Hostname: page-component-84b7d79bbc-5lx2p Total loading time: 0 Render date: 2024-07-26T18:06:37.461Z Has data issue: false hasContentIssue false

Multi-stage proofreading in DNA replication

Published online by Cambridge University Press:  17 March 2009

Robert A. Beckman
Affiliation:
Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111
Lawrence A. Loeb
Affiliation:
Joseph Gottstein Memorial Cancer Research Laboratory, Department of Pathology SM-30, University of Washington, Seattle, WA 98195

Extract

The mechanisms by which DNA polymerases achieve their remarkable fidelity, including base selection and proofreading, are briefly reviewed. Nine proofreading models from the current literature are evaluated in the light of steady-state and transient kinetic studies of E. coli DNA polymerase I, the beststudied DNA polymerase.

Type
Research Article
Copyright
Copyright © Cambridge University Press 1993

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abbotts, J. & Loeb, L. A. (1984). On the fidelity of DNA replication. Lack of primer position effect on the fidelity of mammalian DNA polymerases. J. biol. Chem. 259, 67126714.CrossRefGoogle ScholarPubMed
Abbotts, J. & Loeb, L. A. (1985). DNA polymerase-α and models for proofreading. Nucleic Acids Res. 13, 261274.CrossRefGoogle ScholarPubMed
Abbotts, J., SenGupta, D. N., Zon, G. & Wilson, S. H. (1988). Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Effect of template sequence and substrate variation on termination of synthesis, J. biol. Chem. 263, 1509415103.CrossRefGoogle ScholarPubMed
Agarwal, S. S., Dube, D. K. & Loeb, L. A. (1979). On the fidelity of DNA replication. VII. Accuracy of E. coli DNA polymerase I. J. biol. Chem. 254, 101106.CrossRefGoogle Scholar
Allen, D. J. & Benkovic, S. J. (1989). Resonance energy transfer measurements between substrate binding sites within the large (Klenow) fragment of Escherichia coli DNA polymerase I. Biochemistry 28, 95869593.CrossRefGoogle ScholarPubMed
Baldwin, A. N. & Berg, P. (1966). Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase. j. biol. Chem. 241, 839845.CrossRefGoogle ScholarPubMed
Bambara, R. A., Uyemura, D. & Lehman, I. R. (1976). On the processive mechanism of Escherichia coli DNA polymerase I. Delayed initiation of polymerization. J. biol. Chem. 251, 40904094.CrossRefGoogle ScholarPubMed
Basu, A. & Modak, M. J. (1987). Identification and amino acid sequence of the deoxynucleoside triphosphate binding site in Escherichia coli DNA polymerase I. Biochemistry 26, 17041709.CrossRefGoogle ScholarPubMed
Battula, N. & Loeb, L. A. (1976). On the fidelity of DNA replication. Lack of exodeoxyribonuclease activity and error correcting function in avian myeloblastosis virus DNA polymerase. J. biol. Chem. 251, 982986.CrossRefGoogle ScholarPubMed
Beckman, R. A., Mildvan, A. S. & Loeb, L. A. (1985). On the fidelity of DNA replication: Manganese mutagenesis in vitro. Biochemistry 24, 58105817.CrossRefGoogle ScholarPubMed
Berg, O. G., Winter, R. B. & Von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20, 69266948.CrossRefGoogle ScholarPubMed
Berg, O. G., Winter, R. B. & Von Hippel, P. H. (1982). How do genome-regulatory proteins locate their DNA target sites? Trends biochem. Sci. 7, 5255.CrossRefGoogle Scholar
Bernad, A., Blanco, L., Lazaro, J. M., Martin, G. & Salas, M. (1989). A conserved 3′ → 5′ exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 59, 219228.CrossRefGoogle ScholarPubMed
Bernardi, F., Saghi, M., Dorizzi, M. & Ninio, J. (1979). A new approach to DNA polymerase kinetics. J. mol. Biol. 129, 93112.CrossRefGoogle ScholarPubMed
Bessman, M. J., Muzyczka, N., Goodman, M. F. & Schnaar, R. L. (1974). Studies on the biochemical basis of spontaneous mutation. II. The incorporation of a base and its analogue into DNA by wild-type, mutator and antimutator DNA polymerases. J. mol. Biol. 88, 409421.CrossRefGoogle ScholarPubMed
Blomberg, C. (1977). A kinetic recognition process for tRNA at the ribosome. J. theor. Biol. 66, 307325.CrossRefGoogle ScholarPubMed
Boosalis, M. S., Petruska, J. & Goodman, M. F. (1987). DNA polymerase insertion fidelity. Gel assay for site-specific kinetics. J. biol. Chem. 262, 1468914696.CrossRefGoogle ScholarPubMed
Boosalis, M. S., Mosbaugh, D. W., Hamatake, R., Sugino, A., Kunkel, T. A. & Goodman, M. F. (1989). DNA polymerase insertion fidelity. J. biol. Chem. 264, 1136011366.CrossRefGoogle Scholar
Brody, R. S. & Frey, P. A. (1981). Unambiguous determination of the stereochemistry of nucleotidyl transfer catalyzed by DNA polymerase I from Escherichia coli. Biochemistry 20, 12451252.CrossRefGoogle ScholarPubMed
Brown, T. C. & Jiricny, J. (1988). Different base/base mispairs are corrected with different efficiencies and specificies in monkey kidney cells. Cell 54, 705711.CrossRefGoogle Scholar
Brutlag, D. & Kornberg, A. (1972). Enzymatic synthesis of deoxyribonucleic acid. XXXVI. A proofreading function for the 3′ →5′ exonuclease activity in deoxyribonucleic acid polymerases. J. biol. Chem. 247, 241248.CrossRefGoogle Scholar
Bryant, F. R., Johnson, K. A. & Benkovic, S. J. (1983). Elementary steps in the DNA polymerase I reaction pathway. Biochemistry 22, 35373546.CrossRefGoogle ScholarPubMed
Burgers, P. M. J. & Eckstein, F. (1979). A study of the mechanism of DNA polymerase I from Escherichia coli with diastereomeric phosphorothioate analogs of deoxyadenosine triphosphate. J. biol. Chem. 254, 68896893.CrossRefGoogle ScholarPubMed
Byrnes, J. J., Downey, K. M., Que, B. G., Lee, M. Y. M., Black, V. L. & So, A. G. (1977). Selective inhibition of the 3′ to 5′ exonuclease activity associated with DNA polymerases: a mechanism of mutagenesis. Biochemistry 16, 37403746.CrossRefGoogle ScholarPubMed
Capson, T. L., Peliska, J. A., Kaboord, B. F., Frey, M. W., Lively, C., Dahlberg, M. & Benkovic, S. J. (1992). Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4. Biochemistry 32, 1098410994.CrossRefGoogle Scholar
Catalano, C. E. & Benkovic, S. J. (1989). Inactivation of DNA polymerase I (Klenow fragment) by adenosine 2′, 3′-epoxide 5′-triphosphate: evidence for the formation of a tight-binding inhibitor. Biochemistry 28, 43744382.CrossRefGoogle ScholarPubMed
Clayton, L. K., Goodman, M. F., Branscomb, E. W. & Galas, D. J. (1979). Error induction and correction by mutant and wild type T4 DNA polymerases: Kinetic error discrimination mechanisms. j. biol. Chem. 254, 19021912.CrossRefGoogle ScholarPubMed
Cotterill, S. M., Reyland, M. E., Loeb, L. A. & Lehman, I. R. (1987). A cryptic proofreading 3′ → 5′ exonuclease associated with the polymerase subunit of the DNA polymerase-primase from Drosophila melanogaster. Proc. natn. Acad. Sci. U.S.A. 84, 56355639.CrossRefGoogle ScholarPubMed
Cowart, M., Gibson, K. H., Allen, D. J. & Benkovic, S. J. (1989). DNA substrate structural requirements for the exonuclease and polymerase activities of procaryotic and phage DNA polymerases. Biochemistry 8, 19751983.CrossRefGoogle Scholar
Crick, F. H. C. (1975). General discussion following: A discussion on the physics and chemistry of biological recognition. Phil. Trans. R. Soc. Lond. B 272, 193194.Google Scholar
Dahlberg, M. E. & Benkovic, S. J. (1991). Kinetic mechanism of DNA polymerase I (Klenow fragment): identification of a second conformational change and evaluation of the internal equilibrium constant. Biochemistry 30, 48354843.CrossRefGoogle ScholarPubMed
Derbyshire, V., Freemont, P. S., Sanderson, M. R., Beese, L., Friedman, J. M., Joyce, C. M. & Steitz, T. A. (1988). Genetic and crystallographic studies of the 3′ → 5′ exonucleolytic site of DNA polymerase I. Science 240, 199201.CrossRefGoogle ScholarPubMed
Detera, S. D., Becerra, S. P., Swack, J. A. & Wilson, S. H. (1981). Studies on the mechanism of DNA polymerase. Nascent chain elongation, steady state kinetics, and the initiation phase of DNA synthesis. j. biol. Chem. 256, 69336943.CrossRefGoogle ScholarPubMed
Detera, S. D. & Wilson, S. H. (1982). Studies on the mechanism of Escherichia coli DNA polymerase I large fragment. Chain termination and modulation by polynucleotides. j. biol. Chem. 257, 97709780.CrossRefGoogle ScholarPubMed
Deutscher, M. & Kornberg, A. (1969). Enzymatic synthesis of deoxyribonucleic acid. j. mol. Biol. 244, 30193028.Google ScholarPubMed
DiGiuseppe, J. A., Wright, G. E. & Dresler, S. L. (1989). A kinetic study of rat recombinant DNA polymerase β: detection of a slow (hysteretic) transition in polymerase activity and inhibition by butylphenyl-deoxyguanosine triphosphate. Nucleic Acids Research 1, 30793088.CrossRefGoogle Scholar
Donlin, M. J., Patel, S. S. & Johnson, K. A. (1991). Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction. Biochemistry 30, 538546.CrossRefGoogle ScholarPubMed
Drake, J. W. (1969). Comparative rates of spontaneous mutation. Nature 221, 11321133.CrossRefGoogle ScholarPubMed
Dube, D. K. & Loeb, L. A. (1989). Mutants generated by the insertion of random oligonucleotides into the active site of the β-lactamase gene. Biochemistry 28, 57035707.CrossRefGoogle ScholarPubMed
Echols, H., Lu, C. & Burgers, P. M. J. (1983). Mutator strains of Escherichia coli, mutD and dnaQ, with defective exonucleolytic editing by DNA polymerase III holoenzyme. Proc. natn. Acad. Sci. U.S.A. 80, 21892192.CrossRefGoogle ScholarPubMed
Eger, B. T., Kuchta, R. D., Carroll, S. S., Benkovic, P. A., Dahlberg, M. E., Joyce, C. M. & Benkovic, S. J. (1991). Mechanism of DNA replication fidelity for three mutants of DNA polymerase I: Klenow fragment KF(exo+), KF(polA5), and KF(exo –). Biochemistry 30, 14411448.CrossRefGoogle Scholar
Ehrenberg, M. & Blomberg, C. (1980). Thermodynamic constraints on kinetic proofreading in biosynthetic pathways. Biophys. J. 31, 333358.CrossRefGoogle ScholarPubMed
Eigen, M., Gardiner, W., Schuster, P. & Winkler-Oswatitsch, R. (1981). Origin of genetic information. Scientific American 244, 7894.CrossRefGoogle ScholarPubMed
Eldred, E. W. & Schimmel, P. (1972). Rapid deacylation by isoleucyl transfer ribonucleic acid synthetase of isoleucine-specific transfer ribonucleic acid aminoacylated with valine. J. biol. Chem. 247, 29612965.CrossRefGoogle ScholarPubMed
Engel, J. D. & von Hippel, P. H. (1978). D (M6ATP) as a probe of the fidelity of base incorporation into polynucleotides by Escherichia coli DNA polymerase I. J. biol. Chem. 253, 935939.CrossRefGoogle ScholarPubMed
Englund, P. T., Huberman, J., Jovin, T. & Kornberg, A. (1969). Enzymatic synthesisof deoxyribonucleic acid. XXX. Binding of triphosphates to deoxyribonucleic acid polymerase. j. biol. Chem. 244, 30383044.CrossRefGoogle Scholar
Ferrin, L. J., Beckman, R. A., Loeb, L. A. & Mildvan, A. S. (1986). Kinetic and magnetic resonance studies of the interaction of Mn2+, substrates and templates with DNA polymerases. In Manganese in Metabolism and Enzyme Function (eds. Schramm, V. L. & Wedler, F. C.), pp. 259273. New York: Academic Press.CrossRefGoogle Scholar
Ferrin, L. J. & Mildvan, A. S. (1985). Nuclear Overhauser effect studies of the conformations and binding site environments of deoxynucleoside triphosphate substrates bound to DNA polymerase I and its large fragment. Biochemistry 24, 69046913.CrossRefGoogle ScholarPubMed
Ferrin, L. J. & Mildvan, A. S. (1986). NMR studies of conformations and interactions of substrates and ribonucleotide templates bound to the large fragment of DNA polymerase I. Biochemistry 25, 51315145.CrossRefGoogle Scholar
Fersht, A. R. (1977). Editing mechanisms in protein synthesis. Rejection of valine by the isoleucyl-tRNA synthetase. Biochemistry 16, 10251030.CrossRefGoogle ScholarPubMed
Fersht, A. R. (1979 a). Fidelity of replication of phage φΧ174 DNA by DNA polymerase III holoenzyme: spontaneous mutation by misincorporation. Proc. natn. Acad. Sci. U.S.A. 76, 49464950.CrossRefGoogle Scholar
Fersht, A. R. (1979 b). Editing mechanisms in the aminoacylation of tRNA. In Transfer RNA (ed. Schimmel, P., Soll, D. and Abelson, J.), pp. 247254. Cold Spring Harbor: Cold Spring Harbor Laboratory.Google Scholar
Fersht, A. R. & Dingwall, C. (1979 a). An editing mechanism for the methionyl-tRNA synthetase in the selection of amino acids in protein synthesis. Biochemistry 18, 12501256.CrossRefGoogle ScholarPubMed
Fersht, A. R. & Dingwall, C. (1979 b). Establishing the misacylation/deacylation of the tRNA pathway for the editing mechanism of prokaryotic and eukaryotic valyl-tRNA synthetases. Biochemistry 18, 12381245.CrossRefGoogle ScholarPubMed
Fersht, A. R. & Kaethner, M. (1976). Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing. Biochemistry 15, 33423346.CrossRefGoogle ScholarPubMed
Fersht, A. R. & Knill-Jones, J. W. (1983 a). Fidelity of replication of bacteriophage φΧ174 DNA in vitro and in vivo. J. mol. Biol. 165, 633654.CrossRefGoogle Scholar
Fersht, A. R. & Knill-Jones, J. W. (1983 b). Contribution of 3′ leads to 5′ exonuclease activity of DNA polymerase III holoenzyme from Escherichia coli to specificity. J. mol. Biol. 165, 669682.CrossRefGoogle ScholarPubMed
Focher, F., Ferrari, E., Spadari, S. & Hubscher, U. (1988). Do DNA polymerases δ and α act accordingly as leading and lagging strand replicases? FEBS Letters 229, 610.CrossRefGoogle Scholar
Freemont, P. S., Ollis, D. L., Steitz, T. A. & Joyce, C. M. (1986). A domain of the Klenow fragment of Escherichia coli DNA polymerase I has polymerase but no exonuclease activity. Proteins: Struct., Funct., Genet. 1, 6673.CrossRefGoogle ScholarPubMed
Freemont, P. S., Friedman, J. M., Beese, L. S., Sanderson, M. R. & Steitz, T. A. (1988). Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc. natn. Acad. Sci. U.S.A. 85, 89248928.CrossRefGoogle ScholarPubMed
Freist, W. (1989). Mechanisms of aminoacyl-tRNA synthetases: a critical consideration of recent results. Biochemistry 28, 67876795.CrossRefGoogle ScholarPubMed
Freist, W., Pardowitz, I. & Cramer, F. (1985). Isoleucyl-tRNA synthetase from baker's yeast: multistep proofreading in discriminatioin between isoleucine and valine with modulated accuracy, a scheme for molecular recognition by energy dissipation. Biochemistry 24, 70147023.CrossRefGoogle ScholarPubMed
Freist, W. & Sternbach, H. (1988). Tyrosyl-tRNA synthetase from baker's yeast. Order of substrate addition, discrimination of 20 amino acids in aminoacylation of tRNATyr-C-C-A and tRNATyr-C-C-A(3′NH2). Eur.J. Biochem. 177, 425433.CrossRefGoogle Scholar
Freist, W., Sternbach, H. & Cramer, F. (1987). Isoleucyl-tRNA synthetase from baker's yeast and from Escherichia coli MRE 600. Discrimination of 20 amino acids in aminoacylation of tRNA (Ile)-C-C-A(3′NH2). Eur.J. Biochem. 169, 3339.CrossRefGoogle Scholar
Freist, W., Sternbach, M. & Cramer, F. (1988). Isoleucyl-tRNA synthetase from baker's yeast and from Escherichia coli MRE 600. Discrimination of 20 amino acids in aminoacylation of tRNA (Ile)-C-C-A. Eur. J. Biochem. 173, 2734.CrossRefGoogle ScholarPubMed
Fresco, J. R. & Alberts, B. M. (1960). The accommodation of noncomplementary bases in helical polyribonucleotides and deoxyribonucleic acids. Proc. natn. Acad. Sci. U.S.A. 46, 311321.CrossRefGoogle ScholarPubMed
Freter, R. P. & Savageau, M. A. (1980). Proofreading systems of multiple stages for improved accuracy of biological discrimination. J. theor. Biol. 85, 99123.CrossRefGoogle ScholarPubMed
Frey, M. W., Nossal, N. G., Capson, T. L. & Benkovic, S. J. (1993). Construction and characterization of a bacteriophage T4 DNA polymerase deficient in 3′→ 5′ exonuclease activity. Proc natn. Acad. Sci. U.S.A. 90, 25792583.CrossRefGoogle ScholarPubMed
Frieden, C. (1979). Slow transitions and hysteric behavior in enzymes. A. Rev. Biochem. 48, 471489.CrossRefGoogle Scholar
Fry, M. & Loeb, L. A. (1986). Animal Cell DNA Polymerases. Boca Raton: CRC Press.Google Scholar
Galas, D. J. & Branscomb, E. W. (1978). The enzymatic determinants of DNA polymerase accuracy: Theory of T4 polymerase mechanisms. J. mol. Biol. 124, 653687.CrossRefGoogle ScholarPubMed
Gillin, F. D. & Nossal, N. G. (1975). T4 DNA polymerase has a lower apparent KM for deoxynucleoside triphosphates complementary rather than noncomplementary to the template. Biochem. biophys. Res. Commun. 64, 457464.CrossRefGoogle Scholar
Goscin, L. P. & Byrnes, J. J. (1982). DNA polymerase δ: One polypeptide, two activities. Biochemistry 21, 25132518.CrossRefGoogle ScholarPubMed
Grosse, F., Krauss, G., Knill-Jones, J. W. & Fersht, A. R. (1983). Accuracy of DNA polymerase-α in copying natural DNA. The EMBO Journal 2, 15151519.CrossRefGoogle ScholarPubMed
Guest, C. R., Hochstrasser, R. A., Allen, D. J., Benkovic, S. J. & Millar, D. P. (1991). Interaction of DNA with the Klenow fragment of DNA polymerase I studied by time-resolved fluorescence spectroscopy. Biochemistry 30, 87598770.CrossRefGoogle ScholarPubMed
Gupta, A., DeBrosse, C.Alpha, S & Benkovic, S. J. (1982). Template-primerdependent turnover of (Sp)-dATP alpha S by T4 DNA polymerase. The stereochemistry of the associated 3′ goes to 5′-exonuclease. J. biol. Chem. 257, 76897692.CrossRefGoogle Scholar
Hamatake, R. K., Hasegawa, H., Clark, A. B., Bebenek, K., Kunkel, T. A. & Sugino, A. (1990). Purification and characterization of DNA polymerase II from the yeast Saccharomyces cerevisiae. Identification of the catalytic core and a possible holoenzyme form of the enzyme. J. biol. Chem. 265, 40724083.CrossRefGoogle Scholar
Hershfield, M. S. (1973). On the role of deoxyribonucleic acid polymerase in determining mutation rates. J. biol. Chem. 248, 14171423.CrossRefGoogle ScholarPubMed
Hopfield, J. J. (1974). Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. natn. Acad. Sci. U.S.A. 71, 41354139.CrossRefGoogle ScholarPubMed
Hopfield, J. J. (1980). The energy relay: A proofreading scheme based on dynamic cooperativity and lacking all characteristic symptoms of kinetic proofreading in DNA replication and protein synthesis. Proc. natn. Acad. Sci. U.S.A. 77, 52485252.CrossRefGoogle ScholarPubMed
Hopfield, J. J. & Yamane, T. (1979). The fidelity of protein synthesis. In Ribosomes: Structure, Function, and Genetics (eds. Chambliss, G., Craven, G. R., Davies, I., Davies, K., Kahna, L. & Nomura, M.), pp. 585596. Baltimore: University Park Press.Google Scholar
Huberman, J. A. & Kornberg, A. (1970). Enzymatic synthesis of deoxyribonucleic acid. XXXV. A 3′ hydroxylribonucleotide binding site of Escherichia coli deoxyribonucleic acid polymerase. J. biol. Chem. 245, 53265334.CrossRefGoogle ScholarPubMed
Jencks, W. P. (1970). Free energies of hydrolysis and decarboxylation. In Handbook of Biochemistry, 2nd ed. (ed. Sober, H. A.), p. J-181. Cleveland: Chemical Rubber Company.Google Scholar
Jordan, F. & Sostman, M. D. (1973). Molecular orbital (CNDO/2 and MINDO) calculations on protonated deoxyribonucleic acid bases. The effects of base protonation on intermolecular interactions. J. Am. Chem. Soc. 95, 65446554.CrossRefGoogle ScholarPubMed
Jovin, T. M., Englund, P. T. & Kornberg, A. (1969). Enzymatic synthesis of deoxyribonucleic acid. XXVII. Chemical modifications of deoxyribonucleic acid polymerase. J. biol. Chem. 244, 30093018.CrossRefGoogle ScholarPubMed
Joyce, C. M., Fujii, D. M., Laks, H. S., Hughes, C. M. & Grindley, N. D. F. (1985). Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli. J. mol. Biol. 186, 283293.CrossRefGoogle ScholarPubMed
Joyce, C. M., Ollis, D. L., Rush, J., Steitz, T. A., Kongisberg, W. H. & Grindley, N. D. F. (1986). Relating structure to function for DNA polymerase I of Escherichia coli. UCLA Symp. mol. cell. Biol. 39, 197205.Google Scholar
Joyce, C. M. & Steitz, T. A. (1987). DNA polymerase I: from crystal structure to function via genetics. Trends in Biochem. Sci. 12, 288292.CrossRefGoogle Scholar
Kahn, J. D. & Hearst, J. E. (1989). Reversibility of nucleotide incorporation by Escherichia coli RNA polymerase, and its effects on fidelity. J. mol. Biol. 205, 291314.CrossRefGoogle ScholarPubMed
Kati, W. M., Johnson, K. A., Jova, L. F. & Anderson, K. S. (1992). Mechanism and fidelity of HIV reverse transcriptase. J. biol. Chem. 257, 2598825997.CrossRefGoogle Scholar
Kelly, W. S. & Grindley, N. D. F. (1976). polA6, a mutation affecting the DNA binding capacity of DNA polymerase I. Nucleic Acids Res. 3, 29712983.CrossRefGoogle ScholarPubMed
Kennard, O. (1985). Structural studies of DNA fragments: the G. T wobble base pair in A, B and Z DNA; the C. A base pair in B-DNA. J. biol. mol. struct. Dyn. 3, 205226.Google Scholar
Knowles, J. R. (1987). Tinkering with enzymes: What are we learning? Science 236, 12521258.CrossRefGoogle ScholarPubMed
Kornberg, A. & Baker, T. A. (1992). DNA Replication, 2nd ed.New York: W. H. Freeman & Co.Google Scholar
Krugh, T. R. (1971). Proximity of the nucleoside monophosphate and triphosphate binding sites on deoxyribonucleic acid polymerases. Biochemistry 10, 25942599.CrossRefGoogle Scholar
Kuchta, R. D., Benkovic, P. & Benkovic, S. J. (1988). Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 27, 67166725.CrossRefGoogle ScholarPubMed
Kuchta, R. D., Mizrahi, V., Benkovic, P. A., Johnson, K. A. & Benkovic, S. J. (1987). Kinetic mechanisms of DNA polymerase I (Klenow). Biochemistry 26, 84108417.CrossRefGoogle ScholarPubMed
Kunkel, T. A. (1985 a). The mutational specificity of DNA polymerases-α and -γ during in vitro DNA synthesis. J. biol. Chem. 260, 1286612874.CrossRefGoogle ScholarPubMed
Kunkel, T. A. (1985 b). The mutational specificity of DNA polymeraseβ during in vitro DNA synthesis: Production of frameshift, base substitution and deletion mutations. J. biol. Chem. 260, 57875796.CrossRefGoogle ScholarPubMed
Kunkel, T. A., Beckman, R. A. & Loeb, L. A. (1986). On the fidelity of DNA synthesis: Pyrophosphate-induced misincorporation allows detection of two proofreading mechanisms. J. biol. Chem. 261, 1361013616.CrossRefGoogle ScholarPubMed
Kunkel, T. A., Eckstein, F., Mildvan, A. S., Koplitz, R. M. & Loeb, L. A. (1981 a). Deoxynucleoside [1-thio]triphosphates prevent proofreading during in vitro DNA synthesis. Proc. natn. Acad. Sci. U.S.A. 78, 67346738.CrossRefGoogle ScholarPubMed
Kunkel, T. A., James, E. A. & Loeb, L. A. (1983). The use of φδ174 amber mutations to study DNA repair. In DNA Repair: A Laboratory Manual of Research Procedures, (eds. Friedberg, E. C. & Hanawalt, P. C.) pp. 223237. New York: Marcel Dekker Inc.Google Scholar
Kunkel, T. A. & Loeb, L. A. (1981). Fidelity of mammalian DNA polymerases. Science 213,765767.CrossRefGoogle ScholarPubMed
Kunkel, T. A. & Mosbaugh, D. W. (1989). Exonucleolytic proofreading by a mammalian DNA polymerase-γ. Biochemistry 28, 988995.CrossRefGoogle Scholar
Kunkel, T. A., Sabatino, R. D. & Bambara, R. A. (1987). Exonucleolytic proofreading by calf thymus DNA polymerase δ. Proc. natn. Acad. Sci. U.S.A. 84, 48654869.CrossRefGoogle ScholarPubMed
Kunkel, T. A., Schaaper, R. M., Beckman, R. A. & Loeb, L. A. (1981 b). On the fidelity of DNA replication. XII. Effect of the next nucleotide on proofreading. J. biol. Chem. 256, 98839889.CrossRefGoogle Scholar
Kunkel, T. A. & Soni, A. (1988). Exonucleolytic proofreading enhances the fidelity of DNA synthesis by chick embryo DNA polymerase-gamma. J. biol. Chem. 263, 44504459.CrossRefGoogle ScholarPubMed
Kurland, C. G. (1978). The role of guanine nucleotides in protein biosynthesis. Biophys.J. 22, 373392.CrossRefGoogle ScholarPubMed
Leavitt, M. C. & Ito, J. (1989). T5 DNA polymerase: structural-functional relationships to other DNA polymerases. Proc. natn. Acad. Sci. U.S.A. 86,44654469.CrossRefGoogle ScholarPubMed
Lecomte, P., Doubleday, O. P. & Radman, M. (1986). Evidence for an intermediate in DNA synthesis involving pyrophosphate exchange. A possible role in fidelity. j. mol. Biol. 189, 643652.CrossRefGoogle Scholar
Lee, M. Y. W. T., Tan, C. K., Downey, K. & So, A. G. (1984). Further studies on calf thymus DNA polymerase-δ purified to homogeneity by a new procedure. Biochemistry 23, 19061913.CrossRefGoogle ScholarPubMed
Lehman, I. R., Kaguni, L. S., DiFrancesco, R. L. & Cotterill, S. M. (1987). Assembly of a DNA replication complex from Drosophila melanogaster embryos. In DNA Replication and Recombination (ed. McMacken, R. and Kelly, T.), pp 89100. New York: Liss.Google Scholar
Lehninger, A. L. (1975). Bioenergetic principles and the ATP cycle. In Biochemistry, pp. 398411. New York: Worth.Google Scholar
Liu, C. C., Burke, R. L., Hibner, U., Barry, J. & Alberts, B. (1979). Probing DNA replication mechanisms with the T4 bacteriophage in vitro system. Cold Spring Harb. Symp. quant. Biol. 43, 469487.CrossRefGoogle ScholarPubMed
Loeb, L. A. (1991). Mutator phenotype may be required for multistage carcinogenesis. Cancer Research 51, 30753079.Google ScholarPubMed
Loeb, L. A., Dube, D. K., Beckman, R. A., Koplitz, M. & Gopinathan, K. P. (1981). On the fidelity of DNA replication: Nucleoside monophosphate generation during polymerization. J. biol. Chem. 256, 39783987.CrossRefGoogle ScholarPubMed
Loeb, L. A. & Reyland, M. E. (1987). Fidelity of DNA synthesis. In Nucleic Acids and Molecular Biology (ed. Eckstein, F. and Lilley, D. M. J.), pp. 157173. Berlin: Springer-Verlag.CrossRefGoogle Scholar
Lohrmann, R. & Orgel, L. E. (1980). Efficient catalysis of polycytidylic acid-directed oligoguanylate formation by Pb2+. J. mol. Biol. 142, 555567.CrossRefGoogle ScholarPubMed
Loftfield, R. B. (1963). The frequency of errors in protein biosynthesis. Biochem. J. 89, 8292.CrossRefGoogle ScholarPubMed
Loftfield, R. B. & Eigner, E. A. (1966). The specificity of enzymic reactions. Aminoacyl-soluble RNA ligases. Biochim. biophys. Acta 130, 426448.CrossRefGoogle ScholarPubMed
Lu, A. L., Clark, S. & Modrich, P. (1983). Methyl-directed repair of DNA base-pair mismatches in vitro. Proc. natn. Acad. Sci. U.S.A. 80, 46394643.CrossRefGoogle ScholarPubMed
Maki, H. & Kornberg, A. (1987). Proofreading by DNA polymerase III of Escherichia coli depends on cooperative interaction of the polymerase and exonuclease subunits. Proc. natn. Acad. Sci. U.S.A. 84, 43894392.CrossRefGoogle ScholarPubMed
McClure, W. R. & Chow, Y. (1980). The kinetics and processivity of nucleic acid polymerases. Methods Enzymol. 64, 277292.CrossRefGoogle ScholarPubMed
McClure, W. R. & Jovin, T. M. (1975). The steady state kinetic parameters and nonprocessivity of Escherichia coli deoxyribonucleic acid polymerase I. J. biol. Chem. 250, 40734080.CrossRefGoogle ScholarPubMed
McHenry, C. (1991). DNA polymerase III holoenzyme. Components, structure, and mechanism of a true replicative complex. J. biol. Chem. 266, 1912719130.CrossRefGoogle ScholarPubMed
Mendelman, L. V., Petruska, J. & Goodman, M. F. (1990). Base mispair extension kinetics. Comparison of DNA polymerase α and reverse transcriptase. J. biol. Chem. 265, 23382346.CrossRefGoogle ScholarPubMed
Mildvan, A. S. (1974). Mechanisms of enzyme action. A. Rev. Biochem. 43, 357399.CrossRefGoogle ScholarPubMed
Mildvan, A. S., Stein, P. J., Abboud, M. M., Koren, R. & Bean, B. L. (1978). In Protons and Ions Involved in Fast Dynamic Phenomena, pp. 413433. Amsterdam: Elsevier.Google Scholar
Mizrahi, V., Benkovic, P. A. & Benkovic, S. J. (1986 a). Mechanism of the idlingturnover reaction of the large (Klenow) fragment of Escherichia coli DNA polymerase I. Proc. natn. Acad. Sci. U.S.A. 83, 231235.CrossRefGoogle ScholarPubMed
Mizrahi, V., Benkovic, P. A. & Benkovic, S. J. (1986 b). Mechanism of DNA polymerase I: exonuclease/polymerase activity switch and DNA sequence dependence of pyrophosphorolysis and misincorporation reactions. Proc. natn. Acad. Sci. U.S.A. 83, 57695773.CrossRefGoogle ScholarPubMed
Mizrahi, V., Henrie, R. N., Marlier, J. F., Johnson, K. A. & Benkovic, S. J. (1985). Rate-limiting steps in the DNA polymerase I reaction pathway. Biochemistry 24, 40104018.CrossRefGoogle ScholarPubMed
Mohan, P. M., Basu, A., Basu, S., Abraham, K. J. & Modak, M. J. (1988). DNA binding domain of Escherichia coli DNA polymerase I: identification of arginine-841 as an essential residue. Biochemistry 27, 226233.CrossRefGoogle ScholarPubMed
Mosbaugh, D. W. & Meyer, R. R. (1980). Interaction of mammalian deoxyribonuclease V, double strand 3′ → 5′ and 5′ →3′ exonuclease with deoxyribonucleic acid polymerase-β from Novikoff hepatoma. J. biol. Chem. 2551, 1023910247.CrossRefGoogle Scholar
Mullen, G. P., Serpersu, E. H., Ferrin, L. J., Loeb, L. A. & Mildvan, A. S. (1990 b). Metal binding to DNA polymerase I, its large fragment, and two 3′, 5′ exonuclease mutants of the large fragment. J. biol. Chem. 2651, 1432714334.CrossRefGoogle Scholar
Mullen, G. P., Shenbagamurthi, P. & Mildvan, A. S. (1989). Substrate and DNA binding to a 50-residue peptide fragment of DNA polymerase I. J. biol. Chem. 264, 1963719647.CrossRefGoogle ScholarPubMed
Mullen, G. P., Vaughn, J. B., Shenbagamurthi, P. & Mildvan, A. S. (1990 a). NMR studies of the active site of DNA polymerase I and of a 50-residue peptide fragment of the enzyme. Biochem. Pharmacol. 40, 6981.CrossRefGoogle ScholarPubMed
Mulvey, R. S. & Fersht, A. R. (1977). Editing mechanisms in aminoacylation of tRNA: ATP consumption and the binding of aminoacyl-tRNA by elongation factor Tu. Biochemistry 16, 47314737.CrossRefGoogle ScholarPubMed
Munir, K. M., French, D. C., Dube, D. K. & Loeb, L. A. (1992). Permissible amino acid substitutions within the putative nucleoside-binding site of herpes simplex virus type 1 encoded thymidine kinase established by random sequence mutagenesis. j. biol. Chem. 267, 65846589.CrossRefGoogle ScholarPubMed
Munir, K. M., French, D. C. & Loeb, L. A. (1993). Thymidine kinase mutants obtained by random sequence selection. Proc. natn. Acad. Sci. U.S.A. 90, 40124016.CrossRefGoogle ScholarPubMed
Muzyczka, N., Poland, R. L. & Bessman, M. J. (1972). Studies on the biochemical basis of spontaneous mutation. I. A comparison of the deoxyribonucleic acid polymerases of mutator, antimutator, and wild type strains of bacteriophage T4. j biol. Chem. 247, 71167122.CrossRefGoogle Scholar
Muzyczka, N., Schnaar, R. L., Goodman, M. F., Gore, W. C. & Bessman, M. J. (1973). Base selectivity of mutant and wild-type DNA polymerases. Fedn Proc. Fedn Am. Socs. exp. Biol. 32, 491.Google Scholar
Neet, K. E. & Ainslee, G. R. (1980). Hysteretic enzymes. Methods Enzymol. 64, 192226.CrossRefGoogle ScholarPubMed
Ninio, J. (1975). Kinetic amplification of enzyme discrimination. Biochimie 57, 587595.CrossRefGoogle ScholarPubMed
O'Donnell, M. E. & Kornberg, A. (1985). Dynamics of DNA polymerase III holoenzyme of Escherichia coli in replication of a multiprimed template. J. biol. Chem. 260, 1287512883.CrossRefGoogle ScholarPubMed
Ollis, D. L., Brick, P., Hamlin, R., Yuong, N. G. & Steitz, T. A. (1985). Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature Lond. 28, 762766.CrossRefGoogle Scholar
Pandey, V. N., Williams, K. R., Stone, K. L. & Modak, M. J. (1987). Photoaffinity labeling of the thymidine triphosphate binding domain in Escherichia coli DNA polymerase I: identification of histidine-881 as the site of cross-linking. Biochemistry 26, 17041709.CrossRefGoogle ScholarPubMed
Papanicolaou, C., Dorizzi, M. & Ninio, J. (1984). A memory effect in DNA replication. Biochimie 66, 4348.CrossRefGoogle ScholarPubMed
Papanicolaou, C., Lecomte, P. & Ninio, J. (1986). Mnemonic aspects of Escherichia coli DNA polymerase I. Interaction with one template influences the next interaction with another template. J. mol. Biol. 189, 435448.CrossRefGoogle ScholarPubMed
Patel, S. S., Wong, I. & Johnson, K. A. (1991). Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonucleasedeficient mutant. Biochemistry 30, 511522.CrossRefGoogle ScholarPubMed
Pauling, L. (1957). The probability of errors in the process of synthesis of protein molecules. In Festschrift für Prof. Dr. Arthur Stoll Siebzigsten Geburtstag, pp. 597602. Basel: Birkhauser.Google Scholar
Perrino, F. W., Preston, B. D., Sandell, L. L. & Loeb, L. A. (1989). Extension of mismatched 3′ termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase. Proc. natn. Acad. Sci. U.S.A. 86, 83438347.CrossRefGoogle Scholar
Petros, A. M., Mueller, L. & Kopple, K. D. (1990). NMR identification of protein surfaces using paramagnetic probes. Biochemistry 29, 1004110048.CrossRefGoogle ScholarPubMed
Petruska, J. & Goodman, M. F. (1985). Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity. J. biol. Chem. 260, 75337536.CrossRefGoogle ScholarPubMed
Petruska, J., Goodman, M. F., Boosalis, M. S., Sowers, L. C., Cheong, C. & Tinoco, I. (1988). Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc. natn. Acad. Sci. U.S.A. 85, 62526256.CrossRefGoogle ScholarPubMed
Petruska, J., Sowers, L. C. & Goodman, M. F. (1986). Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Proc. natn. Acad. Sci. U.S.A. 83, 15591562.CrossRefGoogle ScholarPubMed
Phear, G., Nalbartoglu, J. & Meuth, M. (1987). Next-nucleotide effects in mutations driven by DNA precursor pool imbalances at the aprt locus of Chinese hamster ovary cells. Proc. natn. Acad. Sci. U.S.A. 84, 44504454.CrossRefGoogle ScholarPubMed
Pless, R. C. & Bessman, M. J. (1983). Influence of local nucleotide sequence on substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro. Biochemistry 22, 49054915.CrossRefGoogle ScholarPubMed
Preston, B. D., Poiesz, B. J. & Loeb, L. A. (1988). Fidelity of HIV-1 reverse transcriptase. Science 242, 11681171.CrossRefGoogle ScholarPubMed
Que, B. G., Downey, K. M. & So, A. G. (1978). Mechanisms of selective inhibition of 3′ to 5′ exonuclease activity of Escherichia coli DNA polymerase 1 by nucleoside 5′- monophosphates. Biochemistry 17, 16031606.CrossRefGoogle ScholarPubMed
Raszka, M. & Kaplan, N. O. (1972). Association by hydrogen bonding of mononucleotides in aqueous solution. Proc. natn. Acad. Sci. U.S.A. 69, 20252029.CrossRefGoogle ScholarPubMed
Record, M. T. Jr, Lohman, T. M. & DeHaseth, P. L. (1976). Na+ effects on transition of DNA and polynucleotides of variable linear charge density. J. mol. Biol. 107, 145158.CrossRefGoogle Scholar
Reha-Krantz, L. J. (1988). Amino acid changes coded by bacteriophage T4 DNA polymerase mutator mutants. Relating structure to function. J. mol. Biol. 202,711724.CrossRefGoogle ScholarPubMed
Roberts, J. D., Preston, B. D., Johnston, L. A., Soni, A., Loeb, L. A. & Kunkel, T. A. (1989). Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis in vitro. Mol. cell. Biol. 9, 469476.Google ScholarPubMed
Scheuermann, R. H. & Echols, H. (1984). A separate editing exonuclease for DNA replication: the ε subunit of Escherichia coli DNA polymerase III holoenzyme. Proc. natn. Acad. Sci. U.S.A. 81, 77477751.CrossRefGoogle ScholarPubMed
Seal, G. & Loeb, L. A. (1976). On the fidelity of DNA replication. Enzyme activities associated with DNA polymerases from RNA tumor viruses. J. biol. Chem. 254, 975981.CrossRefGoogle Scholar
Segel, I. H. (1975). Steady-state kinetics of multireactant enzymes. In Enzyme Kinetics, pp. 274344, 506–665. New York: John Wiley & Sons.Google Scholar
Skarnes, W., Bonin, P. & Baril, E. (1986). Exonuclease activity associated with a multiprotein form of HeLa cell DNA polymerase-α. J. biol. Chem. 261, 66296636.CrossRefGoogle ScholarPubMed
Sloan, D. L., Loeb, L. A., Mildvan, A. S. & Feldman, R. J. (1975). Comparison of the geometry of nucleoside triphosphates on DNA polymerase and pyruvate kinase asdetermined by NMR. J. biol. Chem. 250, 89138920.CrossRefGoogle Scholar
Spanos, A., Sedgwick, S. G., Yarranton, G. J., Hubscher, U. & Banks, G. R. (1981). Detection of the catalytic activities of DNA polymerases and their associated exonucleases following SDS-polyacrylamide gel electrophoresis. Nucleic Acids Research 9, 18251839.CrossRefGoogle ScholarPubMed
Stephenson, C. & Karran, P. (1988). Selective binding to DNA base pair mismatches by proteins from human cells. J. biol. Chem. 264, 2117721182.CrossRefGoogle Scholar
Sweasy, J. B. & Loeb, L. A. (1992). Mammalian DNA polymerase β can substitute for DNA polymerase I during DNA replication in Escherichia coli. J. biol. Chem. 267, 14071410.CrossRefGoogle ScholarPubMed
Sweasy, J. B. & Loeb, L. A. (1993). Detection and characterization of mammalian DNA polymerase β mutants by functional complementation in Escherichia coli. Proc. natn. Acad. Sci. U.S.A. 90, 46264630.CrossRefGoogle ScholarPubMed
Thomas, D. C., Roberts, J. D., Sabatino, D., Myers, T. W., Tan, C. -K., Downey, K. M., So, A. G., Bambara, R. A. & Kunkel, T. A. (1991). Fidelity of mammalian DNA replication and replicative DNA polymerases. Biochemistry 30, 1175111759.CrossRefGoogle ScholarPubMed
Topal, M. D. & Fresco, J. R. (1976). Complementary base pairing and the origin of substitution mutations. Nature, Lond. 263, 285289.CrossRefGoogle ScholarPubMed
Travaglini, E. C., Mildvan, A. S. & Loeb, L. A. (1975). Kinetic analysis of Escherichia coli deoxyribonucleic acid polymerase I. J. biol. Chem. 250, 86478656.CrossRefGoogle ScholarPubMed
Vishwanatha, J. K., Coughlin, S. A., Wesolowski-Owen, M. & Baril, E. F. (1986). Multiprotein form of DNA polymerase-α from HeLa cells. j. biol. Chem. 261, 66196628.CrossRefGoogle ScholarPubMed
Wang, A. C. & Kallenbach, N. R. (1971). Helical complexes of polyriboinosinic acid with copolymers of polyribocytidylic acid containing inosine, adenosine and uridine residues. J. mol. Biol. 62, 591611.CrossRefGoogle ScholarPubMed
Warwicker, J., Ollis, D. L., Richards, F. M. & Steitz, T. A. (1985). Electrostatic field of the large fragment of Escherichia coli DNA polymerase I. J. mol. Biol. 186, 645649.CrossRefGoogle ScholarPubMed
Weymouth, L. A. & Loeb, L. A. (1978). Mutagenesis during in vitro DNA synthesis. Proc. natn. Acad. Sci. U.S.A. 75, 19241928.CrossRefGoogle ScholarPubMed
Winter, R. B., Berg, O. G. & von Hippel, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor–operator interaction: kinetic measurements and conclusions. Biochemistry 20, 69016977.Google ScholarPubMed
Wong, I., Patel, S. S. & Johnson, K. A. (1991). An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry 30, 526537.CrossRefGoogle ScholarPubMed
Yarus, M. (1972). Phenylalanyl-tRNA synthetase and isoleucyl-tRNA Phe: apossible verification mechanism for aminocyl-tRNA. Proc. natn. Acad. Sci. U.S.A. 69, 19151919.CrossRefGoogle Scholar