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Volumn 44, Issue 48, 2005, Pages 15674-15684

Using 2-aminopurine fluorescence to detect bacteriophage T4 DNA polymerase-DNA complexes that are important for primer extension and proofreading reactions

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; COMPLEXATION; CONFORMATIONS; DNA; FLUORESCENCE; QUENCHING; REACTION KINETICS;

EID: 28544438811     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi051462y     Document Type: Article
Times cited : (43)

References (39)
  • 1
    • 0031587827 scopus 로고    scopus 로고
    • Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69
    • Wang, J., Sattar, A. K. M. A., Wang, C. C., Karam, J. D., Konigsberg, W. H., and Steitz, T. A. (1997) Crystal structure of a pol α family replication DNA polymerase from bacteriophage RB69, Cell 89, 1087-1099.
    • (1997) Cell , vol.89 , pp. 1087-1099
    • Wang, J.1    Sattar, A.K.M.A.2    Wang, C.C.3    Karam, J.D.4    Konigsberg, W.H.5    Steitz, T.A.6
  • 2
    • 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
  • 3
    • 0032535528 scopus 로고    scopus 로고
    • Crystal structures of open and closed forms of binary and ternary complexes 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 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
  • 4
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of bacteriophage T7 DNA replication complex at 2.2 Å resolution
    • Doublié, S., Tabor, S., Long, A., Richardson, C. C., and Ellenberger, T. (1998) Crystal structure of bacteriophage T7 DNA replication complex at 2.2 Å resolution, Nature 391, 251-258.
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublié, S.1    Tabor, S.2    Long, A.3    Richardson, C.C.4    Ellenberger, T.5
  • 5
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replication complex of a pol α family DNA polymerase
    • Franklin, M. C., Wang, J., and Steitz, T. A. (2001) Structure of the replication complex of a pol α family DNA polymerase, Cell 105, 657-667.
    • (2001) Cell , vol.105 , pp. 657-667
    • Franklin, M.C.1    Wang, J.2    Steitz, T.A.3
  • 6
    • 2342537864 scopus 로고    scopus 로고
    • Crystallographic snapshots of a replication DNA polymerase encountering an abasic site
    • Hogg, M., Wallace, S. S., and Doublié, S. (2004) Crystallographic snapshots of a replication DNA polymerase encountering an abasic site, EMBO J. 23, 1483-1993.
    • (2004) EMBO J. , vol.23 , pp. 1483-1993
    • Hogg, M.1    Wallace, S.S.2    Doublié, S.3
  • 7
    • 2342484512 scopus 로고    scopus 로고
    • Lesion (in)tolerance reveals insights in DNA replication fidelity
    • Freisinger, E., Grollman, A. P., Miller, H., and Kisker, C. (2004) Lesion (in)tolerance reveals insights in DNA replication fidelity, EMBO J. 23, 1494-1505.
    • (2004) EMBO J. , vol.23 , pp. 1494-1505
    • Freisinger, E.1    Grollman, A.P.2    Miller, H.3    Kisker, C.4
  • 8
    • 4544273926 scopus 로고    scopus 로고
    • Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase
    • Hsu, G. W., Ober, M., Carrell, T., and Beese, L. S. (2004) Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase, Nature 431, 217-221.
    • (2004) Nature , vol.431 , pp. 217-221
    • Hsu, G.W.1    Ober, M.2    Carrell, T.3    Beese, L.S.4
  • 9
    • 1642588255 scopus 로고    scopus 로고
    • Structures of mismatch replication errors observed in a DNA polymerase
    • Johnson, S. J., and Beese, L. S. (2004) Structures of mismatch replication errors observed in a DNA polymerase, Cell 116, 803-816.
    • (2004) Cell , vol.116 , pp. 803-816
    • Johnson, S.J.1    Beese, L.S.2
  • 10
    • 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
  • 11
    • 0037154094 scopus 로고    scopus 로고
    • Determinants of DNA mismatch recognition within the polymerase domain of the Klenow fragment
    • Thompson, E. H., Z., Bailey, M. F., van der Schans, D. J. C., Joyce, C. M., and Millar, D. P. (2002) Determinants of DNA mismatch recognition within the polymerase domain of the Klenow fragment, Biochemistry 41, 713-722.
    • (2002) Biochemistry , vol.41 , pp. 713-722
    • Thompson, E.H.Z.1    Bailey, M.F.2    Van Der Schans, D.J.C.3    Joyce, C.M.4    Millar, D.P.5
  • 12
    • 0000812659 scopus 로고
    • Base pairing and mutagenesis: Observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR
    • Sowers, L. C., Fazakerley, G. V., Eritja, R., Kaplan, B. E., and Goodman, M. F. (1986) Base pairing and mutagenesis: Observation of a protonated base pair between 2-aminopurine and cytosine in an oligonucleotide by proton NMR, Proc, Natl. Acad. Sci. U.S.A. 83, 5434-5438.
    • (1986) Proc. Natl. Acad. Sci. U.S.A. , vol.83 , pp. 5434-5438
    • Sowers, L.C.1    Fazakerley, G.V.2    Eritja, R.3    Kaplan, B.E.4    Goodman, M.F.5
  • 13
    • 0019879372 scopus 로고
    • Nonrandom substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro
    • Pless, R. C., Levitt, L. M., and Bessman, M. J. (1981) Nonrandom substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro, Biochemistry 20, 6235-6244.
    • (1981) Biochemistry , vol.20 , pp. 6235-6244
    • Pless, R.C.1    Levitt, L.M.2    Bessman, M.J.3
  • 14
    • 0027493457 scopus 로고
    • Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment
    • Bloom, L. B., Otto, M. R., Beechem, J. M., and Goodman, M. F. (1993) Influence of 5′-nearest neighbors on the insertion kinetics of the fluorescent nucleotide analog 2-aminopurine by Klenow fragment, Biochemistry 32, 11247-11258.
    • (1993) Biochemistry , vol.32 , pp. 11247-11258
    • Bloom, L.B.1    Otto, M.R.2    Beechem, J.M.3    Goodman, M.F.4
  • 15
    • 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
    • Prey, M. A., 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
    • Prey, M.A.1    Sowers, L.C.2    Millar, D.P.3    Benkovic, S.J.4
  • 16
    • 0037006992 scopus 로고    scopus 로고
    • Using 2-aminopurine fluorescence to detect base unstacking in the template strand during nucleotide incorporation by the bacteriophage T4 DNA polymerase
    • Mandal, S. S., Fidalgo da Silva, and Reha-Krantz, L. J. (2002) Using 2-aminopurine fluorescence to detect base unstacking in the template strand during nucleotide incorporation by the bacteriophage T4 DNA polymerase, Biochemistry 41, 4399-4406.
    • (2002) Biochemistry , vol.41 , pp. 4399-4406
    • Mandal, S.S.1    Fidalgo Da Silva2    Reha-Krantz, L.J.3
  • 17
    • 0037174863 scopus 로고    scopus 로고
    • Using 2-aminopurine fluorescence to measure incorporation of incorrect nucleotides by wild type and mutant bacteriophage T4 DNA polymerases
    • Fidalgo da Silva, E., Mandal, S. S., and Reha-Krantz, L. J. (2002) Using 2-aminopurine fluorescence to measure incorporation of incorrect nucleotides by wild type and mutant bacteriophage T4 DNA polymerases, J. Biol. Chem. 277, 40640-40649.
    • (2002) J. Biol. Chem. , vol.277 , pp. 40640-40649
    • Fidalgo Da Silva, E.1    Mandal, S.S.2    Reha-Krantz, L.J.3
  • 18
    • 0017652144 scopus 로고
    • Studies on the biochemical basis of spontaneous mutation. V. Effect of temperature on mutation frequency
    • Bessman, M. J., and Reha-Krantz, L. J. (1977) Studies on the biochemical basis of spontaneous mutation. V. Effect of temperature on mutation frequency, J. Mol. Biol. 116, 115-123.
    • (1977) J. Mol. Biol. , vol.116 , pp. 115-123
    • Bessman, M.J.1    Reha-Krantz, L.J.2
  • 19
    • 0028246076 scopus 로고
    • Pre-steady-state kinetic analysis of sequence-dependent nucleotide excision by the 3′-exonuclease activity of bacteriophage T4 DNA polymerase
    • Bloom, L. B., 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 3′-exonuclease activity of bacteriophage T4 DNA polymerase, Biochemistry 33, 7576-7586.
    • (1994) Biochemistry , vol.33 , pp. 7576-7586
    • Bloom, L.B.1    Otto, M.R.2    Eritja, R.3    Reha-Krantz, L.J.4    Goodman, M.F.5    Beechem, J.M.6
  • 20
    • 0014669561 scopus 로고
    • Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives
    • Ward, D. C., Reich, E., and Stryer, L. (1969) Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives. J. Biol. Chem. 244, 1228-1237.
    • (1969) J. Biol. Chem. , vol.244 , pp. 1228-1237
    • Ward, D.C.1    Reich, E.2    Stryer, L.3
  • 22
    • 0035969959 scopus 로고    scopus 로고
    • Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence
    • Rachofsky, E. L., Osman, R., and Ross, J. B. A. (2001) Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence, Biochemistry 40, 946-956.
    • (2001) Biochemistry , vol.40 , pp. 946-956
    • Rachofsky, E.L.1    Osman, R.2    Ross, J.B.A.3
  • 24
    • 0029802609 scopus 로고    scopus 로고
    • Using 2-aminopurine fluorescence and mutational analysis to demonstrate an active role of bacteriophage T4 DNA polymerase in strand separation required for 3′ → 5′ exonuclease activity
    • Marquez, L. A., and Reha-Krantz, L. J. (1996) Using 2-aminopurine fluorescence and mutational analysis to demonstrate an active role of bacteriophage T4 DNA polymerase in strand separation required for 3′ → 5′ exonuclease activity, J. Biol. Chem. 271, 28903-28911.
    • (1996) J. Biol. Chem. , vol.271 , pp. 28903-28911
    • Marquez, L.A.1    Reha-Krantz, L.J.2
  • 25
    • 0021867612 scopus 로고
    • Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity
    • Petruska, J., and Goodman, M. F. (1985) Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity, J. Biol. Chem. 260, 7533-7539.
    • (1985) J. Biol. Chem. , vol.260 , pp. 7533-7539
    • Petruska, J.1    Goodman, M.F.2
  • 27
    • 0027717954 scopus 로고
    • Genetic and biochemical studies of bacteriophage T4 DNA polymerase 3′ → 5′ exonuclease activity
    • Reha-Krantz, L. J., and Nonay, R. L. (1993) Genetic and biochemical studies of bacteriophage T4 DNA polymerase 3′ → 5′ exonuclease activity, J. Biol. Chem. 268, 27100-27108.
    • (1993) J. Biol. Chem. , vol.268 , pp. 27100-27108
    • Reha-Krantz, L.J.1    Nonay, R.L.2
  • 28
    • 0027998846 scopus 로고
    • Motif a of bacteriophage T4 DNA polymerase: Role in primer extension and DNA replication fidelity
    • Reha-Krantz, L. J., and Nonay, R. L. (1994) Motif A of bacteriophage T4 DNA polymerase: Role in primer extension and DNA replication fidelity, J. Biol. Chem. 269, 5635-5643.
    • (1994) J. Biol. Chem. , vol.269 , pp. 5635-5643
    • Reha-Krantz, L.J.1    Nonay, R.L.2
  • 29
    • 36449000480 scopus 로고
    • Stroboscopic optical boxcar technique for the determination of fluorescence lifetimes
    • James, D. R., Siemiarczuk, A., and Ware, W. R. (1992) Stroboscopic optical boxcar technique for the determination of fluorescence lifetimes, Rev. Sci. Instrum. 63, 1710-1716.
    • (1992) Rev. Sci. Instrum. , vol.63 , pp. 1710-1716
    • James, D.R.1    Siemiarczuk, A.2    Ware, W.R.3
  • 30
    • 0028143392 scopus 로고
    • Melting of a DNA helix terminus within the active site of a DNA polymerase
    • Hochstrasser, R. A., Carver, T. E., Sowers, L. C., and Millar, D. P. (1994) Melting of a DNA helix terminus within the active site of a DNA polymerase, Biochemistry 33, 11971-11979.
    • (1994) Biochemistry , vol.33 , pp. 11971-11979
    • Hochstrasser, R.A.1    Carver, T.E.2    Sowers, L.C.3    Millar, D.P.4
  • 31
    • 0034077645 scopus 로고    scopus 로고
    • Sequence dependence of energy transfer in DNA oligonucleotides
    • Xu, D. G., and Nordlund, T. M. (2000) Sequence dependence of energy transfer in DNA oligonucleotides, Biophys. J. 78, 1042-1058.
    • (2000) Biophys. J. , vol.78 , pp. 1042-1058
    • Xu, D.G.1    Nordlund, T.M.2
  • 32
    • 0035969981 scopus 로고    scopus 로고
    • Conformation and dynamics of abasic sites in DNA investigated by time-resoloved fluorescence of 2-aminopurine
    • Rachofsky, E. L., Seibert, E., Stivers, J. T., Osman, R., and Ross, J. B. A. (2001) Conformation and dynamics of abasic sites in DNA investigated by time-resoloved fluorescence of 2-aminopurine, Biochemistry 40, 957-967.
    • (2001) Biochemistry , vol.40 , pp. 957-967
    • Rachofsky, E.L.1    Seibert, E.2    Stivers, J.T.3    Osman, R.4    Ross, J.B.A.5
  • 33
    • 0018800392 scopus 로고
    • Error induction and correction by mutant and wild-type T4 DNA polymerase. Kinetic error discrimination mechanisms
    • Clayton, L. K., Goodman, M. F., Branscomb, E. W., and Galas, D. J. (1979) Error induction and correction by mutant and wild-type T4 DNA polymerase. Kinetic error discrimination mechanisms, J. Biol. Chem. 254, 1902-1912.
    • (1979) J. Biol. Chem. , vol.254 , pp. 1902-1912
    • Clayton, L.K.1    Goodman, M.F.2    Branscomb, E.W.3    Galas, D.J.4
  • 34
    • 0017226230 scopus 로고
    • An antimutator deoxyribonucleic acid polymerase. II. In vitro studies of its temperature sensitivity
    • Lo, K.-Y., and Bessman, M. J. (1976) An antimutator deoxyribonucleic acid polymerase. II. In vitro studies of its temperature sensitivity, J. Biol. Chem. 251, 2480-2486.
    • (1976) J. Biol. Chem. , vol.251 , pp. 2480-2486
    • Lo, K.-Y.1    Bessman, M.J.2
  • 35
    • 0028892405 scopus 로고
    • Dynamics of bacteriophage T4 DNA polymerase function: Identification of amino acid residues that affect switching between polymerase and 3′ → 5′ 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 3′ → 5′ 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
  • 36
    • 0032584187 scopus 로고    scopus 로고
    • Identification of a transient excision intermediate at the crossroads between DNA polymerase extension and proofreading pathways
    • Baker, R. P., and Reha-Krantz, L. J. (1998) Identification of a transient excision intermediate at the crossroads between DNA polymerase extension and proofreading pathways, Proc. Natl. Acad. Sci. U.S.A. 95, 3507-3512.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 3507-3512
    • Baker, R.P.1    Reha-Krantz, L.J.2
  • 38
    • 0030693128 scopus 로고    scopus 로고
    • -) activity on damaged DNA templates: Effect of proximal and distal template damage on DNA synthesis
    • -) activity on damaged DNA templates: Effect of proximal and distal template damage on DNA synthesis, Biochemistry 36, 15336-15342.
    • (1997) Biochemistry , vol.36 , pp. 15336-15342
    • Miller, H.1    Grollman, A.P.2
  • 39
    • 0026702250 scopus 로고
    • Interaction of Drosophila DNA polymerase α holoenzyme with synthetic template-primers containing mismatched primer bases or propanodeoxyguanosine adducts at various position in template and primer regions
    • Weiss, S. J., and Fisher, P. A. (1992) Interaction of Drosophila DNA polymerase α holoenzyme with synthetic template-primers containing mismatched primer bases or propanodeoxyguanosine adducts at various position in template and primer regions, J. Biol. Chem. 267, 18520-18526.
    • (1992) J. Biol. Chem. , vol.267 , pp. 18520-18526
    • Weiss, S.J.1    Fisher, P.A.2


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