메뉴 건너뛰기




Volumn 46, Issue 43, 2007, Pages 12289-12297

Conformational dynamics of DNA polymerase probed with a novel fluorescent DNA base analogue

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL TRANSITIONS; ENZYMATIC CYCLES; FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET); PHOSPHODIESTERS;

EID: 35648934962     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi700755m     Document Type: Article
Times cited : (58)

References (46)
  • 2
    • 0025040632 scopus 로고
    • An attempt to unify the structure of polymerases
    • Delarue, M., Poch, O., Tordo, N., Moras, D., and Argos, P. (1990) An attempt to unify the structure of polymerases, Protein Eng. 3, 461-467.
    • (1990) Protein Eng , vol.3 , pp. 461-467
    • Delarue, M.1    Poch, O.2    Tordo, N.3    Moras, D.4    Argos, P.5
  • 3
    • 0036107982 scopus 로고    scopus 로고
    • Evolution of DNA polymerase families: Evidences for multiple gene exchange between cellular and viral proteins
    • Fillee, J., Forterre, P., Sen-Lin, T., and Laurent, J. (2002) Evolution of DNA polymerase families: evidences for multiple gene exchange between cellular and viral proteins, J. Mol. Evol. 54, 763-773.
    • (2002) J. Mol. Evol , vol.54 , pp. 763-773
    • Fillee, J.1    Forterre, P.2    Sen-Lin, T.3    Laurent, J.4
  • 4
    • 0021984004 scopus 로고
    • Structure of the large fragment of Escherichia coli DNA polymerase I complexed with dTMP
    • Ollis, D. L., Brick, P., Hamlin, R., Xuong, N. G., and Steitz, T. A. (1985) Structure of the large fragment of Escherichia coli DNA polymerase I complexed with dTMP, Nature 313, 162-166.
    • (1985) Nature , vol.313 , pp. 162-166
    • Ollis, D.L.1    Brick, P.2    Hamlin, R.3    Xuong, N.G.4    Steitz, T.A.5
  • 5
    • 0029056926 scopus 로고
    • Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-Å resolution: Structural basis for thermostability
    • Korolev, S., Nayal, M., Barnes, W.M., Di Cera, E., and Waksman, G. (1995) Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5-Å resolution: Structural basis for thermostability, Proc. Natl. Acad. Sci. U.S.A. 92, 9264-9268.
    • (1995) Proc. Natl. Acad. Sci. U.S.A , vol.92 , pp. 9264-9268
    • Korolev, S.1    Nayal, M.2    Barnes, W.M.3    Di Cera, E.4    Waksman, G.5
  • 6
    • 0028983795 scopus 로고
    • Crystal structure of Thermus aquaticus DNA polymerase
    • Kim, Y., Eom, S. H., Wang, J., Lee, D. S., Suh, S. W., and Steitz, T. A. (1995) Crystal structure of Thermus aquaticus DNA polymerase, Nature 376, 612-616.
    • (1995) Nature , vol.376 , pp. 612-616
    • Kim, Y.1    Eom, S.H.2    Wang, J.3    Lee, D.S.4    Suh, S.W.5    Steitz, T.A.6
  • 7
    • 0031568308 scopus 로고    scopus 로고
    • Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution
    • Kiefer, J. R., Mao, C., Hansen, C. J., Basehore, S. L., Hogrefe, H. H., Braman, J. C., and Beese, L. S. (1997) Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 Å resolution. Structure 5, 95-108.
    • (1997) Structure , vol.5 , pp. 95-108
    • Kiefer, J.R.1    Mao, C.2    Hansen, C.J.3    Basehore, S.L.4    Hogrefe, H.H.5    Braman, J.C.6    Beese, L.S.7
  • 8
    • 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
  • 10
    • 0028136070 scopus 로고
    • Crystal structure of rat DNA polymerase β: Evidence for a common polymerase mechanism
    • Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H., and Kraut, J. (1994) Crystal structure of rat DNA polymerase β: evidence for a common polymerase mechanism, Science 246, 1930-1935.
    • (1994) Science , vol.246 , pp. 1930-1935
    • Sawaya, M.R.1    Pelletier, H.2    Kumar, A.3    Wilson, S.H.4    Kraut, J.5
  • 11
    • 0034857266 scopus 로고    scopus 로고
    • Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain
    • Zhou, B.-L., Pata, J. D., and Steitz, T. A. (2001) Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain, Mol. Cell 8, 427-437.
    • (2001) Mol. Cell , vol.8 , pp. 427-437
    • Zhou, B.-L.1    Pata, J.D.2    Steitz, T.A.3
  • 12
    • 0034847259 scopus 로고    scopus 로고
    • Structure of the catalytic core of S. cerevisiae DNA polymerase η: 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 η: 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
  • 14
    • 0026693137 scopus 로고
    • Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexes with an inhibitor
    • Kohlstaedt, L. A., Wang, J., Friedman, J. M., Rice, P. A., and Steitz, T. A. (1992) Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexes with an inhibitor, Science 256, 1783-1790.
    • (1992) Science , vol.256 , pp. 1783-1790
    • Kohlstaedt, L.A.1    Wang, J.2    Friedman, J.M.3    Rice, P.A.4    Steitz, T.A.5
  • 16
    • 0026026192 scopus 로고
    • An induced fit kinetic mechanism for DNA polymerase fidelity: Direct measurement by single turnover kinetics
    • Wong, I., Patel, S. S., and Johnson, K. A. (1991) An induced fit kinetic mechanism for DNA polymerase 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
  • 17
    • 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
  • 18
    • 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 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    Dahlberg6    Benkovic, S.J.7
  • 19
    • 0031053276 scopus 로고    scopus 로고
    • DNA polymerase β: Structure-fidelity relationships 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 relationships 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
  • 20
    • 0035966270 scopus 로고    scopus 로고
    • Yeast DNA polymerase η utilizes an induced-fit mechanism of nucleotide incorporation
    • Washington, M. T., Prakash, L., and Prakash, S. (2001) Yeast DNA polymerase η 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
  • 21
    • 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
  • 22
    • 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
  • 23
    • 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
  • 24
    • 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., Kong, 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    Kong, Y.2    Korolev, S.3    Waksman, G.4
  • 25
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replicating complex of a pol α family DNA polymerase
    • Franklin, M. C., Wang, J., and Steitz, T. A. (2001) Structure of the replicating 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
  • 26
    • 0032573488 scopus 로고    scopus 로고
    • Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance
    • Huang, H., Chopra, R., Verdine, G. L., and Harrison, S. C. (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance, Science 282, 1669-1675.
    • (1998) Science , vol.282 , pp. 1669-1675
    • Huang, H.1    Chopra, R.2    Verdine, G.L.3    Harrison, S.C.4
  • 27
    • 0036295231 scopus 로고    scopus 로고
    • Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se
    • Yang, L., Beard, W. A., Wilson, S. H., Broyde, S., and Schlik, T. (2002) Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. J. Mol. Biol. 317, 651-671.
    • (2002) J. Mol. Biol , vol.317 , pp. 651-671
    • Yang, L.1    Beard, W.A.2    Wilson, S.H.3    Broyde, S.4    Schlik, T.5
  • 28
    • 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
  • 29
    • 0034812469 scopus 로고    scopus 로고
    • highly fluorescent DNA base analogue that forms Watson-Crick base pairs with guanine
    • Wilhelmsson, M., Holmen, A., Lincoln, P., Nielsen, P. E., and Norden, B. A. (2001) highly fluorescent DNA base analogue that forms Watson-Crick base pairs with guanine, J. Am. Chem. Soc. 123, 2434-2435.
    • (2001) J. Am. Chem. Soc , vol.123 , pp. 2434-2435
    • Wilhelmsson, M.1    Holmen, A.2    Lincoln, P.3    Nielsen, P.E.4    Norden, B.A.5
  • 30
    • 4844229802 scopus 로고    scopus 로고
    • DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization
    • Engman, K. C., Sandin, P., Osborne, S., Brown, T., Billeter, M., Lincoln, P., Norden, B., Albinsson, B., and Wilhelmsson, M. L. (2004) DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization, Nucleic Acids Res. 32, 5087-95.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5087-5095
    • Engman, K.C.1    Sandin, P.2    Osborne, S.3    Brown, T.4    Billeter, M.5    Lincoln, P.6    Norden, B.7    Albinsson, B.8    Wilhelmsson, M.L.9
  • 31
    • 0024456523 scopus 로고
    • Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI reognition sequence: Fluorescence, molecular dynamics and NMR studies
    • Nordlund, T. M., Andersson, S., Nilsson, L., and Rigler, R. R. (1989) Structure and dynamics of a fluorescent DNA oligomer containing the EcoRI reognition sequence: Fluorescence, molecular dynamics and NMR studies, Biochemistry 28, 9095-9103.
    • (1989) Biochemistry , vol.28 , pp. 9095-9103
    • Nordlund, T.M.1    Andersson, S.2    Nilsson, L.3    Rigler, R.R.4
  • 33
    • 0035969959 scopus 로고    scopus 로고
    • Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence
    • Rachovsky, 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
    • Rachovsky, E.L.1    Osman, R.2    Ross, J.B.A.3
  • 34
    • 0030823054 scopus 로고    scopus 로고
    • Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides
    • Driscoll, S. L., Hawkins, M. E., Balis, F. M., Pfleiderer, W., and Laws, W. R. (1997) Fluorescence properties of a new guanosine analog incorporated into small oligonucleotides, Biophys. J. 73, 3277-3286.
    • (1997) Biophys. J , vol.73 , pp. 3277-3286
    • Driscoll, S.L.1    Hawkins, M.E.2    Balis, F.M.3    Pfleiderer, W.4    Laws, W.R.5
  • 35
    • 0025353207 scopus 로고
    • Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base
    • Wu, P., Nordlund, T. M., Gildea, B., and McLaughlin, L. W. (1990) Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base, Biochemistry 29, 6508-6514.
    • (1990) Biochemistry , vol.29 , pp. 6508-6514
    • Wu, P.1    Nordlund, T.M.2    Gildea, B.3    McLaughlin, L.W.4
  • 36
    • 0035969613 scopus 로고    scopus 로고
    • Facile synthesis of a fluorescent deoxycytidine analogue suitable for probing the RecA nucleoprotein filament
    • Singleton, S. F., Shan, F., Kanan, M. W., Mcintosh, C. M., Sterman, C. J., Helm, J. S., and Webb, K. J. (2001) Facile synthesis of a fluorescent deoxycytidine analogue suitable for probing the RecA nucleoprotein filament, Org. Lett. 3, 3919-3922.
    • (2001) Org. Lett , vol.3 , pp. 3919-3922
    • Singleton, S.F.1    Shan, F.2    Kanan, M.W.3    Mcintosh, C.M.4    Sterman, C.J.5    Helm, J.S.6    Webb, K.J.7
  • 37
    • 24944436333 scopus 로고    scopus 로고
    • Fluorescent properties of base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield
    • Sandin, P., Wilhelmsson, M. L., Lincoln, P, Powers, V. E., Brown, T., and Albinsson, B. (2005) Fluorescent properties of base analogue tC upon incorporation into DNA - negligible influence of neighbouring bases on fluorescence quantum yield, Nucleic Acids Res. 33, 5019-5025.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5019-5025
    • Sandin, P.1    Wilhelmsson, M.L.2    Lincoln, P.3    Powers, V.E.4    Brown, T.5    Albinsson, B.6
  • 38
    • 0028827318 scopus 로고    scopus 로고
    • Joyce, C. M., and V. Derbyshire, V. (1995) Purification of Escherichia coli DNA polymerase I and Klenow fragment, Methods Enzymol. 262, 3-13.
    • Joyce, C. M., and V. Derbyshire, V. (1995) Purification of Escherichia coli DNA polymerase I and Klenow fragment, Methods Enzymol. 262, 3-13.
  • 40
    • 0842311287 scopus 로고    scopus 로고
    • Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase
    • Bailey, M. F., Van der Schans, E. J. C., and Millar, D. P. (2004) Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase, J. Mol. Biol. 336, 673-693.
    • (2004) J. Mol. Biol , vol.336 , pp. 673-693
    • Bailey, M.F.1    Van der Schans, E.J.C.2    Millar, D.P.3
  • 41
    • 0032478136 scopus 로고    scopus 로고
    • Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment
    • Furey, W. S., Joyce, C. M., Osborne, M. A., Klenerman, D., Peliska, J. A., and Balasubramanian, S. (1998) Use of fluorescence resonance energy transfer to investigate the conformation of DNA substrates bound to the Klenow fragment, Biochemistry 37, 2979-2990.
    • (1998) Biochemistry , vol.37 , pp. 2979-2990
    • Furey, W.S.1    Joyce, C.M.2    Osborne, M.A.3    Klenerman, D.4    Peliska, J.A.5    Balasubramanian, S.6
  • 42
    • 0033525079 scopus 로고    scopus 로고
    • Interaction of Escherichia coli DNA polymerase I (Klenow fragment) with primer-templates containing N-acetyl-2-aminofluorene or N-2-aminofluorene adducts in the active site
    • Dzantiev, L., and Romano, L. J. (1999) Interaction of Escherichia coli DNA polymerase I (Klenow fragment) with primer-templates containing N-acetyl-2-aminofluorene or N-2-aminofluorene adducts in the active site, J. Biol. Chem. 274 3279-3284.
    • (1999) J. Biol. Chem , vol.274 , pp. 3279-3284
    • Dzantiev, L.1    Romano, L.J.2
  • 43
    • 0041823551 scopus 로고    scopus 로고
    • Use of 2-aminopurine to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment)
    • Purohit, V. Grindley, N. D. F., and Joyce, C. M. (2003) Use of 2-aminopurine to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment), Biochemistry 42, 10200-10211.
    • (2003) Biochemistry , vol.42 , pp. 10200-10211
    • Purohit, V.1    Grindley, N.D.F.2    Joyce, C.M.3
  • 44
    • 34248370198 scopus 로고    scopus 로고
    • A unified kinetic mechanism applicable to multiple DNA polymerases
    • Bakhtina, M., Roettger, M. P., Kumar, S., and Tsai, M.-D. (2007) A unified kinetic mechanism applicable to multiple DNA polymerases, Biochemistry 46, 5463-5472.
    • (2007) Biochemistry , vol.46 , pp. 5463-5472
    • Bakhtina, M.1    Roettger, M.P.2    Kumar, S.3    Tsai, M.-D.4
  • 45
    • 33747462891 scopus 로고    scopus 로고
    • A new paradigm for DNA polymerase specificity
    • Tsai, C.-H., and Johnson, K. A. (2006) A new paradigm for DNA polymerase specificity, Biochemistry 45, 9675-9687.
    • (2006) Biochemistry , vol.45 , pp. 9675-9687
    • Tsai, C.-H.1    Johnson, K.A.2
  • 46
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.