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Volumn 361, Issue 3, 2006, Pages 537-550

Directed Evolution of DNA Polymerase, RNA Polymerase and Reverse Transcriptase Activity in a Single Polypeptide

Author keywords

directed evolution; DNA polymerases; enzyme evolution; PCR; protein engineering

Indexed keywords

DEOXYRIBONUCLEOTIDE; DNA DIRECTED DNA POLYMERASE BETA; DNA POLYMERASE; POLYPEPTIDE; RIBONUCLEOTIDE; RNA DIRECTED DNA POLYMERASE; RNA POLYMERASE;

EID: 33746347051     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.06.050     Document Type: Article
Times cited : (87)

References (36)
  • 1
    • 0026639873 scopus 로고
    • DNA replication fidelity
    • Kunkel T.A. DNA replication fidelity. J. Biol. Chem. 267 (1992) 18251-18254
    • (1992) J. Biol. Chem. , vol.267 , pp. 18251-18254
    • Kunkel, T.A.1
  • 2
    • 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. 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 (1998) 7514-7525
    • (1998) EMBO J. , vol.17 , pp. 7514-7525
    • Li, Y.1    Korolev, S.2    Waksman, G.3
  • 3
    • 0032518398 scopus 로고    scopus 로고
    • Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution (see comments)
    • Doublié S., Tabor S., Long A.M., Richardson C.C., and Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution (see comments). Nature 391 (1998) 251-258
    • (1998) Nature , vol.391 , pp. 251-258
    • Doublié, S.1    Tabor, S.2    Long, A.M.3    Richardson, C.C.4    Ellenberger, T.5
  • 4
    • 0032518524 scopus 로고    scopus 로고
    • Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
    • Kiefer J.R., Mao C., Braman J.C., and Beese L.S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature 391 (1998) 304-307
    • (1998) Nature , vol.391 , pp. 304-307
    • Kiefer, J.R.1    Mao, C.2    Braman, J.C.3    Beese, L.S.4
  • 5
    • 1642588255 scopus 로고    scopus 로고
    • Structures of mismatch replication errors observed in a DNA polymerase
    • Johnson S.J., and Beese L.S. Structures of mismatch replication errors observed in a DNA polymerase. Cell 116 (2004) 803-816
    • (2004) Cell , vol.116 , pp. 803-816
    • Johnson, S.J.1    Beese, L.S.2
  • 6
    • 0037388383 scopus 로고    scopus 로고
    • Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations
    • Johnson S.J., Taylor J.S., and Beese L.S. Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations. Proc. Natl Acad. Sci. USA 100 (2003) 38895-38900
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 38895-38900
    • Johnson, S.J.1    Taylor, J.S.2    Beese, L.S.3
  • 7
    • 0034711010 scopus 로고    scopus 로고
    • Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases
    • Morales J.C., and Kool E.T. Functional hydrogen-bonding map of the minor groove binding tracks of six DNA polymerases. Biochemistry 39 (2000) 12979-12988
    • (2000) Biochemistry , vol.39 , pp. 12979-12988
    • Morales, J.C.1    Kool, E.T.2
  • 8
    • 0035997351 scopus 로고    scopus 로고
    • Active site tightness and substrate fit in DNA replication
    • Kool E.T. Active site tightness and substrate fit in DNA replication. Annu. Rev. Biochem. 71 (2002) 191-219
    • (2002) Annu. Rev. Biochem. , vol.71 , pp. 191-219
    • Kool, E.T.1
  • 9
    • 13544276569 scopus 로고    scopus 로고
    • Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication
    • Hsu G.W., Huang X., Luneva N.P., Geacintov N.E., and Beese L.S. Structure of a high fidelity DNA polymerase bound to a benzo[a]pyrene adduct that blocks replication. J. Biol. Chem. 280 (2005) 3764-3770
    • (2005) J. Biol. Chem. , vol.280 , pp. 3764-3770
    • Hsu, G.W.1    Huang, X.2    Luneva, N.P.3    Geacintov, N.E.4    Beese, L.S.5
  • 10
    • 4544273926 scopus 로고    scopus 로고
    • Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase
    • Hsu G.W., Ober M., Carell T., and Beese L.S. Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature 431 (2004) 2172-2221
    • (2004) Nature , vol.431 , pp. 2172-2221
    • Hsu, G.W.1    Ober, M.2    Carell, T.3    Beese, L.S.4
  • 11
    • 0033578332 scopus 로고    scopus 로고
    • Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation
    • Li Y., Mitaxov V., and Waksman G. Structure-based design of Taq DNA polymerases with improved properties of dideoxynucleotide incorporation. Proc. Natl Acad. Sci. USA 96 (1999) 9491-9496
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 9491-9496
    • Li, Y.1    Mitaxov, V.2    Waksman, G.3
  • 12
    • 0031028380 scopus 로고    scopus 로고
    • Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection
    • Gao G., Orlova M., Georgiadis M.M., Hendrickson W.A., and Goff S.P. Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection. Proc. Natl Acad. Sci. USA 94 (1997) 407-411
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 407-411
    • Gao, G.1    Orlova, M.2    Georgiadis, M.M.3    Hendrickson, W.A.4    Goff, S.P.5
  • 13
    • 0032562549 scopus 로고    scopus 로고
    • How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides
    • Astatke M., Grindley N.D., and Joyce C.M. How E. coli DNA polymerase I (Klenow fragment) distinguishes between deoxy- and dideoxynucleotides. J. Mol. Biol. 278 (1998) 147-165
    • (1998) J. Mol. Biol. , vol.278 , pp. 147-165
    • Astatke, M.1    Grindley, N.D.2    Joyce, C.M.3
  • 14
    • 0242317682 scopus 로고    scopus 로고
    • An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides
    • DeLucia A.M., Grindley N.D., and Joyce C.M. An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides. Nucl. Acids Res. 31 (2003) 4129-4137
    • (2003) Nucl. Acids Res. , vol.31 , pp. 4129-4137
    • DeLucia, A.M.1    Grindley, N.D.2    Joyce, C.M.3
  • 15
    • 0034704124 scopus 로고    scopus 로고
    • Multiple amino acid substitutions allow DNA polymerases to synthesize RNA
    • Patel P.H., and Loeb L.A. Multiple amino acid substitutions allow DNA polymerases to synthesize RNA. J. Biol. Chem. 275 (2000) 40266-40272
    • (2000) J. Biol. Chem. , vol.275 , pp. 40266-40272
    • Patel, P.H.1    Loeb, L.A.2
  • 16
    • 0037076311 scopus 로고    scopus 로고
    • Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase
    • Xia G., Chen L., Sera T., Fa M., Schultz P.G., and Romesberg F.E. Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase. Proc. Natl Acad. Sci. USA 99 (2002) 6597-6602
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 6597-6602
    • Xia, G.1    Chen, L.2    Sera, T.3    Fa, M.4    Schultz, P.G.5    Romesberg, F.E.6
  • 17
    • 1242314258 scopus 로고    scopus 로고
    • Expanding the substrate repertoire of a DNA polymerase by directed evolution
    • Fa M., Radeghieri A., Henry A.A., and Romesberg F.E. Expanding the substrate repertoire of a DNA polymerase by directed evolution. J. Am. Chem. Soc. 126 (2004) 1748-1754
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 1748-1754
    • Fa, M.1    Radeghieri, A.2    Henry, A.A.3    Romesberg, F.E.4
  • 18
    • 24744447201 scopus 로고    scopus 로고
    • Polymerase evolution: efforts toward expansion of the genetic code
    • Leconte A.M., Chen L., and Romesberg F.E. Polymerase evolution: efforts toward expansion of the genetic code. J. Am. Chem. Soc. 127 (2005) 12470-12471
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 12470-12471
    • Leconte, A.M.1    Chen, L.2    Romesberg, F.E.3
  • 19
    • 0035836707 scopus 로고    scopus 로고
    • Directed evolution of polymerase function by compartmentalized self-replication
    • Ghadessy F.J., Ong J.L., and Holliger P. Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl Acad. Sci. USA 98 (2001) 4552-4557
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 4552-4557
    • Ghadessy, F.J.1    Ong, J.L.2    Holliger, P.3
  • 20
    • 0031854986 scopus 로고    scopus 로고
    • Man-made cell-like compartments for molecular evolution
    • Tawfik D.S., and Griffiths A.D. Man-made cell-like compartments for molecular evolution. Nature Biotechnol. 16 (1998) 652-656
    • (1998) Nature Biotechnol. , vol.16 , pp. 652-656
    • Tawfik, D.S.1    Griffiths, A.D.2
  • 21
    • 2542525398 scopus 로고    scopus 로고
    • Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution
    • Ghadessy F.J., Ramsay N., Boudsocq F., Loakes D., Brown A., Iwai S., et al. Generic expansion of the substrate spectrum of a DNA polymerase by directed evolution. Nature Biotechnol. 22 (2004) 755-759
    • (2004) Nature Biotechnol. , vol.22 , pp. 755-759
    • Ghadessy, F.J.1    Ramsay, N.2    Boudsocq, F.3    Loakes, D.4    Brown, A.5    Iwai, S.6
  • 22
    • 2642699794 scopus 로고
    • Rapid and efficient site-specific mutagenesis without phenotypic selection
    • Kunkel T.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc. Natl Acad. Sci. USA 82 (1985) 488-492
    • (1985) Proc. Natl Acad. Sci. USA , vol.82 , pp. 488-492
    • Kunkel, T.A.1
  • 23
    • 0028834955 scopus 로고
    • Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies
    • Creighton S., Bloom L.B., and Goodman M.F. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods Enzymol. 262 (1995) 232-256
    • (1995) Methods Enzymol. , vol.262 , pp. 232-256
    • Creighton, S.1    Bloom, L.B.2    Goodman, M.F.3
  • 24
    • 0033613841 scopus 로고    scopus 로고
    • Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment)
    • Minnick D.T., Bebenek K., Osheroff W.P., Turner R.M.J., Astatke M., Liu L., et al. Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment). J. Biol. Chem. 274 (1999) 3067-3075
    • (1999) J. Biol. Chem. , vol.274 , pp. 3067-3075
    • Minnick, D.T.1    Bebenek, K.2    Osheroff, W.P.3    Turner, R.M.J.4    Astatke, M.5    Liu, L.6
  • 25
    • 0035846958 scopus 로고    scopus 로고
    • In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates
    • Matsumura I., and Ellington A.D. In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305 (2001) 331-339
    • (2001) J. Mol. Biol. , vol.305 , pp. 331-339
    • Matsumura, I.1    Ellington, A.D.2
  • 26
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30 (1976) 409-425
    • (1976) Annu. Rev. Microbiol. , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 28
    • 0029091457 scopus 로고
    • A mutant T7 RNA polymerase as a DNA polymerase
    • Sousa R., and Padilla R. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14 (1995) 4609-4621
    • (1995) EMBO J. , vol.14 , pp. 4609-4621
    • Sousa, R.1    Padilla, R.2
  • 29
    • 0033559119 scopus 로고    scopus 로고
    • Efficient synthesis of nucleic acids heavily modified with non-canonical ribose 2′-groups using a mutantT7 RNA polymerase (RNAP)
    • Padilla R., and Sousa R. Efficient synthesis of nucleic acids heavily modified with non-canonical ribose 2′-groups using a mutantT7 RNA polymerase (RNAP). Nucl. Acids Res. 27 (1999) 1561-1563
    • (1999) Nucl. Acids Res. , vol.27 , pp. 1561-1563
    • Padilla, R.1    Sousa, R.2
  • 30
    • 0025988479 scopus 로고
    • Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase
    • Myers T.W., and Gelfand D.H. Reverse transcription and DNA amplification by a Thermus thermophilus DNA polymerase. Biochemistry 30 (1991) 7661-7666
    • (1991) Biochemistry , vol.30 , pp. 7661-7666
    • Myers, T.W.1    Gelfand, D.H.2
  • 31
    • 0034657619 scopus 로고    scopus 로고
    • Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC)
    • Xiong Y., and Sundaralingam M. Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). Nucl. Acids Res. 28 (2000) 2171-2176
    • (2000) Nucl. Acids Res. , vol.28 , pp. 2171-2176
    • Xiong, Y.1    Sundaralingam, M.2
  • 32
    • 0027190862 scopus 로고
    • The DNA strand in DNA.RNA hybrid duplexes is neither B-form nor A-form in solution
    • Salazar M., Fedoroff O.Y., Miller J.M., Ribeiro N.S., and Reid B.R. The DNA strand in DNA.RNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry 32 (1993) 4207-4215
    • (1993) Biochemistry , vol.32 , pp. 4207-4215
    • Salazar, M.1    Fedoroff, O.Y.2    Miller, J.M.3    Ribeiro, N.S.4    Reid, B.R.5
  • 33
    • 0031556022 scopus 로고    scopus 로고
    • Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis
    • Fedoroff O.Y., Ge Y., and Reid B.R. Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis. J. Mol. Biol. 269 (1997) 225-239
    • (1997) J. Mol. Biol. , vol.269 , pp. 225-239
    • Fedoroff, O.Y.1    Ge, Y.2    Reid, B.R.3
  • 34
    • 0037112343 scopus 로고    scopus 로고
    • Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication
    • Yang M.Y., Bowmaker M., Reyes A., Vergani L., Angeli P., Gringeri E., et al. Biased incorporation of ribonucleotides on the mitochondrial L-strand accounts for apparent strand-asymmetric DNA replication. Cell 111 (2002) 495-505
    • (2002) Cell , vol.111 , pp. 495-505
    • Yang, M.Y.1    Bowmaker, M.2    Reyes, A.3    Vergani, L.4    Angeli, P.5    Gringeri, E.6
  • 35
    • 0017849404 scopus 로고
    • DNA sequencing by partial ribosubstitution
    • Barnes W.M. DNA sequencing by partial ribosubstitution. J. Mol. Biol. 119 (1978) 83-99
    • (1978) J. Mol. Biol. , vol.119 , pp. 83-99
    • Barnes, W.M.1
  • 36
    • 0028834955 scopus 로고
    • Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies
    • Creighton S., Bloom L.B., and Goodman M.F. Gel fidelity assay measuring nucleotide misinsertion, exonucleolytic proofreading, and lesion bypass efficiencies. Methods Enzymol. 262 (1995) 232-256
    • (1995) Methods Enzymol. , vol.262 , pp. 232-256
    • Creighton, S.1    Bloom, L.B.2    Goodman, M.F.3


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