
    • Mechanistic Studies of the Bypass of a Bulky Single-base Lesion Catalyzed by a Y-family DNA Polymerase
    • Sherrer, S. M., Brown, J. A., Pack, L. R., Jasti, V. P., Fowler, J. D., Basu, A. K., and Suo, Z. (2009) Mechanistic Studies of the Bypass of a Bulky Single-base Lesion Catalyzed by a Y-family DNA Polymerase J. Biol. Chem. 284, 6379-6388
    • (2009) J. Biol. Chem. , vol.284 , pp. 6379-6388
    • Sherrer, S.M.1    Brown, J.A.2    Pack, L.R.3    Jasti, V.P.4    Fowler, J.D.5    Basu, A.K.6    Suo, Z.7
  • 99
    • 24644443795 scopus 로고    scopus 로고
    • Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase π
    • Johnson, R. E., Prakash, L., and Prakash, S. (2005) Distinct mechanisms of cis-syn thymine dimer bypass by Dpo4 and DNA polymerase π Proc. Natl. Acad. Sci. U.S.A. 102, 12359-12364
    • (2005) Proc. Natl. Acad. Sci. U.S.A. , vol.102 , pp. 12359-12364
    • Johnson, R.E.1    Prakash, L.2    Prakash, S.3
  • 101
    • 84886721590 scopus 로고    scopus 로고
    • Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a y family DNA polymerase
    • Kirouac, K. N., Basu, A. K., and Ling, H. (2013) Structural mechanism of replication stalling on a bulky amino-polycyclic aromatic hydrocarbon DNA adduct by a Y family DNA polymerase J. Mol. Biol. 425, 4167-4176
    • (2013) J. Mol. Biol. , vol.425 , pp. 4167-4176
    • Kirouac, K.N.1    Basu, A.K.2    Ling, H.3
  • 102
    • 84879179094 scopus 로고    scopus 로고
    • Replication past the butadiene diepoxide-derived DNA adduct S-[4-(N(6)-deoxyadenosinyl)-2,3-dihydroxybutyl]glutathione by DNA polymerases
    • Cho, S. H. and Guengerich, F. P. (2013) Replication past the butadiene diepoxide-derived DNA adduct S-[4-(N(6)-deoxyadenosinyl)-2,3-dihydroxybutyl] glutathione by DNA polymerases Chem. Res. Toxicol. 26, 1005-1013
    • (2013) Chem. Res. Toxicol. , vol.26 , pp. 1005-1013
    • Cho, S.H.1    Guengerich, F.P.2
  • 103
    • 34247183642 scopus 로고    scopus 로고
    • Sloppy bypass of an abasic lesion catalyzed by a Y-family DNA polymerase
    • Fiala, K. A. and Suo, Z. (2007) Sloppy bypass of an abasic lesion catalyzed by a Y-family DNA polymerase J. Biol. Chem. 282, 8199-8206
    • (2007) J. Biol. Chem. , vol.282 , pp. 8199-8206
    • Fiala, K.A.1    Suo, Z.2
  • 104
    • 79959352056 scopus 로고    scopus 로고
    • High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing
    • Yuan, B., Wang, J., Cao, H., Sun, R., and Wang, Y. (2011) High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing Nucleic Acids Res. 39, 5945-5954
    • (2011) Nucleic Acids Res. , vol.39 , pp. 5945-5954
    • Yuan, B.1    Wang, J.2    Cao, H.3    Sun, R.4    Wang, Y.5
  • 106
    • 35448977252 scopus 로고    scopus 로고
    • A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment
    • Bauer, J., Xing, G., Yagi, H., Sayer, J. M., Jerina, D. M., and Ling, H. (2007) A structural gap in Dpo4 supports mutagenic bypass of a major benzo[a]pyrene dG adduct in DNA through template misalignment Proc. Natl. Acad. Sci. U.S.A. 104, 14905-14910
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 14905-14910
    • Bauer, J.1    Xing, G.2    Yagi, H.3    Sayer, J.M.4    Jerina, D.M.5    Ling, H.6
  • 107
    • 67650546933 scopus 로고    scopus 로고
    • Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: Guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes
    • Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2009) Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: Guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes J. Biol. Chem. 284, 17687-17699
    • (2009) J. Biol. Chem. , vol.284 , pp. 17687-17699
    • Zhang, H.1    Eoff, R.L.2    Kozekov, I.D.3    Rizzo, C.J.4    Egli, M.5    Guengerich, F.P.6
  • 108
    • 36048931023 scopus 로고    scopus 로고
    • Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase π
    • Alt, A., Lammens, K., Chiocchini, C., Lammens, A., Pieck, J. C., Kuch, D., Hopfner, K. P., and Carell, T. (2007) Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase π Science 318, 967-970
    • (2007) Science , vol.318 , pp. 967-970
    • Alt, A.1    Lammens, K.2    Chiocchini, C.3    Lammens, A.4    Pieck, J.C.5    Kuch, D.6    Hopfner, K.P.7    Carell, T.8
  • 109
    • 84865490707 scopus 로고    scopus 로고
    • Quantitative analysis of the mutagenic potential of 1-aminopyrene-DNA adduct bypass catalyzed by Y-family DNA polymerases
    • Sherrer, S. M., Taggart, D. J., Pack, L. R., Malik, C. K., Basu, A. K., and Suo, Z. (2012) Quantitative analysis of the mutagenic potential of 1-aminopyrene-DNA adduct bypass catalyzed by Y-family DNA polymerases Mutat. Res. 737, 25-33
    • (2012) Mutat. Res. , vol.737 , pp. 25-33
    • Sherrer, S.M.1    Taggart, D.J.2    Pack, L.R.3    Malik, C.K.4    Basu, A.K.5    Suo, Z.6
  • 110
    • 53049095093 scopus 로고    scopus 로고
    • Kinetic analysis of translesion synthesis opposite bulky N2- and O6-alkylguanine DNA adducts by human DNA polymerase REV1
    • Choi, J. Y. and Guengerich, F. P. (2008) Kinetic analysis of translesion synthesis opposite bulky N2- and O6-alkylguanine DNA adducts by human DNA polymerase REV1 J. Biol. Chem. 283, 23645-23655
    • (2008) J. Biol. Chem. , vol.283 , pp. 23645-23655
    • Choi, J.Y.1    Guengerich, F.P.2
  • 111
    • 0033080970 scopus 로고    scopus 로고
    • An open and closed case for all polymerases
    • Doublie, S., Sawaya, M. R., and Ellenberger, T. (1999) An open and closed case for all polymerases Structure 7, R31-R35
    • (1999) Structure , vol.7
    • Doublie, S.1    Sawaya, M.R.2    Ellenberger, T.3
  • 112
    • 0028049441 scopus 로고
    • Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP
    • Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H., and Kraut, J. (1994) Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP Science 264, 1891-1903
    • (1994) Science , vol.264 , pp. 1891-1903
    • Pelletier, H.1    Sawaya, M.R.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 113
    • 35349009532 scopus 로고    scopus 로고
    • A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1
    • Rothwell, P. J. and Waksman, G. (2007) A pre-equilibrium before nucleotide binding limits fingers subdomain closure by Klentaq1 J. Biol. Chem. 282, 28884-28892
    • (2007) J. Biol. Chem. , vol.282 , pp. 28884-28892
    • Rothwell, P.J.1    Waksman, G.2
  • 114
    • 39549088486 scopus 로고    scopus 로고
    • An intramolecular FRET system monitors fingers subdomain opening in Klentaq1
    • Allen, W. J., Rothwell, P. J., and Waksman, G. (2008) An intramolecular FRET system monitors fingers subdomain opening in Klentaq1 Protein Sci. 17, 401-408
    • (2008) Protein Sci. , vol.17 , pp. 401-408
    • Allen, W.J.1    Rothwell, P.J.2    Waksman, G.3
  • 115
    • 33747462891 scopus 로고    scopus 로고
    • A new paradigm for DNA polymerase specificity
    • Tsai, Y. C. and Johnson, K. A. (2006) A new paradigm for DNA polymerase specificity Biochemistry 45, 9675-9687
    • (2006) Biochemistry , vol.45 , pp. 9675-9687
    • Tsai, Y.C.1    Johnson, K.A.2
  • 116
    • 77952388742 scopus 로고    scopus 로고
    • Nucleotide-dependent conformational change governs specificity and analog discrimination by HIV reverse transcriptase
    • Kellinger, M. W. and Johnson, K. A. (2010) Nucleotide-dependent conformational change governs specificity and analog discrimination by HIV reverse transcriptase Proc. Natl. Acad. Sci. U.S.A. 107, 7734-7739
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 7734-7739
    • Kellinger, M.W.1    Johnson, K.A.2
  • 118
    • 43049105331 scopus 로고    scopus 로고
    • Snapshots of a Y-family DNA polymerase in replication: Substrate-induced conformational transitions and implications for fidelity of Dpo4
    • Wong, J. H., Fiala, K. A., Suo, Z., and Ling, H. (2008) Snapshots of a Y-family DNA polymerase in replication: Substrate-induced conformational transitions and implications for fidelity of Dpo4 J. Mol. Biol. 379, 317-330
    • (2008) J. Mol. Biol. , vol.379 , pp. 317-330
    • Wong, J.H.1    Fiala, K.A.2    Suo, Z.3    Ling, H.4
  • 120
  • 121
    • 34748886033 scopus 로고    scopus 로고
    • Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence
    • DeLucia, A. M., Grindley, N. D., and Joyce, C. M. (2007) Conformational changes during normal and error-prone incorporation of nucleotides by a Y-family DNA polymerase detected by 2-aminopurine fluorescence Biochemistry 46, 10790-10803
    • (2007) Biochemistry , vol.46 , pp. 10790-10803
    • Delucia, A.M.1    Grindley, N.D.2    Joyce, C.M.3
  • 122
    • 70350508554 scopus 로고    scopus 로고
    • Global conformational dynamics of a Y-family DNA polymerase during catalysis
    • Xu, C., Maxwell, B. A., Brown, J. A., Zhang, L., and Suo, Z. (2009) Global conformational dynamics of a Y-family DNA polymerase during catalysis PLoS Biol. 7, e1000225
    • (2009) PLoS Biol. , vol.7 , pp. 1000225
    • Xu, C.1    Maxwell, B.A.2    Brown, J.A.3    Zhang, L.4    Suo, Z.5
  • 123
    • 61349147834 scopus 로고    scopus 로고
    • Kinetic analysis of correct nucleotide insertion by a Y-family DNA polymerase reveals conformational changes both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence
    • Beckman, J. W., Wang, Q., and Guengerich, F. P. (2008) Kinetic analysis of correct nucleotide insertion by a Y-family DNA polymerase reveals conformational changes both prior to and following phosphodiester bond formation as detected by tryptophan fluorescence J. Biol. Chem. 283, 36711-36723
    • (2008) J. Biol. Chem. , vol.283 , pp. 36711-36723
    • Beckman, J.W.1    Wang, Q.2    Guengerich, F.P.3
  • 124
    • 84897043136 scopus 로고    scopus 로고
    • Conformational dynamics of a Y-Family DNA polymerase during substrate binding and catalysis as revealed by inter-domain Forster resonance energy transfer
    • Maxwell, B. A., Xu, C., and Suo, Z. (2014) Conformational dynamics of a Y-Family DNA polymerase during substrate binding and catalysis as revealed by inter-domain Forster resonance energy transfer Biochemistry 53, DOI: 10.1021/bi5000146
    • (2014) Biochemistry , vol.53
    • Maxwell, B.A.1    Xu, C.2    Suo, Z.3
  • 125
    • 84859765696 scopus 로고    scopus 로고
    • DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis
    • Maxwell, B. A., Xu, C., and Suo, Z. (2012) DNA Lesion Alters Global Conformational Dynamics of Y-family DNA Polymerase during Catalysis J. Biol. Chem. 287, 13040-13047
    • (2012) J. Biol. Chem. , vol.287 , pp. 13040-13047
    • Maxwell, B.A.1    Xu, C.2    Suo, Z.3
  • 126
    • 73649091713 scopus 로고    scopus 로고
    • Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W
    • Zhang, H. and Guengerich, F. P. (2010) Effect of N2-guanyl modifications on early steps in catalysis of polymerization by Sulfolobus solfataricus P2 DNA polymerase Dpo4 T239W J. Mol. Biol. 395, 1007-1018
    • (2010) J. Mol. Biol. , vol.395 , pp. 1007-1018
    • Zhang, H.1    Guengerich, F.P.2
  • 127
    • 29344432100 scopus 로고    scopus 로고
    • Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass
    • Wang, Y., Arora, K., and Schlick, T. (2006) Subtle but variable conformational rearrangements in the replication cycle of Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) may accommodate lesion bypass Protein Sci. 15, 135-151
    • (2006) Protein Sci. , vol.15 , pp. 135-151
    • Wang, Y.1    Arora, K.2    Schlick, T.3
  • 128
    • 68949136996 scopus 로고    scopus 로고
    • Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4
    • Eoff, R. L., Sanchez-Ponce, R., and Guengerich, F. P. (2009) Conformational changes during nucleotide selection by Sulfolobus solfataricus DNA polymerase Dpo4 J. Biol. Chem. 284, 21090-21099
    • (2009) J. Biol. Chem. , vol.284 , pp. 21090-21099
    • Eoff, R.L.1    Sanchez-Ponce, R.2    Guengerich, F.P.3
  • 129
    • 84890939582 scopus 로고    scopus 로고
    • Direct Probing of Solvent Accessibility and Mobility at the Binding Interface of Polymerase (Dpo4)-DNA Complex
    • Qin, Y., Yang, Y., Zhang, L., Fowler, J. D., Qiu, W., Wang, L., Suo, Z., and Zhong, D. (2013) Direct Probing of Solvent Accessibility and Mobility at the Binding Interface of Polymerase (Dpo4)-DNA Complex J. Phys. Chem. A 117, 13926-13934
    • (2013) J. Phys. Chem. A , vol.117 , pp. 13926-13934
    • Qin, Y.1    Yang, Y.2    Zhang, L.3    Fowler, J.D.4    Qiu, W.5    Wang, L.6    Suo, Z.7    Zhong, D.8
  • 130
    • 77957954447 scopus 로고    scopus 로고
    • Backbone assignment of the catalytic core of a Y-family DNA polymerase
    • Ma, D., Fowler, J. D., Yuan, C., and Suo, Z. (2010) Backbone assignment of the catalytic core of a Y-family DNA polymerase Biomol. NMR Assignments 4, 207-209
    • (2010) Biomol. NMR Assignments , vol.4 , pp. 207-209
    • Ma, D.1    Fowler, J.D.2    Yuan, C.3    Suo, Z.4
  • 131
    • 84855394776 scopus 로고    scopus 로고
    • Backbone assignment of the little finger domain of a Y-family DNA polymerase
    • Ma, D., Fowler, J. D., and Suo, Z. (2011) Backbone assignment of the little finger domain of a Y-family DNA polymerase Biomol. NMR Assignments 5, 195-198
    • (2011) Biomol. NMR Assignments , vol.5 , pp. 195-198
    • Ma, D.1    Fowler, J.D.2    Suo, Z.3
  • 132
    • 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. U.S.A. 104, 12610-12615
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , pp. 12610-12615
    • Luo, G.1    Wang, M.2    Konigsberg, W.H.3    Xie, X.S.4
  • 134
    • 75849150495 scopus 로고    scopus 로고
    • Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution
    • Christian, T. D., Romano, L. J., and Rueda, D. (2009) Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution Proc. Natl. Acad. Sci. U.S.A. 106, 21109-21114
    • (2009) Proc. Natl. Acad. Sci. U.S.A. , vol.106 , pp. 21109-21114
    • Christian, T.D.1    Romano, L.J.2    Rueda, D.3
  • 136
    • 84876534117 scopus 로고    scopus 로고
    • Single-molecule Investigation of Substrate Binding Kinetics and Protein Conformational Dynamics of a B-family Replicative DNA Polymerase
    • Maxwell, B. A. and Suo, Z. (2013) Single-molecule Investigation of Substrate Binding Kinetics and Protein Conformational Dynamics of a B-family Replicative DNA Polymerase J. Biol. Chem. 288, 11590-11600
    • (2013) J. Biol. Chem. , vol.288 , pp. 11590-11600
    • Maxwell, B.A.1    Suo, Z.2
  • 137
    • 84863826327 scopus 로고    scopus 로고
    • Single-molecule Forster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase i
    • Berezhna, S. Y., Gill, J. P., Lamichhane, R., and Millar, D. P. (2012) Single-molecule Forster resonance energy transfer reveals an innate fidelity checkpoint in DNA polymerase I J. Am. Chem. Soc. 134, 11261-11268
    • (2012) J. Am. Chem. Soc. , vol.134 , pp. 11261-11268
    • Berezhna, S.Y.1    Gill, J.P.2    Lamichhane, R.3    Millar, D.P.4


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