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Volumn 44, Issue 39, 2005, Pages 13101-13110

The use of nonnatural nucleotides to probe the contributions of shape complementarity and π-electron surface area during DNA polymerization

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CATALYST ACTIVITY; ELECTRONS; ENZYME KINETICS; ENZYMES; POLYMERIZATION; SYNTHESIS (CHEMICAL);

EID: 25444443087     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi050585f     Document Type: Article
Times cited : (50)

References (37)
  • 1
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Sponer, J., Leszczynski, J., and Hobza, P. (2002) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 61, 3-31.
    • (2002) Biopolymers , vol.61 , pp. 3-31
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 2
    • 0029045480 scopus 로고
    • Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns
    • Horlacher, J., Hottiger, M., Podust, V. N., Hubscher, U., and Benner, S. A. (1995) Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns. Proc. Natl. Acad. Sci. U.S.A. 92, 6329-6333.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 6329-6333
    • Horlacher, J.1    Hottiger, M.2    Podust, V.N.3    Hubscher, U.4    Benner, S.A.5
  • 3
    • 0030967829 scopus 로고    scopus 로고
    • A thymidine triphosphate shape analogue lacking Watson-Crick pairing ability is replicated with high sequence selectivity
    • Moran, S., Ren, R. X., and Kool, E. T. (1997) A thymidine triphosphate shape analogue lacking Watson-Crick pairing ability is replicated with high sequence selectivity. Proc. Natl. Acad. Sci. U.S.A. 94, 10506-10511.
    • (1997) Proc. Natl. Acad. Sci. U.S.A. , vol.94 , pp. 10506-10511
    • Moran, S.1    Ren, R.X.2    Kool, E.T.3
  • 4
    • 0033572961 scopus 로고    scopus 로고
    • Efforts toward the expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base
    • McMinn, D. L., Ogawa, A. K., Wu, Y. O., Shultz, P. G., and Romesberg, F. E. (1999) Efforts toward the expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base. J. Am. Chem. Soc. 121. 11585-11586.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 11585-11586
    • McMinn, D.L.1    Ogawa, A.K.2    Wu, Y.O.3    Shultz, P.G.4    Romesberg, F.E.5
  • 5
    • 0042318760 scopus 로고    scopus 로고
    • Enzymatic incorporation of an unnatural base pair between 4-propynyl-pyrrole-2-carbaldehyde and 9-methyl-imidazo [(4, 5)b]pyridine into nucleic acids
    • Mitsui, T., Kimoto, M., Harada, Y., Sato, A., Kitamura, A., To, T., Hirao, I., and Yokoyama, S. (2002) Enzymatic incorporation of an unnatural base pair between 4-propynyl-pyrrole-2-carbaldehyde and 9-methyl-imidazo [(4, 5)b]pyridine into nucleic acids. Nucleic Acids Res. (Suppl. 2), 219-220.
    • (2002) Nucleic Acids Res. , Issue.SUPPL. 2 , pp. 219-220
    • Mitsui, T.1    Kimoto, M.2    Harada, Y.3    Sato, A.4    Kitamura, A.5    To, T.6    Hirao, I.7    Yokoyama, S.8
  • 6
    • 0033578081 scopus 로고    scopus 로고
    • A specific partner for abasic damage in DNA
    • Matray, T. J., and Kool, E. T. (1999) A specific partner for abasic damage in DNA. Nature 399, 704-709.
    • (1999) Nature , vol.399 , pp. 704-709
    • Matray, T.J.1    Kool, E.T.2
  • 8
    • 0037133706 scopus 로고    scopus 로고
    • Quantitative measurement of translesion replication in human cells: Evidence for bypass of abasic sites by a replicative DNA polymerase
    • Avkin, S., Adar, S., Blander, G., and Livneh, Z. (2002) Quantitative measurement of translesion replication in human cells: evidence for bypass of abasic sites by a replicative DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 99, 3764-3769.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 3764-3769
    • Avkin, S.1    Adar, S.2    Blander, G.3    Livneh, Z.4
  • 9
    • 0030971099 scopus 로고    scopus 로고
    • Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the "A rule"
    • Shibutani, S., Takeshita, M., and Grollman, A. P. (1997) Translesional synthesis on DNA templates containing a single abasic site. A mechanistic study of the "A rule". J. Biol. Chem. 272, 13916-13922.
    • (1997) J. Biol. Chem. , vol.272 , pp. 13916-13922
    • Shibutani, S.1    Takeshita, M.2    Grollman, A.P.3
  • 10
    • 0031034183 scopus 로고    scopus 로고
    • Mechanism of bypass synthesis through an abasic site analogue by DNA polymerase I
    • Paz-Elizur, T., Takeshita, M., and Livneh, Z. (1997) Mechanism of bypass synthesis through an abasic site analogue by DNA polymerase I. Biochemistry 36, 1766-1773.
    • (1997) Biochemistry , vol.36 , pp. 1766-1773
    • Paz-Elizur, T.1    Takeshita, M.2    Livneh, Z.3
  • 11
    • 0023664684 scopus 로고
    • Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/ apyrimidinic endonucleases
    • Takeshita, M., Chang, C. N., Johnson, F., Will, S., and Grollman, A. P. (1987) Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/ apyrimidinic endonucleases. J. Biol. Chem. 262, 10171-10179.
    • (1987) J. Biol. Chem. , vol.262 , pp. 10171-10179
    • Takeshita, M.1    Chang, C.N.2    Johnson, F.3    Will, S.4    Grollman, A.P.5
  • 12
    • 0027518205 scopus 로고
    • Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase
    • Cai, H., Bloom, L. B., Eritja, R., and Goodman, M. F. (1993) Kinetics of deoxyribonucleotide insertion and extension at abasic template lesions in different sequence contexts using HIV-1 reverse transcriptase. J. Biol. Chem. 268, 23567-23572.
    • (1993) J. Biol. Chem. , vol.268 , pp. 23567-23572
    • Cai, H.1    Bloom, L.B.2    Eritja, R.3    Goodman, M.F.4
  • 13
    • 0035912947 scopus 로고    scopus 로고
    • Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase
    • Berdis, A. J. (2001) Dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 exonuclease-deficient DNA polymerase. Biochemistry 40, 7180-7191.
    • (2001) Biochemistry , vol.40 , pp. 7180-7191
    • Berdis, A.J.1
  • 14
    • 0346463162 scopus 로고    scopus 로고
    • Evaluating the contribution of base stacking during translesion DNA replication
    • Reineks, E. Z., and Berdis, A. J. (2004) Evaluating the contribution of base stacking during translesion DNA replication. Biochemistry 43, 393-404.
    • (2004) Biochemistry , vol.43 , pp. 393-404
    • Reineks, E.Z.1    Berdis, A.J.2
  • 15
    • 0027984280 scopus 로고
    • 5-Nitroindole as an universal base analogue
    • Loakes, D., and Brown, D. M. (1994) 5-Nitroindole as an universal base analogue. Nucleic Acids Res. 22, 4039-4043.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4039-4043
    • Loakes, D.1    Brown, D.M.2
  • 16
    • 3042798863 scopus 로고    scopus 로고
    • Evaluating the contributions of desolvation and base-stacking during translesion DNA synthesis
    • Zhang, X., Lee, I., and Berdis, A. J. (2004) Evaluating the contributions of desolvation and base-stacking during translesion DNA synthesis. Org. Biomol. Chem. 2, 1703-1711.
    • (2004) Org. Biomol. Chem. , vol.2 , pp. 1703-1711
    • Zhang, X.1    Lee, I.2    Berdis, A.J.3
  • 17
    • 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
  • 18
    • 0027394216 scopus 로고
    • Construction and characterization of a bacteriophage T4 DNA polymerase deficient in 3′-5′ exonuclease activity
    • Frey, M. W., Nossal, N. G., Capson, T. I., and Benkovic, S. J. (1993) Construction and characterization of a bacteriophage T4 DNA polymerase deficient in 3′-5′ exonuclease activity. Proc. Natl. Acad. Sci. U.S.A. 90, 2579-2583.
    • (1993) Proc. Natl. Acad. Sci. U.S.A. , vol.90 , pp. 2579-2583
    • Frey, M.W.1    Nossal, N.G.2    Capson, T.I.3    Benkovic, S.J.4
  • 19
    • 0024955649 scopus 로고
    • Rapid purification of overexpressed T4 DNA polymerase
    • Rush, J., and Konigsberg, W. H. (1989) Rapid purification of overexpressed T4 DNA polymerase. Prepr. Biochem. 19, 329-340.
    • (1989) Prepr. Biochem. , vol.19 , pp. 329-340
    • Rush, J.1    Konigsberg, W.H.2
  • 20
    • 0029036729 scopus 로고
    • 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR
    • Loakes, D., Brown, D. M., Linde, S., and Hill, F. (1995) 3-Nitropyrrole and 5-nitroindole as universal bases in primers for DNA sequencing and PCR. Nucleic Acids Res. 23, 2361-2366.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 2361-2366
    • Loakes, D.1    Brown, D.M.2    Linde, S.3    Hill, F.4
  • 21
    • 0001627456 scopus 로고
    • Synthesis of some 5-substituted indoles
    • Yang, Y., Martin, A., Nelson, D. L., and Regan, J. (1992) Synthesis of some 5-substituted indoles. Heterocycles 34, 1169-1175.
    • (1992) Heterocycles , vol.34 , pp. 1169-1175
    • Yang, Y.1    Martin, A.2    Nelson, D.L.3    Regan, J.4
  • 22
    • 44049116120 scopus 로고
    • Synthesis of 5-arylated indoles via palladium-catalyzed cross-coupling reaction of 5-indoylboronic acid with aryl and heteroaryl halides
    • Yang, Y., and Martin, A. (1992) Synthesis of 5-arylated indoles via palladium-catalyzed cross-coupling reaction of 5-indoylboronic acid with aryl and heteroaryl halides. Heterocycles 34, 1395-1398.
    • (1992) Heterocycles , vol.34 , pp. 1395-1398
    • Yang, Y.1    Martin, A.2
  • 24
    • 0022537369 scopus 로고
    • Mechanism of DNA polymerase I: Exonuclease/polymerase activity switch and DNA sequence dependence of pyrophosphorolysis and misincorporation reactions
    • Mizrahi, V., Benkovic, P. A., and Benkovic, S. J. (1986) Mechanism of DNA polymerase I: exonuclease/polymerase activity switch and DNA sequence dependence of pyrophosphorolysis and misincorporation reactions. Proc. Natl. Acad. Sci. U.S.A. 83, 5769-5773.
    • (1986) Proc. Natl. Acad. Sci. U.S.A. , vol.83 , pp. 5769-5773
    • Mizrahi, V.1    Benkovic, P.A.2    Benkovic, S.J.3
  • 25
    • 0028916224 scopus 로고
    • Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates
    • Johnson, K. A. (1995) Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates. Methods Enzymol. 249, 38-61.
    • (1995) Methods Enzymol. , vol.249 , pp. 38-61
    • Johnson, K.A.1
  • 26
    • 0034430847 scopus 로고    scopus 로고
    • Kinetics: A tool to study molecular motors
    • Gilbert, S. P., and Mackey, A. T. (2000) Kinetics: a tool to study molecular motors. Methods 22, 337-354.
    • (2000) Methods , vol.22 , pp. 337-354
    • Gilbert, S.P.1    Mackey, A.T.2
  • 28
    • 0034979126 scopus 로고    scopus 로고
    • Hydrogen bonding, base stacking, and steric effects in DNA replication
    • Kool, E. T. (2001) Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu. Rev. Biophys. Biomol. Struct. 30, 1-22.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 1-22
    • Kool, E.T.1
  • 29
    • 0037196080 scopus 로고    scopus 로고
    • New structural and mechanistic insight into the A-rule and the instructional and noninstructional behavior of DNA photoproducts and other lesions
    • Taylor, J. S. (2002) New structural and mechanistic insight into the A-rule and the instructional and noninstructional behavior of DNA photoproducts and other lesions. Mutat. Res. 510, 55-70.
    • (2002) Mutat. Res. , vol.510 , pp. 55-70
    • Taylor, J.S.1
  • 30
    • 0026738750 scopus 로고
    • Structure and function of the bacteriophage T4 DNA polymerase holoenzyme
    • Young, M. C. Reddy, M. K., and Von Hippel, P. H. (1992) Structure and function of the bacteriophage T4 DNA polymerase holoenzyme. Biochemistry 31, 8675-8690.
    • (1992) Biochemistry , vol.31 , pp. 8675-8690
    • Young, M.C.1    Reddy, M.K.2    Von Hippel, P.H.3
  • 31
    • 0031587827 scopus 로고    scopus 로고
    • Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69
    • Wang, J., Sattar, A. K., Wang, C. C., Karam, J. D., Konigsberg, W. H., and Steitz, T. A. (1997) Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. Cell 89, 1087-1099.
    • (1997) Cell , vol.89 , pp. 1087-1099
    • Wang, J.1    Sattar, A.K.2    Wang, C.C.3    Karam, J.D.4    Konigsberg, W.H.5    Steitz, T.A.6
  • 33
    • 0035369086 scopus 로고    scopus 로고
    • Structure of the replicating complex of a pol alpha family DNA polymerase
    • Franklin, M. C., Wang, J., and Steitz, T. A. (2001) Structure of the replicating complex of a pol alpha 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
  • 34
    • 2342537864 scopus 로고    scopus 로고
    • Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site
    • Hogg, M., Wallace, S. 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.S.2    Doublie, S.3
  • 35
    • 4243067681 scopus 로고    scopus 로고
    • Protein stabilization by removal of unsatisfied polar groups: Computational approaches and experimental tests
    • Hendsch, Z. S., Jonsson, T., Sauer, R. T., and Tidor, B. (1996) Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests. Biochemistry 35, 7621-7625.
    • (1996) Biochemistry , vol.35 , pp. 7621-7625
    • Hendsch, Z.S.1    Jonsson, T.2    Sauer, R.T.3    Tidor, B.4
  • 36
    • 0035997351 scopus 로고    scopus 로고
    • Active site tightness and substrate fit in DNA replication
    • Kool, E. T. (2002) Active site tightness and substrate fit in DNA replication. Annu. Rev. Biochem. 71, 191-219.
    • (2002) Annu. Rev. Biochem. , vol.71 , pp. 191-219
    • Kool, E.T.1
  • 37
    • 0042318450 scopus 로고    scopus 로고
    • Facile polymerization of dNTPs bearing unnatural base analogues by DNA polymerase alpha and Klenow fragment (DNA polymerase I)
    • Chiaramonte, M., Moore, C. L., Kincaid, K., and Kuchta, R. D. (2003) Facile polymerization of dNTPs bearing unnatural base analogues by DNA polymerase alpha and Klenow fragment (DNA polymerase I). Biochemistry 42, 10472-10481.
    • (2003) Biochemistry , vol.42 , pp. 10472-10481
    • Chiaramonte, M.1    Moore, C.L.2    Kincaid, K.3    Kuchta, R.D.4


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