Biochemical Basis of DNA Replication Fidelity

References

• Watson J. D., Crick F. H.C. Genetical implications of the structure of deoxyribonucleic acid. Nature 1953; 171: 964
   PubMed Web of Science ®Google Scholar
• Watson J. D., Crick F. H. C. The structure of DNA. Cold Spring Harbor Symp. Quant. Biol. 1953; 18: 123
   PubMedGoogle Scholar
• Kornberg A., Baker T. A. DNA Replication. W. H. Freeman, New York 1992, chap. 4.
   Google Scholar
• Brutlag D., Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. XXXVI. A proofreading function for the 35 exonuclease activity in deoxyribonucleic acid polymerases. J. Biol. Chem. 1972; 247: 241
   PubMed Web of Science ®Google Scholar
• Muzyczka N., Poland R. L., Bessman M. J. Studies on the biochemical basis of spontaneous mutation. I. A. comparison of the deoxyribonucleic acid polymerase of mutator, antimutator, and wild-type strains of bacteriophage T4. J. Biol. Chem. 1972; 247: 7116
   PubMed Web of Science ®Google Scholar
• Scheuermann R., Tarn S., Burgers P. M., Lu C., Echols H. Identification of the epsilonsubunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: a fidelity subunit for DNA replication. Proc. Natl. Acad. Sci. U.S.A. 1983; 80: 7085
   PubMed Web of Science ®Google Scholar
• DiFrancesco R., Bhatnagar S. K., Brown A., Bessman M. J. The interaction of DNA polymerase III and the product of the Escherichia coli mutator gene, mutD. J. Biol. Chem. 1984; 259: 5567
   PubMed Web of Science ®Google Scholar
• Radman M., Wagner R. Mismatch repair in Escherichia coli. Annu. Rev. Genet. 1986; 20: 523
   PubMed Web of Science ®Google Scholar
• Modrich P. DNA mismatch correction. Annu. Rev. Biochem. 1987; 56: 435
   PubMed Web of Science ®Google Scholar
• Modrich P. Methyl-directed DNA mismatch correction. J. Biol. Chem. 1989; 264: 6597
   PubMed Web of Science ®Google Scholar
• Au K. G., Clark S., Miller J. H., Modrich P. Escherichia coli mutY gene encodes an adenine glycosylase active in GA mispairs. Proc. Natl. Acad. Sci. U.S.A. 1989; 86: 8877
   PubMed Web of Science ®Google Scholar
• Tchou J., Kasai H., Shibutani S., Chung M. H., Laval J., Grollman A. P., Nishimura S. 8-Oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity. Proc. Natl. Acad. Sci. U.S.A. 1991; 88: 4690
   PubMed Web of Science ®Google Scholar
• Michaels M. L., Miller J. H. The GO system protects organism from the mutagenic effect of spontaneous lesion 8-hydroxyguanine (7,8-Dihydro-8-Oxoguanine). J. Bacteriol. 1992; 174: 6321
   PubMed Web of Science ®Google Scholar
• Echols H., Goodman M. F. Fidelity mechanisms in DNA replication. Annu. Rev. Biochem. 1991; 60: 477
   PubMed Web of Science ®Google Scholar
• Bessman M. J., Muzyczka N., Goodman M. F., Schnaar R. L. 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. 1974; 88: 409
   PubMed Web of Science ®Google Scholar
• Fersht A. R. Enzyme Structure and Mechanism. W. H. Freeman, New York 1985; 112
   Google Scholar
• Segal I. H. Enzyme Kinetics. John Wiley & Sons, New York 1975; 564
   Google Scholar
• Randall S. K., Eritja R., Kaplan B. E., Petruska J., Goodman M. F. Nucleotide insertion kinetics opposite abasic lesions in DNA. J. Biol. Chem. 1987; 262: 6864
   PubMed Web of Science ®Google Scholar
• Boosalis M. S., Petruska J., Goodman M. F. DNA polymerase insertion fidelity: gel assay for site-specific kinetics. J. Biol. Chem. 1987; 262: 14689
   PubMed Web of Science ®Google Scholar
• Mendelman L. V., Boosalis M. S., Petruska J., Goodman M. F. Nearest neighbor influences on DNA polymerases insertion fidelity. J. Biol. Chem. 1989; 264: 14415
   PubMed Web of Science ®Google Scholar
• Yu H., Goodman M. F. Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates. J. Biol. Chem. 1992; 267: 10888
   PubMed Web of Science ®Google Scholar
• Creighton S., Huang M. M., Cai H., Arnheim N., Goodman M. F. Base mispair extension kinetics: binding of avian myeloblastosis reverse transcriptase to matched and mismatched base pair termini. J. Biol. Chem. 1992; 267: 2633
   PubMed Web of Science ®Google Scholar
• Clarke A. B., Disney R. L. Probability And Random Processes: a First Course With Applications. John Wiley & Sons, New York 1985
   Google Scholar
• Reddy M. K., Weitzel S. E., von Hippel P. H. Processive proofreading is intrinsic to T4 DNA polymerase. J. Biol. Chem. 1992; 267: 14157
   PubMed Web of Science ®Google Scholar
• Kuchta R. D., Mizrahi V., Benkovic P. A., Johnson K. A., Benkovic S. J. Kinetic mechanism of DNA polymerase I (Klenow). Biochemistry 1987; 26: 8410
   PubMed Web of Science ®Google Scholar
• Clayton L. K., Goodman M. F., Branscomb E. W., Galas D. J. Error induction and correction by mutant and wild-type T4 DNA polymerases: kinetic error discrimination mechanisms. J. Biol. Chem. 1902; 254: 1979
   Google Scholar
• Fersht A. R. Fidelity of replication of phage πX174 DNA by DNA polymerase III holoenzyme; spontaneous mutation by misincorporation. Proc. Natl. Acad. Sci. U.S.A. 1979; 76: 4946
   PubMed Web of Science ®Google Scholar
• Kornberg A., Baker T. A. DNA Replication. W. H. Freeman, New York 1992, chap. 5.
   Google Scholar
• Fersht A. R., Knill-Jones J. W., Tsui W. C. Kinetic basis of spontaneous mutation. Misinsertion frequencies, proofreading specificities and cost of proofreading by DNA polymerases of Escherichia coli. J. Mol. Biol. 1982; 156: 37
   PubMed Web of Science ®Google Scholar
• Schaaper R. M. Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair. Proc. Nad. Acad. Sci. U.S.A. 1988; 85: 8126
   PubMed Web of Science ®Google Scholar
• Sinha N. K., Haimes M. D. Molecular mechanisms of substitution mutagenesis. An experimental test of the Watson-Crick and topal-fresco models of base mispairings. J. Biol. Chem. 1981; 256: 10671
   PubMed Web of Science ®Google Scholar
• Sinha N. K., Goodman M. F. Fidelity of DNA replication. Bacteriophage T4, C. K. Mathews, E. M. Kutter, G. Mosig, P. B. Berget. Am. Soc. Microbiol., Washington, D. C. 1983; 131
   Google Scholar
• Kunkel T. A., Loeb L. A., Goodman M. F. On the fidelity of DNA replication. The accuracy of T4 DNA polymerases in copying πX174 DNA in vitro. J. Biol. Chem. 1984; 259: 1539
   PubMed Web of Science ®Google Scholar
• Cox E. C. Bacterial mutator genes and the control of spontaneous mutagenesis. Annu. Rev. Genet. 1976; 10: 135
   PubMed Web of Science ®Google Scholar
• Cox E. C., Horner D. L. Dominant mutators in Escherichia coli. Genetics 1982; 100: 7
   PubMed Web of Science ®Google Scholar
• Degnan G. E., Cox E. C. Conditional mutator gene in Escherichia coli Isolation, mapping, and effector studies. J. Bacteriol. 1974; 117: 477
   PubMed Web of Science ®Google Scholar
• Schaaper R. M., Bond B. I., Fowler R. G. AT CG transversions and their prevention by the Escherichia coli mutT and murHLS pathways. Mol. Gen. Genet. 1989; 219: 1
   PubMedGoogle Scholar
• Schaaper R. M., Radman M. The extreme mutator effect of Escherichia coli mutD5 results from saturation of mismatch repair by excessive DNA replication errors. EMBO J. 1989; 8: 3511
   PubMed Web of Science ®Google Scholar
• Reha-Krantz L. J., Stocki S., Nonay R. L., Dimayuga E., Goodrich L. D., Konigsberg W. H., Spicer E. K. DNA polymerization in the absence of exonucleolytic proofreading: in vivo and in vitro studies. Proc. Natl. Acad. Sci. U.S.A. 1991; 88: 2417
   PubMed Web of Science ®Google Scholar
• Young M. C., Reddy M. K., von Hippel P. H. Structure and function of the bacteriophage T4 DNA polymerase holoenzyme. Biochemistry 1992; 31: 8675
   PubMed Web of Science ®Google Scholar
• Speyer J. F. Mutagenic DNA polymerase. Biochem. Biophys. Res. Comtn. 1965; 21: 6
   PubMed Web of Science ®Google Scholar
• Freese E. B., Freese E. F. On the specificity of DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 1967; 57: 650
   PubMed Web of Science ®Google Scholar
• Drake J. W., Allen E. F. Antimutagenic DNA polymerases of bacteriophage T4. Cold Spring Harbor Symp. Quant. Biol. 1968; 33: 339
   PubMedGoogle Scholar
• Lo K. Y., Bessman M. J. An antimutator deoxyribonucleic acid polymerase. I. Purification and properties of the enzyme. J. Biol. Chem. 1976; 251: 2475
   PubMed Web of Science ®Google Scholar
• Speyer J. F., Karam J. D., Lenny A. B. On the role of DNA polymerase in base selection. Cold Spring Harbor Symp. Quant. Biol. 1966; 31: 693
   PubMedGoogle Scholar
• Drake J. W. Comparative rates of spontaneous mutation. Nature 1969; 221: 1132
   PubMed Web of Science ®Google Scholar
• Drake J. W., Allen E. F., Forsberg S. A., Preparata R., Greening E. O. Spontaneous mutation. Genetic control of mutation rates in bacteriophage T4. Nature 1969; 221: 1128
   PubMed Web of Science ®Google Scholar
• Ripley L. S., Shoemaker N. B. A major role for bacteriophage T4 DNA polymerase in frameshift mutagenesis. Genetics 1983; 103: 353
   PubMed Web of Science ®Google Scholar
• Petruska J., Goodman M. F., Boosalis M. S., Sowers L. C., Cheong C., Tinoco I., Jr. Comparison between DNA melting thermodynamics and DNA polymerase fidelity. Proc. Natl. Acad. Sci. U.S.A. 1988; 85: 6252
   PubMed Web of Science ®Google Scholar
• Perrino F. W., Loeb L. A. Differential extension of 3 mispairs is a major contribution to the high fidelity of calf thymus DNA polymerase-alpha. J. Biol. Chem. 1989; 264: 2898
   PubMed Web of Science ®Google Scholar
• Mendelman L. V., Petruska J., Goodman M. F. Base mispair extension kinetics: comparison of DNA polymerase α and reverse transcriptase. J. Biol. Chem. 1990; 265: 2338
   PubMed Web of Science ®Google Scholar
• Perrino F. W., Preston B. D., Sandell L. L., Loeb L. A. Extension of mismtached 3 termini of DNA is a major determinant of the infidelity of human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl. Acad. Sci. U.S.A. 1989; 86: 8343
   PubMed Web of Science ®Google Scholar
• Kuchta R. D., Benkovic P., Benkovic S. J. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity. Biochemistry 1988; 27: 6716
   PubMed Web of Science ®Google Scholar
• Petruska J., Sowers L. C., Goodman M. F. Comparison of nucleotide interactions in water, proteins, and vacuum: model for DNA polymerase fidelity. Proc. Natl. Acad. Sci. U.S.A. 1986; 83: 1559
   PubMed Web of Science ®Google Scholar
• Cohen S. S. Virus-Induced Enzymes. Columbia University Press, New York 1968
   Google Scholar
• Mathews C. K. Bacteriophage biochemistry. ACS Monograph No. 164. Van Nostrand Reinhold, New York 1971
   Google Scholar
• Tomich P. K., Chiu C. S., Wovcha M. G., Greenberg G. R. Evidence for a complex regulating the in vivo activities of early enzymes induced by bacteriophage T4. J. Biol. Chem. 1974; 249: 7613
   PubMed Web of Science ®Google Scholar
• Reddy G. P. V., Singh A., Stafford M. E., Mathews C. K. Enzyme associations in T4 phage DNA precursor synthesis. Proc. Natl. Acad. Sci. U.S.A. 1977; 74: 3152
   PubMed Web of Science ®Google Scholar
• Thylen C., Mathews C. K. Essential role of T4 phage deoxycytidylate hydroxymethylase in a multienzyme complex for deoxyribonucleotide synthesis. J. Biol. Chem. 1989; 264: 15169
   PubMed Web of Science ®Google Scholar
• Ollis D. L., Brick P., Hamlin R., Xuong N. G., Steitz T. A. Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP. Nature 1985; 313: 762
   PubMed Web of Science ®Google Scholar
• Derbyshire V., Freemont P. S., Sanderson M. R., Beese L., Friedman J. M., Joyce C. M., Steitz T. A. Genetic and crystallographic studies of the 3, 5-exonucleolytic site of DNA polymerase I. Science 1988; 240: 199
   PubMed Web of Science ®Google Scholar
• Reha-Krantz L. J. Amino acid changes coded by bacteriophage T4 DNA polymerase mutator mutants: relating structure to function. J. Mol. Biol. 1988; 202: 711
   PubMed Web of Science ®Google Scholar
• Spicer E. K., Rush J., Fung C., Reha Krantz L. J. Primary structure of T4 DNA polymerase: evolutionary relatedness to eukaryotic and other prokaryotic DNA polymerases. J. Biol. Chem. 1988; 263: 7478
   PubMed Web of Science ®Google Scholar
• Cowart M. C., Gibson K. J., Allen D. J., Benkovic S. J. DNA substrate structural requirements for the exonuclease and polymerase activities of prokaryotic and phage DNA polymerases. Biochemistry 1989; 28: 1975
   PubMed Web of Science ®Google Scholar
• Joyce C. M. How DNA travels between the separate polymerase and 3 5 exonuclease sites of DNA polymerase I (Klenow fragment). J. Biol. Chem. 1989; 264: 10858
   PubMed Web of Science ®Google Scholar
• Goodman M. F., Gore W. C., Muzyczka N., Bessman M. J. Studies on the biochemical basis of spontaneous mutation. III. Rate model for DNA polymerase-effected nucleotide misincoporation. J. Mol. Biol. 1974; 88: 423
   Web of Science ®Google Scholar
• Sinha N. K. Specificity and efficiency of editing of mismatches involved in the formation of base substitution mutations by the 35 exonuclease activity of phage T4 DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 1987; 84: 915
   PubMed Web of Science ®Google Scholar
• Brenowitz S., Kwack S., Goodman M. F., O'Donnell M., Echols H. Specificity and enzymatic mechanism of the editing exonuclease of Escherichia coli DNA polymerase III. J. Biol. Chem. 1991; 266: 7888
   PubMed Web of Science ®Google Scholar
• Reha-Krantz L. J., Bessman M. J. Studies on the biochemical basis of spontaneous mutation. IV. Effect on amino acid substitution on the enzymatic and biological properties of the T4 DNA polymerase. J. Mol. Biol. 1977; 116: 99
   PubMed Web of Science ®Google Scholar
• Bessman M. J., Reha-Krantz L. J. Studies on the biochemical basis of spontaneous mutation. V. Effects of temperature on mutation frequency. J. Mol. Biol. 1977; 116: 115
   PubMed Web of Science ®Google Scholar
• Hershfield M. S., Nossal N. G. Hydrolysis of template and newly synthesized deoxyribonucleic acid by the 3 to 5 exonuclease activity of the T4 deoxyribonucleic acid polymerase. J. Biol. Chem. 1972; 247: 3393
   PubMed Web of Science ®Google Scholar
• Nossal N. G., Hershfleld M. S. Exonuclease activity of wild-type and mutant T4 DNA polymerases: hydrolysis during DNA synthesis in vitro. DNA Synthesis In Vitro, R. D. Wells, R. B. Inman. University Park Press, Baltimore 1973; 47
   Google Scholar
• Hershfleld M. S. On the role of deoxyribonucleic acid polymerase in determining mutation rates: characterization of the defect in the T4 deoxyribonucleic acid polymerase caused by the ts88 mutation. J. Biol. Chem. 1973; 248: 1417
   PubMed Web of Science ®Google Scholar
• Reha-Krantz L. J. Locations of amino acid substitutions in bacteriophage T4tsL56 DNA polymerase predict an N-terminal exonuclease domain. J. Virol. 1989; 63: 4762
   PubMed Web of Science ®Google Scholar
• Gillen F. D., Nossal N. G. Control of mutation frequency by bacteriophage T4 DNA polymerase. I. The CB120 antimutator DNA polymerase is defective in strand displacement. J. Biol. Chem. 1976; 251: 5219
   PubMed Web of Science ®Google Scholar
• Reha-Krantz L. J. Genetic and biochemical studies of the bacteriophage T4 DNA polymerase. UCLA Symp. Mol. Cell. Biol. New Ser, T. J. Kelly, R. McMacken. Alan R. Liss, New York 1987; 47: 501
   Google Scholar
• Cai H., Bloom L. B., Reha-Krantz L. J., Goodman M. F. 1992, unpublished
   Google Scholar
• Wong I., Patel S. S., Johnson K. A. An induced-fit kinetic mechanism for DNA replication fidelity: direct measurement by single-turnover kinetics. Biochemistry 1991; 30: 526
   PubMed Web of Science ®Google Scholar
• Detera S. D., Becerra S. P., Swack J. A., Wilson S. H. Studies on the mechanism of DNA polymerase alpha. Nascent chain elongation, steady state kinetics, and the initiation phase of DNA synthesis. J. Biol. Chem. 1981; 256: 6933
   PubMed Web of Science ®Google Scholar
• Fisher P. A., Korn D. Ordered sequential mechanism of substrate recognition and binding by KB cell DNA polymerase alpha. Biochemistry 1981; 20: 4560
   PubMed Web of Science ®Google Scholar
• Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985; 230: 1350
   PubMed Web of Science ®Google Scholar
• Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988; 239: 487
   PubMed Web of Science ®Google Scholar
• Li H., Cui X., Arnheim N. Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reaction. Proc. Natl. Acad. Sci. U.S.A. 1990; 87: 4580
   PubMed Web of Science ®Google Scholar
• Ehlen T., Dubeau L. Detection of ras point mutations by polymerase chain reaction using mutation-specific., inosine-containing oligonucleotide primers. Biochem. Biophys. Res. Comm. 1989; 160: 441
   PubMed Web of Science ®Google Scholar
• Gibbs R. A., Nguyen P. N., Caskey C. T. Detection of single DNA base differences by competitive oligonucleotide priming. Nucl. Acids Res. 1989; 17: 2437
   PubMed Web of Science ®Google Scholar
• Newton C. R., Graham A., Heptinstall L. E., Powell S. J., Summers C., Kalsheker N., Smith J. C., Markham A. F. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucl. Acids Res. 1989; 17: 2503
   PubMed Web of Science ®Google Scholar
• Wu D. Y., Ugozzoli L., Pal B. K., Wallace R. B. Allele-specific enzymatic amplification of betaglobin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. U.S.A. 1989; 86: 2757
   PubMed Web of Science ®Google Scholar
• Ugozzoli L., Wallace R. B. Allele-specific polymerase chain reaction, METHODS. A Companion to Methods in Enzyomology 1991; 2: 42
   Google Scholar
• Cha R. S., Zarbl H., Keohavong P., Thilly W. G. Mismatch amplification mutation assay (MAMA): application to the c-H-ras-gene, PCR. Methods and Applications 1992; 2: 14
   Google Scholar
• Huang M. M., Arnheim N., Goodman M. F. Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucl. Acids Res. 1992; 20: 4567
   PubMed Web of Science ®Google Scholar
• Kwok S., Kellogg D. E., McKinney N., Spasic D., Goda L., Levenson C., Sninsky J. J. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucl. Acids Res. 1990; 18: 999
   PubMed Web of Science ®Google Scholar
• Preston B. D., Poiesz B. J., Loeb L. A. Fidelity of HIV-1 reverse transcriptase. Science 1988; 243: 1168
   Google Scholar
• Ricchetti M., BuC H. Reverse tanscriptases and genomic variability: the accuracy of DNA replication is enzyme specific and sequence dependent. EMBO J. 1990; 9: 1583
   PubMed Web of Science ®Google Scholar
• Majumdar C., Abbotts J., Broder S., Wilson S. H. Studies on the mechanism of human immunodeficiency virus reverse transcriptase: steady state kinetics, processivity, and polynucleotide inhibition. J. Biol. Chem. 1988; 263: 15657
   PubMed Web of Science ®Google Scholar
• Majumdar C., Stein C. A., Cohen J. S., Broder S., Wilson S. H. Stepwise mechanism of HIV reverse transcriptase: primer function of phosphorothioate oligodeoxynucleotide. Biochemistry 1989; 28: 1340
   PubMed Web of Science ®Google Scholar
• Huber H. E., McCoy J. M., Seehra J. S., Richardson C. C. Human immunodeficiency virus 1 reverse transcriptase. Template binding, processivity, strand displacement synthesis, and template switching. J. Biol. Chem. 1989; 264: 4669
   PubMed Web of Science ®Google Scholar
• Dudding L. R., Nkabinde N. C., Mizrahi V. Analysis of the RNA- and DNA-dependent DNA polymerase activities of point mutants of HIV-1 reverse transcriptase lacking ribonuclease H activity. Biochemistry 1991; 30: 10498
   PubMed Web of Science ®Google Scholar
• Bakhanashvili M., Hizi A. Fidelity of the RNA-dependent DNA synthesis exhibited by the reverse transcriptases of Human Immunodeficiency Virus Types 1, and 2 and of Murine Leukemia Virus: Mispair extension frequencies. Biochemistry 1992; 31: 9393
   PubMed Web of Science ®Google Scholar
• Reardon J. E., Miller W. H. Human immunodeficiency virus reverse transcriptase. Substrate and inhibitor kinetics with thymidine 5 triphosphate and 3-azido-3-deoxythymidine-5-triphosphate. J. Biol. Chem. 1990; 265: 20302
   PubMed Web of Science ®Google Scholar
• Krug M. S., Berger S. L. Reverse transcriptase from human immunodeficiency virus: a single templateprimer binding site serves two physically separable catalytic functions. Biochemistry 1991; 30: 10614
   PubMed Web of Science ®Google Scholar
• Roberts J. D., Bebenek K., Kunkel T. A. The accuracy of reverse transcriptase from HIV-1. Science 1988; 242: 1171
   PubMed Web of Science ®Google Scholar
• Weber J., Grosse F. Fidelity of human immunodeficiency virus type I reverse transcriptase in copying natural DNA. Nucl. Acids Res. 1989; 17: 1379
   PubMed Web of Science ®Google Scholar
• Bebenek K., Abbotts J., Roberts J. D., Wilson S. H., Kunkel T. A. Specificity and mechanism of error-prone replication by human immunodeficiency virus-1 reverse transcriptase. J. Biol. Chem. 1989; 264: 16948
   PubMed Web of Science ®Google Scholar
• Huebner A., Kruhoffer M., Grosse F., Krauss G. Fidelity of human immunodeficiency virus type I reverse transcriptase in copying natural RNA. J. Mol. Biol. 1992; 223: 595
   PubMed Web of Science ®Google Scholar
• Roberts J. D., Preston B. D., Johnston L. A., Soni A., Loeb L. A., Kunkel T. A. Fidelity of two retroviral reverse transcriptases during DNA-dependent DNA synthesis. in vitro, Mol. Cell. Biol. 1989; 9: 469
   PubMed Web of Science ®Google Scholar
• Streisinger G., Okada Y., Emrich J., Newton J., Tsugita A., Terzaghi E., Inouye M. Frameshift mutations and the genetic code. Cold Spring Harbor Symp. Quant. Biol. 1966; 31: 77
   PubMedGoogle Scholar
• Kunkel T. A. Frameshift mutagenesis by eukaryotic DNA polymerases. in vitro, J. Biol. Chem. 1986; 261: 13581
   PubMedGoogle Scholar
• Kunkel T. A., Soni A. Mutagenesis by transient misalignment. J. Biol. Chem. 1988; 263: 14784
   PubMed Web of Science ®Google Scholar
• Boosalis M. S., Mosbaugh D. W., Hamatake R., Sugino A., Kunkel T. A., Goodman M. F. Kinetic analysis of base substitution mutagenesis by transient misalignment of DNA and by miscoding. J. Biol. Chem. 1989; 264: 11360
   PubMed Web of Science ®Google Scholar
• Fowler R. G., Degnan G. E., Cox E. C. Mutational specificity of conditional E. coli mutator, mutD5. Mol. Gen. Genet. 1974; 133: 179
   PubMedGoogle Scholar
• de Boer J. G., Ripley L. S. Demonstration of the production of frameshift and base-substitution mutations by quasipalindromic DNA sequences. Proc. Natl. Acad. Sci. U.S.A. 1984; 81: 5528
   PubMed Web of Science ®Google Scholar
• Papanicolaou C., Ripley L. S. Polymerasespecific differences in the DNA intermediates of frameshift mutagenesis. In vitro synthesis errors of Escherichia coli DNA polymerase I and its large fragment derivative. J. Mol. Biol. 1989; 207: 335
   PubMed Web of Science ®Google Scholar
• Ripley L. S. Frameshift mutation: determinants of specificity. Annu. Rev. Genet. 1990; 24: 189
   PubMed Web of Science ®Google Scholar
• Allen D. J., Darke P. L., Benkovic S. J. Fluorescent oligonucleotides and deoxynucleotide triphosphates: preparation and their interaction with the large (Klenow) fragment of Escherichia coli DNA polymerase I. Biochemistry 1989; 28: 4601
   PubMed Web of Science ®Google Scholar
• Carroll S. S., Benkovic S. J. Mechanistic aspects of DNA polymerases: Escherichia coli DNA polymerase I (Klenow fragment) as a paradigm. Chem. Rev. 1990; 90: 1291
   Web of Science ®Google Scholar
• Singer B., Chavez F., Goodman M. F., Essigmann J. M., Dosanjh M. K. Effect of 3 flanking neighbors on kinetics of pairing of dCTP or dTTP opposite O6-methylguanine in a defined primed oligonucleotide when Escherichia coli DNA polymerase I is used. Proc. Natl. Acad. Sci. U.S.A. 1989; 86: 8271
   PubMed Web of Science ®Google Scholar
• Dosanjh M. K., Galeros G., Goodman M. F., Singer B. Kinetics of extension of O6-methylguanine paired with cytosine or thymine in defined oligonucleotide sequences. Biochemistry 1991; 30: 11595
   PubMed Web of Science ®Google Scholar
• Voigt J. M., Topal M. D. O6-methylguanine and AC and GT mismatches cause asymmetric structural defects in DNA that are affected by DNA sequence. Biochemistry 1990; 29: 5012
   PubMed Web of Science ®Google Scholar
• Reha-Krantz L. J., Bessman M. J. Studies on the biochemical basis of spontaneous mutation. VI. Selection and characterization of a new bacteriophage T4 mutator DNA polymerase. J. Mol. Biol. 1981; 145: 677
   PubMed Web of Science ®Google Scholar
• Pless R. C., Levitt L. M., Bessman M. J. Nonrandom substitution of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro. Biochemistry 1981; 20: 6235
   PubMed Web of Science ®Google Scholar
• Pless R. C., Bessman M. J. Influence of local nucleotide sequence on substituion of 2-aminopurine for adenine during deoxyribonucleic acid synthesis in vitro. Biochemistry 1983; 22: 4905
   PubMed Web of Science ®Google Scholar
• Freese E. The specific mutagenic effect of base analogues on phage T4. J. Mol. Biol. 1959; 1: 87
   Web of Science ®Google Scholar
• Rudner R. Mutation as an error in base pairing. II. Kinetics of 5-bromodeoxyuridine and 2-amino-purine-induced mutagenesis. Zeitschrift für Vererbungslehre 1961; 92: 361
   PubMedGoogle Scholar
• Ronen A. 2-aminopuririne. Mutat. Res. 1979; 75: 1
   Web of Science ®Google Scholar
• Hopkins R., Goodman M. F. Asymmetry in forming 2-aminopurine hydroxymethylcytosine heteroduplexes; a model giving misincorporation frequencies and rounds of DNA replication from base-pair populations in vivo. J. Mol. Biol. 1979; 135: 1
   PubMed Web of Science ®Google Scholar
• Hopkins R. L., Goodman M. F. Deoxyribonucleotide pools, base pairing and sequence configuration affecting bromodeoxyuradine- and 2-aminopurine-induced mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 1980; 77: 1801
   PubMed Web of Science ®Google Scholar
• Persing D. H., McGinty L., Adams C. W., Fowler R. G. Mutational specificity of the base analogue, 2-aminopurine, in Escherichia coli. Mutat. Res. 1981; 83: 25
   PubMed Web of Science ®Google Scholar
• Goodman M. F., Branscomb E. W. DNA replication fidelity and base mispairing mutagenesis. Accuracy in Molecular Processes: its Control and Relevance to Living Systems, T. B. L. Kirkwood, R. F. Rosenberger, D. J. Galas. Chapman and Hall, New York 1986; 191
   Google Scholar
• Goodman M. F., Hopkins R., Gore W. C. 2-aminopurine-induced mutagenesis in T4 bacteriophage: a model relating mutation frequency to 2-aminopurine incorporation in DNA. Proc. Natl. Acad. Sci. U.S.A. 1977; 74: 4806
   PubMed Web of Science ®Google Scholar
• Mhaskar D. N., Goodman M. F. On the molecular basis of transition mutations. Frequency of forming 2-aminopurine cytosine and adenine cytosine base mispairs in the G AT mutational pathway by T4 DNA polymerase in vitro. J. Biol. Chem. 1984; 259: 11713
   PubMedGoogle Scholar
• Ripley L. S. Influence of diverse gene 43 DNA polymerases on the incorporation and replication in vivo 2-aminopurine at AT base pairs in bacteriophage T4. J. Mol. Biol. 1981; 150: 197
   PubMed Web of Science ®Google Scholar
• Watanabe S. M., Goodman M. F. On the molecular basis of transition mutations: frequencies of forming 2-aminopurine cytosine and adenine cytosine base mispairs in vitro. Proc. Natl. Acad. Sci. U.S.A. 1981; 78: 2864
   PubMed Web of Science ®Google Scholar
• Watanabe S. M., Goodman M. F. Kinetic measurement of 2-aminopurine cytosine and 2-aminopurine thymidine base pairs as a test of DNA polymerase fidelity mechanisms. Proc. Natl. Acad. Sci. U.S.A. 1982; 79: 6429
   PubMed Web of Science ®Google Scholar
• Loeb L. A., Kunkel T. A. Fidelity of DNA synthesis. Annu. Rev. Biochem. 1982; 52: 429
   Web of Science ®Google Scholar
• Fersht A. R., Knill-Jones J. W. Fidelity of replication of bacteriophage X174DNA in vitro and in vivo. J. Mol. Biol. 1983; 165: 633
   PubMed Web of Science ®Google Scholar
• Sloane D. L., Goodman M. F., Echols H. The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme. Nucl. Acids Res. 1988; 16: 6465
   PubMed Web of Science ®Google Scholar
• Sowers L. C., Fazakerley G. V., Eritja R., Kaplan B. E., Goodman M. F. 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. 1986; 83: 5434
   PubMed Web of Science ®Google Scholar
• Eritja R. E., Kaplan B. E., Mhaskar D., Sowers L. C., Petruska J., Goodman M. F. Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine. Nucl. Acids Res. 1986; 14: 5869
   PubMed Web of Science ®Google Scholar
• Petruska J., Goodman M. F. Influence of neighboring bases on DNA polymerase insertion and proofreading fidelity. J. Biol. Chem. 1985; 260: 7533
   PubMed Web of Science ®Google Scholar
• Galas D. J., Branscomb E. W. Enzymatic determinants of DNA polymerase accuracy. Theory of coliphage T4 polymerase mechanisms. J. Mol. Biol. 1978; 88: 653
   Google Scholar
• Goodman M. F. DNA replication fidelity: kinetics and thermodynamics. Mutat. Res. 1988; 200: 11
   PubMed Web of Science ®Google Scholar
• Guest C. R., Hochstrasser R. A., Dupuy C. G., Allen D. J., Benkovic S. J., Miller D. P. Interaction of DNA with the Klenow fragment of DNA polymerase I studied by time-resolved fluorescence spectroscopy. Biochemistry 1991; 30: 8759
   PubMed Web of Science ®Google Scholar
• Jung G. H., Leavitt M. C., Hsieh J. C., Ito J. Bacteriophage PRD1 DNA polymerase: evolution of DNA polymerases. Proc. Natl. Acad. Sci. U.S.A. 1987; 84: 8287
   PubMed Web of Science ®Google Scholar
• Leavitt M. C., Ito J. T5 DNA polymerase: structural functional relationships to other DNA polymerases. Proc. Natl. Acad. Sci. U.S.A. 1989; 86: 4465
   PubMed Web of Science ®Google Scholar
• Bemad A., Zaballos A., Salas M., Blanco L. Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases. EMBO J. 1987; 6: 4219
   PubMed Web of Science ®Google Scholar
• Bernad A., Blanco L., Lazaro J. M., Martin G., Salas M. A conserved 3-5 exonuclease active site in prokaryotic and eukaryotic DNA polymerases. Cell 1989; 59: 219
   PubMed Web of Science ®Google Scholar
• Blanco L., Bernad A., Blasco M. A., Salas M. A general structure for DNA-dependent DNA polymerases. Gene 1991; 100
   PubMed Web of Science ®Google Scholar
• Blanco L., Bernad A., Salas M. Evidence favoring the hypothesis of a conserved 3-5 exonuclease active site in DNA-dependent DNA polymerases. Gene 1992; 112: 139
   PubMed Web of Science ®Google Scholar
• Wong S. W., Wahl A. F., Yuan P. M., Arai N., Pearson B. E., Arai K., Korn D. Human DNA polymerase alpha gene expression is cell proliferation dependent, and its primary structure is similar to both prokaryotic and eukaryotic replicative DNA polymerases. EMBO J. 1988; 7: 37
   PubMed Web of Science ®Google Scholar
• Wang T. S., Wong S. W., Korn D. Human DNA polymerase alpha: predicted functional domains and relationships with viral DNA polymerases. FASEB J. 1989; 3: 14
   PubMed Web of Science ®Google Scholar
• Wang T. S. Eukaryotic DNA polymerases. Annu. Rev. Biochem. 1991; 60: 513
   PubMed Web of Science ®Google Scholar
• Ward D. C., Reich E. Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives. J. Biol. Chem. 1969; 244: 1228
   PubMed Web of Science ®Google Scholar
• Scheit K. H., Rackwitz H. R. Synthesis and physicochemical properties of two analogs of poly(dA):poly(2-aminopurine-9-β-D-deoxyribonucleotide) and poly 2-amino-deoxyadenylic acid. Nucl. Acids Res. 1982; 10: 4059
   PubMed Web of Science ®Google Scholar
• Goodman M. F., Ratliff R. L. Evidence of 2-aminopurine-cytosine base mispairs involving two hydrogen bonds. J. Biol. Chem. 1983; 258: 12842
   PubMedGoogle Scholar
• Topal M. D., Fresco J. R. Molecular basis for substitution mutations. Nature 1976; 263: 285
   PubMed Web of Science ®Google Scholar
• Patel D. J., Kozlowski S. A., Ikuta S., Itakura K. Deoxyadenosine-deoxycytidine pairing in the d(C-G-C-G-A-A-T-T-C-A-C-G) duplex: conformation and dynamics at and adjacent to the dA X dC mismatch site. Biochemistry 1984; 23: 3218
   PubMed Web of Science ®Google Scholar
• Hunter W. N., Brown T., Anand N. N., Kennard O. Structure of an adenine-cytosine base pair in DNA and its implications for mismatch repair. Nature 1986; 320: 552
   PubMed Web of Science ®Google Scholar
• Sowers L. C., Fazakerley G. V., Kim H., Dalton L., Goodman M. F. Variation of nonexchangeable proton resonance chemical shifts as a probe of aberrant base pair formation in DNA. Biochemistry 1986; 25: 3983
   PubMed Web of Science ®Google Scholar
• Wang C., Gao H., Gaffney B. L., Jones R. A. Nitrogen-15-labeled oligodeoxynucleotides. III. Protonation of the adenine N1 in the AC and AG mispairs on the duplexes d[CG(15NI) AGAATTCCCG]2, and d[CGGGAATTC(15NI)ACG]2. J. Am. Chem. Soc. 1991; 113: 5486
   Web of Science ®Google Scholar
• Boulard Y., Cognet J. A., Gabarro A. J., Le B. M., Sowers L. C., Fazakerley G. V. The pH-dependent configurations of the CA mispair in DNA. Nucl. Acids Res. 1933; 20: 1992
   Google Scholar
• Patel D. J., Kozlowski S. A., Ikuta S., Itakura K. Dynamics of DNA duplexes containing internal GT, GA, AC., and TC pairs: hydrogen exchange at and adjacent to mismatch sites. Fed. Proc., Fed. Am. Soc. Exp. Biol. 1984; 43: 2663
   PubMedGoogle Scholar
• Hunter W. N., Kneale G., Brown T., Rabinovich D., Kennard O. Refined crystal structure of an octanucleotide duplex with GT mismatched base pairs. J. Mol. Biol. 1986; 190: 605
   PubMed Web of Science ®Google Scholar
• Kan L. S., Chandrasegaran S., Pulford S. M., Miller P. S. Detection of a guanine X adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 1983; 80: 4263
   PubMed Web of Science ®Google Scholar
• Brown T., Hunter W. N., Kneale G., Kennard O. Molecular structure of the GA base pair in DNA and its implications for the mechanism of trans version mutations. Proc. Natl. Acad. Sci. U.S.A. 1986; 83: 2402
   PubMed Web of Science ®Google Scholar
• Brown T., Leonard G. A., Booth E. D., Chambers J. Crystal structure and stability of a DNA duplex containing A(anti)G(syn) base pairs. J. Mol. Biol. 1989; 207: 455
   PubMed Web of Science ®Google Scholar
• Sowers L. C., Eritja R., Chen F. M., Khwaja T., Kaplan B. E., Goodman M. F., Fazakerley G. V. Characterization of the high pH wobble structure of the 2-aminopurine.cytosine mismatch by N-15 NMR spectroscopy. Biochem. Biophys. Res. Comm. 1989; 165: 89
   PubMed Web of Science ®Google Scholar
• Sowers L. C., Eritja R., Kaplan B., Goodman M. F., Fazakerly G. V. Equilibrium between a wobble and ionized base pair formed between fluorouracil and guanine in DNA as studied by proton and fluorine NMR. J. Biol. Chem. 1988; 263: 14794
   PubMed Web of Science ®Google Scholar
• Sowers L. C., Goodman M. F., Eritja R., Kaplan B., Fazakerley G. V. Ionized and wobble base-pairing for bromouracil-guanine in equilibrium under physiological conditions. A nuclear magnetic resonance study on an oligonucleotide containing a bromouracil-guanine base pair as a function of pH. J. Mol. Biol. 1989; 205: 437
   PubMed Web of Science ®Google Scholar
• Sowers L. C., Ramsay Shaw B., Veigl M. L., Sedwick W. D. DNA base modification: ionized base pairs and mutagenesis. Mutat. Res. 1987; 177: 201
   PubMed Web of Science ®Google Scholar
• Lawley P. D., Brooks P. Ionization of DNA bases or base analogues as a possible explanation of mutagenesis. J. Mol. Biol. 1962; 4: 216
   PubMedGoogle Scholar
• Trautner T. A., Swartz M. N., Kornberg A. Enzymatic synthesis of deoxyribonucleic acid. X. Influence of bromouracil substitutions on replication. Proc. Natl. Acad. Sci. U.S.A. 1962; 48: 449
   PubMed Web of Science ®Google Scholar
• Lasken R. S., Goodman M. F. The biochemical basis of 5-bromouracil-induced mutagenesis. Heteroduplex base mispairs involving bromouracil in GCAT and ATGC mutational pathways. J. Biol. Chem. 1984; 259: 11491
   PubMed Web of Science ®Google Scholar
• Lasken R. S., Goodman M. F. A fidelity assay using “dideoxy” DNA sequencing: a measurement of sequence dependence and frequency of forming 5-bromouracil guanine base mispairs. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 1301
   PubMed Web of Science ®Google Scholar
• Driggers P. H., Beattie K. L. Effect of pH on base-mispairing properties of 5-bromouracil during DNA synthesis. Biochemistry 1988; 27: 1729
   PubMed Web of Science ®Google Scholar
• Yu H., Eritja R., Bloom L. B., Goodman M. F. Ionization of bromuracil and fluorourcial stimulates base mispairing frequencies with guanine. 1992, submitted for publication
   Google Scholar
• Rayssiguier C., Thaler D. S., Radman M. The barrier to recombination between E. coli and Salomonella typhimurium is disrupted in mismatch repair mutants. Nature (London) 1989; 342: 396
   PubMed Web of Science ®Google Scholar
• Tsai-Wu J. J., Liu H. F., Lu A. L. Escherichia coli mutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on AC and AG mispairs. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 8779
   PubMed Web of Science ®Google Scholar
• Michaels M. L., Cruz C., Grollman A. P., Miller J. H. Evidence that MutY and MutM combine to prevent mutations by an oxidatively damaged form of guanine in DNA. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 7022
   PubMed Web of Science ®Google Scholar
• Michaels M. L., Pham L., Cruz C., Miller J. H. MutM, a protein that prevents GC TA trans versions, is formamidopyrimidine-DNA glycosylase. Nucl. Acids Res. 1991; 19: 3629
   PubMed Web of Science ®Google Scholar
• Treffers H. P., Spinelli C., Belser N. O. A factor (or mutator gene) influencing mutation rates in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 1954; 40: 1064
   PubMed Web of Science ®Google Scholar
• Cox E. C. Mutator gene studies in Escherichia coli: the mutT gene. Genetics 1973; 73: 67, Suppl
   PubMed Web of Science ®Google Scholar
• Bhatnagar S. K., Bessman M. J. Studies on the mutator gene, mutT of Escherichia coli Molecular cloning of the gene, purification of the gene product, and identification of a novel nucleoside triphosphatase. J. Biol. Chem. 1988; 263: 8953
   PubMed Web of Science ®Google Scholar
• Bhatnagar S. K., Bullions L. C., Bessman M. J. Characterization of the mutT nucleoside triphosphatase of Escherichia coli. J. Biol. Chem. 1991; 266: 9050
   PubMed Web of Science ®Google Scholar
• Schaaper R. M., Dunn R. L. Escherichia coli mutT mutator effect during in vitro DNA synthesis. Enhanced AG replicational errors. J. Biol. Chem. 1987; 262: 16267
   PubMed Web of Science ®Google Scholar
• Akiyama M., Maki H., Sekiguchi M., Horiuchi T. A specific role of MutT protein: to prevent dGdA mispairing in DNA replication. Proc. Natl. Acad. Sci. U.S.A. 1989; 86: 3949
   PubMed Web of Science ®Google Scholar
• Maki H., Sekiguchi M. MutT protein specifically hydrolyzes a potent mutagenic substrate for DNA synthesis. Nature 1992; 355: 273
   PubMed Web of Science ®Google Scholar
• Boiteux S., O'Connor T. R., Lederer F., Gouyette A., Laval J. Homogeneous Escherichia coli FPG protein. A DNA glycosylase which excised imidazole ring-opened purines and nicks DNA at apurinic/apyrimidinic sites. J. Biol. Chem. 1990; 265: 3916
   PubMed Web of Science ®Google Scholar
• Shibutani S., Takeshita M., Grollman A. P. Insertion of specific bases during DNA synthesis past the hydroxyl-radical damaged base 8-oxodG. Nature 1991; 349: 431
   PubMed Web of Science ®Google Scholar
• Cheng K. C., Cahill D. S., Kasai H., Nishimura S., Loeb L. A. 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G T and A C substitutions. J. Biol. Chem. 1992; 267: 166
   PubMed Web of Science ®Google Scholar
• Walker G. C. Inducible DNA repair systems. Annu. Rev. Biochem. 1985; 54: 425
   PubMed Web of Science ®Google Scholar
• Friedberg E. C. DNA Repair. W. H. Freeman, New York 1985
   Google Scholar
• Lindahl T., Sedgwick B., Sekiguchi M., Nakabeppu Y. Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 1988; 57: 133
   PubMed Web of Science ®Google Scholar
• Radman M. SOS repair hypothesis: phenomenology of an inducible DNA repair which is accompanied by mutagenesis. Molecular Mechanisms for the Repair of DNA, Part A, P. Hanawalt, R. B. Setlow. Plenum Press, New York 1975; 355
   Google Scholar
• Witkin E. M. Ultraviolet mutagenesis and inducible DNA repair in Escherichia coli. Bacteriol. Rev. 1976; 40: 869
   PubMedGoogle Scholar
• Little J. W., Mount D. W. The SOS regulatory system of Escherichia coli. Cell 1982; 29: 11
   PubMed Web of Science ®Google Scholar
• Walker G. C. Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol. Rev. 1984; 48: 60
   PubMedGoogle Scholar
• Echols H., Goodman M. F. Mutation induced by DNA damage: a many protein affair. Mutat. Res. 1990; 236: 301
   PubMed Web of Science ®Google Scholar
• Sancar A., Sancar G. B. DNA repair enzymes. Annu. Rev. Biochem. 1988; 57: 29
   PubMed Web of Science ®Google Scholar
• Bridges B. A., Woodgate R. Mutagenic repair in Escherichia coli: products of the recA gene and of the umuD and umuC genes act at different steps in UV-induced mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 4193
   PubMed Web of Science ®Google Scholar
• Banerjee S. K., Borden A., Christensen R. B., LeClerc J. E., Lawrence C. W. SOS-dependent replication past a single trans-syn T-T cyclobutane dimer gives a different mutation spectrum and increased error rate compared with replication past this lesion in uninduced cells. J. Bacteriol. 1990; 172: 2105
   PubMed Web of Science ®Google Scholar
• Lawrence C. W., Borden A., Banerjee S. K., LeClerc J. E. Mutation frequency and spectrum resulting from a single abasic site in a singlestranded vector. Nucl. Acids Res. 1990; 18: 2153
   PubMed Web of Science ®Google Scholar
• Rajagopalan M., Lu C., Woodgate R., O'Donnell M., Goodman M. F., Echols H. Activity of the purified mutagenesis proteins UmuC., UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase III. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 10777
   PubMed Web of Science ®Google Scholar
• Moore P. D., Bose K. K., Rabkin S. D., Strauss B. S. Sites of termination of in vitro DNA synthesis on ultraviolet- and N-acetylaminofluorene-treated X174 templates by prokaryotic and eukaryotic DNA polymerases. Proc. Natl. Acad. Sci. U.S.A. 1981; 78: 110
   PubMed Web of Science ®Google Scholar
• Banerjee S. K., Christensen R. B., Lawrence C. W., LeClerc J. E. Frequency and spectrum of mutations produced by a single cis-syn thyminethymine cyclobutane dimer in a single-stranded vector. Proc. Natl. Acad. Sci. U.S.A. 1988; 85: 8141
   PubMed Web of Science ®Google Scholar
• Taylor J. S., O'Day C. L. cis-syn thymine dimers are not absolute blocks to replication by DNA polymerase I of Escherichia coli in vitro. Biochemistry 1990; 29: 1624
   PubMed Web of Science ®Google Scholar
• Wang C. I., Taylor J. S. In vitro evidence that UV-induced frameshift and substitution mutations at T tracts are the result of misalignment-mediated replication past a specific thymine dimer. Biochemistry 1992; 31: 3671
   PubMed Web of Science ®Google Scholar
• Hayes R. C., Petrullo L. A., Huang H. M., Wallace S. S., LeClerc J. E. Oxidative damage in DNA. Lack of mutagenicity by thymine glycol lesions. J. Mol. Biol. 1988; 201: 239
   PubMed Web of Science ®Google Scholar
• Ide H., Kow Y. W., Wallace S. S. Thymine glycols and urea residues in M13 DNA constitute replicative blocks in vitro. Nucl. Acids Res. 1985; 13: 8035
   PubMed Web of Science ®Google Scholar
• Loechler E. L., Green C. L., Essigmann J. M. In vivo mutagenesis by O6-methylguanine built into a unique site in a viral genome. Proc. Natl. Acad. Sci. U.S.A. 1984; 81: 6271
   PubMed Web of Science ®Google Scholar
• Eadie J. S., Conrad M., Toorchen D., Topal M. D. Mechanism of mutagenesis by O6-methyl-guanine. Nature 1984; 308: 8
   Google Scholar
• Topal M. D. Mutagenesis by incorporation of alkylated nucleotides. Basic Life Sci. 1985; 31: 339
   PubMedGoogle Scholar
• Chambers R. W., Sledziewska G. E., Hirani H. S., Borowy B. H. uvrA and recA mutations inhibit a site-specific transition produced by a single O6-methylguanine in gene G of bacteriophage X174. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 7173
   PubMed Web of Science ®Google Scholar
• Bhanot O. P., Ray A. The in vivo mutagenic frequency and specificity of O6-methylguanine in X174 replicative form DNA. Proc. Natl. Acad. Sci. U.S.A. 1986; 83: 7348
   PubMed Web of Science ®Google Scholar
• Preston B. D., Singer B., Loeb L. A. Mutagenic potential of O4-methyl thymine in vivo determined by an enzymatic approach to site-specific mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 1986; 83: 8501
   PubMed Web of Science ®Google Scholar
• Rossi S. C., Topal M. D. Mutagenic frequencies of site-specifically located O6-methylguanine in wild-type Escherichia coli and in a strain deficient in ada-methylguanine. J. Bacteriol. 1991; 173: 1201
   PubMed Web of Science ®Google Scholar
• Dosanjh M. K., Essigmann J. M., Goodman M. F., Singer B. Comparative efficiency of forming m4TG vs. m4TA base pairs at a unique site by use of Escherichia coli DNA polymerase I (Klenow fragment) and Drosophila melanogaster polymerase alpha-primase complex. Biochemistry 1990; 29: 4698
   PubMed Web of Science ®Google Scholar
• Loeb L. A., Preston B. D. Mutagenesis by apurinic/apyrimidinic sites. Annu. Rev. Genet. 1986; 20: 201
   PubMed Web of Science ®Google Scholar
• Boiteux S., Laval J. Coding properties of poly(deoxycycytidylic acid) templates containing uracil or apyrimidinic sites: in vitro modulation of mutagenesis by DNA repair enzymes. Biochemistry 1982; 21: 6746
   PubMed Web of Science ®Google Scholar
• Sagher D., Strauss B. S. Insertion of nucleotides opposite apurinic/payrimidinic sites in deoxyribonucleic acid during in vitro synthesis: uniqueness of adenine nucleotides. Biochemistry 1983; 22: 4518
   PubMed Web of Science ®Google Scholar
• Schaaper R. M., Kunkel T. A., Loeb L. A. Infidelity of DNA synthesis associated with bypass of apurinic sites. Proc. Natl. Acad. Sci. U.S.A. 1983; 80: 487
   PubMed Web of Science ®Google Scholar
• Strauss B. S. The 'A rule' of mutagen specificity: a consequence of DNA polymerase bypass of noninstructional lesions. Bioessays 1991; 13: 79
   PubMed Web of Science ®Google Scholar
• Millican T. A., Mock G. A., Chauncey M. A., Patel T. P., Eaton M. A., Gunning J., Cutbush S. D., Neidle S., Mann J. Synthesis and biophysical studies of short oligodeoxynucleotides with novel modifications: a possible approach to the problem of mixed base oligodeoxynucleotide synthesis. Nucl. Acids Res. 1984; 12: 7435
   PubMed Web of Science ®Google Scholar
• Takeshita M., Chang C. N., Johnson F., Will S., Groilman A. P. Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurnic/apyrimidinic endonucleases. J. Biol. Chem. 1987; 262: 10171
   PubMed Web of Science ®Google Scholar
• Ng L., Weiss S. J., Fisher P. A. Recognition and binding of template primers containing defined abasic sites by Drosophila DNA polymerase alpha holoenzyme. J. Biol. Chem. 1989; 264: 13018
   PubMed Web of Science ®Google Scholar
• Cai H., Bloom L. B., Goodman M. F. 1992, unpublished
   Google Scholar
• Cuniasse P., Fazakerley G. V., Guschlbauer W., Kaplan B. E., Sowers L. C. The abasic site as a challenge to DNA polymerase. A nuclear magnetic resonance study of G. C and T opposite a model abasic site. J. Mol. Biol. 1990; 213: 303
   PubMed Web of Science ®Google Scholar
• Kalnik M. W., Chang C. N., Grollman A. P., Patel D. J. NMR studies of basic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-deoxyribose. Biochemistry 1988; 27: 924
   PubMed Web of Science ®Google Scholar
• Fersht A. R., Knill J. J. W. Contribution of 35 exonuclease activity of DNA polymerase III holoenzyme from Escherichia coli to specificity. J. Mol. Biol. 1983; 165: 669
   PubMed Web of Science ®Google Scholar
• Lu C., Scheuermann R. H., Echols H. RecA protein and SOS: correlation of mutagenesis phenotype with binding of mutant RecAs to duplex DNA and LexA cleavage. J. Mol. Biol. 1987; 196: 497
   PubMed Web of Science ®Google Scholar
• Aboul-ela F., Koh D., Tinoco I. J., Martin F. H. Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T). Nucl. Acids Res. 1985; 13: 4811
   PubMed Web of Science ®Google Scholar
• Gaffney B. L., Jones R. A. Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs. Biochemistry 1989; 28: 5881
   PubMed Web of Science ®Google Scholar
• Petruska J., Goodman M. F. 1992, unpublished
   Google Scholar
• Patel S. S., Wong I., Johnson K. A. Presteady state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant. Biochemistry 1991; 30: 511
   PubMed Web of Science ®Google Scholar
• Eger B. T., Benkovic S. J. Minimal kinetic mechanism for misincorporation by DNA polymerase I (Klenow fragment). Biochemistry 1992; 31: 9227
   PubMed Web of Science ®Google Scholar
• Capson T. L., Peliska J. A., Kaboord B. F., Frey M. W., Lively C., Dahlberg M., Benkovic S. J. Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4. Biochemistry 1992; 31: 10984
   PubMed Web of Science ®Google Scholar
• Ornstein R. L., Rein R., Breen D. L., MacElroy R. D. An optimized potential function for the calculation of nucleic acid interaction energies. I. Base stacking. Biopolymers 1978; 17: 2341
   PubMed Web of Science ®Google Scholar