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Volumn 41, Issue 4, 2013, Pages 2466-2478

Unwinding of primer-templates by archaeal family-B DNA polymerases in response to template-strand uracil

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA POLYMERASE; EXONUCLEASE; OLIGODEOXYNUCLEOTIDE; URACIL;

EID: 84876396582     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1364     Document Type: Article
Times cited : (10)

References (43)
  • 2
    • 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
  • 3
  • 4
    • 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
  • 5
    • 47849125401 scopus 로고    scopus 로고
    • Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography
    • Firbank, S.J., Wardle, J., Heslop, P., Lewis, R.J. and Connolly, B.A. (2008) Uracil recognition in archaeal DNA polymerases captured by X-ray crystallography. J. Mol. Biol., 381, 529-539.
    • (2008) J. Mol. Biol. , vol.381 , pp. 529-539
    • Firbank, S.J.1    Wardle, J.2    Heslop, P.3    Lewis, R.J.4    Connolly, B.A.5
  • 6
    • 59749093367 scopus 로고    scopus 로고
    • Recognition of deaminated bases by archaeal family-B DNA polymerases
    • Connolly, B.A. (2009) Recognition of deaminated bases by archaeal family-B DNA polymerases. Biochem. Soc. Trans., 37, 65-68.
    • (2009) Biochem. Soc. Trans. , vol.37 , pp. 65-68
    • Connolly, B.A.1
  • 7
    • 75649109233 scopus 로고    scopus 로고
    • The 30-50 proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases
    • Russell, H.J., Richardson, T.T., Emptage, K. and Connolly, B.A. (2009) The 30-50 proofreading exonuclease of archaeal family-B DNA polymerase hinders the copying of template strand deaminated bases. Nucleic Acids Res., 37, 7603-7611.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 7603-7611
    • Russell, H.J.1    Richardson, T.T.2    Emptage, K.3    Connolly, B.A.4
  • 8
    • 77954697901 scopus 로고    scopus 로고
    • Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues
    • Killelea, T., Ghosh, S., Tan, S.S., Heslop, P., Firbank, S., Kool, E.T. and Connolly, B.A. (2010) Probing the interaction of archaeal DNA polymerases with deaminated bases using X-ray crystallography and non-hydrogen bonding isosteric base analogues. Biochemistry, 49, 5772-5781.
    • (2010) Biochemistry , vol.49 , pp. 5772-5781
    • Killelea, T.1    Ghosh, S.2    Tan, S.S.3    Heslop, P.4    Firbank, S.5    Kool, E.T.6    Connolly, B.A.7
  • 9
    • 0024395470 scopus 로고
    • How DNA travels between the separate polymerase and 30-50 exonuclease sites of DNA polymerase i (Klenow fragment)
    • Joyce, C.M. (1989) How DNA travels between the separate polymerase and 30-50 exonuclease sites of DNA polymerase I (Klenow fragment). J. Biol. Chem., 264, 10858-10866.
    • (1989) J. Biol. Chem. , vol.264 , pp. 10858-10866
    • Joyce, C.M.1
  • 10
    • 0028206048 scopus 로고
    • Function and structure relationships in DNA polymerases
    • Joyce, C.M. and Steitz, T.A. (1994) Function and structure relationships in DNA polymerases. Annu. Rev. Biochem., 63, 777-822.
    • (1994) Annu. Rev. Biochem. , vol.63 , pp. 777-822
    • Joyce, C.M.1    Steitz, T.A.2
  • 11
    • 0032005866 scopus 로고    scopus 로고
    • Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
    • Brautigam, C.A. and Steitz, T.A. (1998) Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol., 8, 54-63.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 54-63
    • Brautigam, C.A.1    Steitz, T.A.2
  • 12
    • 0032692565 scopus 로고    scopus 로고
    • Building a replisome from interacting pieces: Sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex
    • Shamoo, Y. and Steitz, T.A. (1999) Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell, 99, 155-166.
    • (1999) Cell , vol.99 , pp. 155-166
    • Shamoo, Y.1    Steitz, T.A.2
  • 13
    • 77949568225 scopus 로고    scopus 로고
    • DNA polymerase proofreading: Multiple roles maintain genome stability
    • Reha-Krantz, L.J. (2010) DNA polymerase proofreading: Multiple roles maintain genome stability. Biochim. Biophys. Acta, 1804, 1049-1063.
    • (2010) Biochim. Biophys. Acta , vol.1804 , pp. 1049-1063
    • Reha-Krantz, L.J.1
  • 14
    • 67349086074 scopus 로고    scopus 로고
    • Different behaviors in vivo of mutations in the b hairpin loop of the DNA polymerases of the closely related phages T4 and RB69
    • Trzenecka, A., Pzochocka, D. and Bebenek, A. (2009) Different behaviors in vivo of mutations in the b hairpin loop of the DNA polymerases of the closely related phages T4 and RB69. J. Mol. Biol., 289, 797-807.
    • (2009) J. Mol. Biol. , vol.289 , pp. 797-807
    • Trzenecka, A.1    Pzochocka, D.2    Bebenek, A.3
  • 15
    • 44949150331 scopus 로고    scopus 로고
    • Use of 2-aminopurine fluorescence to study the role of the b hairpin in the proofreading pathway catalyzed by the phage T4 and RB69 DNA polymerases
    • Subuddhi, U., Hogg, M. and Reha-Kranz, L.J. (2008) Use of 2-aminopurine fluorescence to study the role of the b hairpin in the proofreading pathway catalyzed by the phage T4 and RB69 DNA polymerases. Biochemistry, 47, 6130-6137.
    • (2008) Biochemistry , vol.47 , pp. 6130-6137
    • Subuddhi, U.1    Hogg, M.2    Reha-Kranz, L.J.3
  • 16
    • 33847706180 scopus 로고    scopus 로고
    • Structural and biochemical investigation of the role in proofreading of a b hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family
    • Hogg, M., Aller, P., Konigsberg, W., Wallace, S.S. and Doublie, S. (2007) Structural and biochemical investigation of the role in proofreading of a b hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family. J. Biol. Chem., 282, 1432-1444.
    • (2007) J. Biol. Chem. , vol.282 , pp. 1432-1444
    • Hogg, M.1    Aller, P.2    Konigsberg, W.3    Wallace, S.S.4    Doublie, S.5
  • 18
    • 0032529485 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: Metal-ion and base sequence effects
    • Stivers, J.T. (1998) 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: metal-ion and base sequence effects. Nucleic Acids Res., 26, 3837-3844.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3837-3844
    • Stivers, J.T.1
  • 19
    • 0035793105 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking
    • Jean, J.M. and Hall, K.B. (2001) 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc. Natl. Acad. Sci. USA, 98, 37-41.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 37-41
    • Jean, J.M.1    Hall, K.B.2
  • 20
    • 0028246076 scopus 로고
    • Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 30-exonuclease activity of bacteriophage T4 DNA polymerase
    • Bloom, L.M., Otto, M.R., Eritja, R., Reha-Krantz, L.J., Goodman, M.F. and Beechem, J.M. (1994) Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 30-exonuclease activity of bacteriophage T4 DNA polymerase. Biochemistry, 33, 7576-7586.
    • (1994) Biochemistry , vol.33 , pp. 7576-7586
    • Bloom, L.M.1    Otto, M.R.2    Eritja, R.3    Reha-Krantz, L.J.4    Goodman, M.F.5    Beechem, J.M.6
  • 21
    • 0032516443 scopus 로고    scopus 로고
    • Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase
    • Beechem, J.M., Otto, M.R., Bloom, L.B., Eritja, R., Reha- Krantz, L.J. and Goodman, M.F. (1998) Exonuclease-polymerase active site partitioning of primer-template DNA strands and equilibrium Mg2+ binding properties of bacteriophage T4 DNA polymerase. Biochemistry, 37, 10144-10155.
    • (1998) Biochemistry , vol.37 , pp. 10144-10155
    • Beechem, J.M.1    Otto, M.R.2    Bloom, L.B.3    Eritja, R.4    Reha- Krantz, L.J.5    Goodman, M.F.6
  • 22
    • 0347752416 scopus 로고    scopus 로고
    • Peculiar 2-aminopurine fluorescence monitors the dynamics of open complex formation by bacteriophage T7 RNA polymerase
    • Bandwar, R.P. and Patel, S.S. (2001) Peculiar 2-aminopurine fluorescence monitors the dynamics of open complex formation by bacteriophage T7 RNA polymerase. J. Biol. Chem., 276, 14075-14082.
    • (2001) J. Biol. Chem. , vol.276 , pp. 14075-14082
    • Bandwar, R.P.1    Patel, S.S.2
  • 23
    • 0033579953 scopus 로고    scopus 로고
    • Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
    • Stivers, J.T., Pankiewicz, K.W. and Watanabe, K.A. (1999) Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase. Biochemistry, 38, 952-963.
    • (1999) Biochemistry , vol.38 , pp. 952-963
    • Stivers, J.T.1    Pankiewicz, K.W.2    Watanabe, K.A.3
  • 24
    • 0033609041 scopus 로고    scopus 로고
    • Measurement of the absolute temporal coupling between DNA binding and base flipping
    • Allan, B.W., Reich, N.O. and Beechem, J.M. (1999) Measurement of the absolute temporal coupling between DNA binding and base flipping. Biochemistry, 38, 5308-5314.
    • (1999) Biochemistry , vol.38 , pp. 5308-5314
    • Allan, B.W.1    Reich, N.O.2    Beechem, J.M.3
  • 26
    • 44349170102 scopus 로고    scopus 로고
    • Differential stabilization of reaction intermediates: Specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies
    • Youngblood, B., Bonnist, E., Dryden, D.T.F., Jones, A.C. and Reich, N.O. (2008) Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies. Nucleic Acids Res., 36, 2917-2925.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2917-2925
    • Youngblood, B.1    Bonnist, E.2    Dryden, D.T.F.3    Jones, A.C.4    Reich, N.O.5
  • 27
    • 0030766474 scopus 로고    scopus 로고
    • The role of base flipping in damage recognition and catalysis by T4 endonuclease v
    • McCullough, A.K., Dodson, M.L., Scharer, O.D. and Lloyd, R.S. (1997) The role of base flipping in damage recognition and catalysis by T4 endonuclease V. J. Biol. Chem., 272, 27210-27217.
    • (1997) J. Biol. Chem. , vol.272 , pp. 27210-27217
    • McCullough, A.K.1    Dodson, M.L.2    Scharer, O.D.3    Lloyd, R.S.4
  • 28
    • 0034160088 scopus 로고    scopus 로고
    • Improving dideoxynucleotide-triphosphate utilization by the hyper-thermophilic DNA polymerase from Pyrococcus furiosus
    • Evans, S.J., Fogg, M.J., Mamone, A., Davis, M., Pearl, L.H. and Connolly, B.A. (2000) Improving dideoxynucleotide-triphosphate utilization by the hyper-thermophilic DNA polymerase from Pyrococcus furiosus. Nucleic Acids Res., 28, 1059-1066.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1059-1066
    • Evans, S.J.1    Fogg, M.J.2    Mamone, A.3    Davis, M.4    Pearl, L.H.5    Connolly, B.A.6
  • 29
    • 53149134620 scopus 로고    scopus 로고
    • Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea
    • Emptage, K., O'Neill, R., Solovyova, A. and Connolly, B.A. (2008) Interplay between DNA polymerase and proliferating cell nuclear antigen switches off base excision repair of uracil and hypoxanthine during replication in archaea. J. Mol. Biol., 383, 762-771.
    • (2008) J. Mol. Biol. , vol.383 , pp. 762-771
    • Emptage, K.1    O'neill, R.2    Solovyova, A.3    Connolly, B.A.4
  • 30
    • 0006585604 scopus 로고
    • Oligodeoxynucleotides contained modified bases
    • Eckstein, F. (ed.) . Oxford University Press, Oxford
    • Connolly, B.A. (1991) Oligodeoxynucleotides contained modified bases. In: Eckstein, F. (ed.), Oligonucleotides and Analogues, a Practical Approach. Oxford University Press, Oxford, pp. 155-183.
    • (1991) Oligonucleotides and Analogues, A Practical Approach , pp. 155-183
    • Connolly, B.A.1
  • 31
    • 0026686711 scopus 로고
    • Synthetic oligodeoxynucleotides containing modified bases
    • Connolly, B.A. (1992) Synthetic oligodeoxynucleotides containing modified bases. Methods Enzymol., 211, 36-53.
    • (1992) Methods Enzymol. , vol.211 , pp. 36-53
    • Connolly, B.A.1
  • 32
    • 84870717515 scopus 로고    scopus 로고
    • A plasmid-based lacZ gene assay for DNA polymerase fidelity measurement
    • Keith, B.J., Jozwiakowski, S.K. and Connolly, B.A. (2013) A plasmid-based lacZ gene assay for DNA polymerase fidelity measurement. Anal. Biochem, 433, 153-161.
    • (2013) Anal. Biochem , vol.433 , pp. 153-161
    • Keith, B.J.1    Jozwiakowski, S.K.2    Connolly, B.A.3
  • 33
    • 0017146579 scopus 로고
    • Ion effects on ligand-nucleic acid interactions
    • Record, M.T., Lohman, T.M. and De Haseth, P. (1976) Ion effects on ligand-nucleic acid interactions. J. Mol. Biol., 107, 145-158.
    • (1976) J. Mol. Biol. , vol.107 , pp. 145-158
    • Record, M.T.1    Lohman, T.M.2    De Haseth, P.3
  • 34
    • 0035957061 scopus 로고    scopus 로고
    • Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: A study using fluorescent oligonucleotides and fluorescence polarisation
    • Reid, S.L., Parry, D., Hsiao-Hui, L. and Connolly, B.A. (2001) Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarisation. Biochemistry, 40, 2484-2494.
    • (2001) Biochemistry , vol.40 , pp. 2484-2494
    • Reid, S.L.1    Parry, D.2    Hsiao-Hui, L.3    Connolly, B.A.4
  • 35
    • 0026019625 scopus 로고
    • Structural basis for the 30-50 exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
    • Beese, L.S. and Steitz, T.A. (1991) Structural basis for the 30-50 exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J., 10, 25-33.
    • (1991) EMBO J. , vol.10 , pp. 25-33
    • Beese, L.S.1    Steitz, T.A.2
  • 36
    • 67650559447 scopus 로고    scopus 로고
    • Local conformations and competitive binding affinities of singleand double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases
    • Datta, K., Johnson, N.P., LiCata, V.J. and von Hippel, P.H. (2009) Local conformations and competitive binding affinities of singleand double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases. J. Biol. Chem., 284, 17180-17193.
    • (2009) J. Biol. Chem. , vol.284 , pp. 17180-17193
    • Datta, K.1    Johnson, N.P.2    Licata, V.J.3    Von Hippel, P.H.4
  • 37
    • 28544438811 scopus 로고    scopus 로고
    • Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions
    • Hariharan, C. and Reha-Krantz, L.J. (2005) Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions. Biochemistry, 44, 15674-15684.
    • (2005) Biochemistry , vol.44 , pp. 15674-15684
    • Hariharan, C.1    Reha-Krantz, L.J.2
  • 38
    • 9144265600 scopus 로고    scopus 로고
    • Evidence of tautomerism in 2-aminopurine from fluorescence lifetime measurements
    • Neely, R.K., Magennis, S.W., Dryden, D.T.F. and Jones, A.C. (2004) Evidence of tautomerism in 2-aminopurine from fluorescence lifetime measurements. J. Phys. Chem. B, 108, 17606-17610.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 17606-17610
    • Neely, R.K.1    Magennis, S.W.2    Dryden, D.T.F.3    Jones, A.C.4
  • 39
    • 0029758746 scopus 로고    scopus 로고
    • Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine
    • Law, S.M., Eritja, R., Goodman, M.F. and Breslauer, K.J. (1996) Spectroscopic and calorimetric characterizations of DNA duplexes containing 2-aminopurine. Biochemistry, 35, 12329-12337.
    • (1996) Biochemistry , vol.35 , pp. 12329-12337
    • Law, S.M.1    Eritja, R.2    Goodman, M.F.3    Breslauer, K.J.4
  • 40
    • 84860390395 scopus 로고    scopus 로고
    • A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex
    • Aller, P., Duclos, S., Wallace, S.S. and Doublie, S. (2011) A crystallographic study of the role of sequence context in thymine glycol bypass by a replicative DNA polymerase serendipitously sheds light on the exonuclease complex. J. Mol. Biol., 412, 22-34.
    • (2011) J. Mol. Biol. , vol.412 , pp. 22-34
    • Aller, P.1    Duclos, S.2    Wallace, S.S.3    Doublie, S.4
  • 41
    • 0028834956 scopus 로고
    • Use of genetic analyses to probe structure, function, and dynamics of bacteriophage T4 DNA polymerase
    • Reha-Krantz, L.J. (1995) Use of genetic analyses to probe structure, function, and dynamics of bacteriophage T4 DNA polymerase. Methods Enzymol., 262, 323-331.
    • (1995) Methods Enzymol. , vol.262 , pp. 323-331
    • Reha-Krantz, L.J.1
  • 42
    • 2342537864 scopus 로고    scopus 로고
    • Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
    • Hogg, M., Wallace, S. and Doublie, S. (2004) Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site. EMBO J., 23, 1483-1493.
    • (2004) EMBO J. , vol.23 , pp. 1483-1493
    • Hogg, M.1    Wallace, S.2    Doublie, S.3
  • 43
    • 0028892405 scopus 로고
    • Dynamics of bacteriophage T4 DNA polymerase function: Identification of amino acid residues that affect switching between polymerase and 30!50 exonuclease activities
    • Stocki, S.A., Nonay, R.L. and Reha-Krantz, L.J. (1995) Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 30!50 exonuclease activities. J. Mol. Biol., 254, 15-28.
    • (1995) J. Mol. Biol. , vol.254 , pp. 15-28
    • Stocki, S.A.1    Nonay, R.L.2    Reha-Krantz, L.J.3


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