An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues

Journal of Molecular Biology

Volumn 255, Issue 4, 1996, Pages 589-603

  Zaccolo, Manuela ^a   Williams, David M ^b   Brown, Daniel M ^b   Gherardi, Ermanno ^a  

^a MEDICAL RESEARCH COUNCIL   (United Kingdom)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

8 oxodeoxyguanosine; dP; PCR; Protein engineering; Pyrimidine analogue; Random mutagenesis

Indexed keywords

ADENINE; DNA POLYMERASE; NUCLEOSIDE ANALOG;

ARTICLE; CODON; CONTROLLED STUDY; DNA LIBRARY; DNA MODIFICATION; DNA TEMPLATE; GENE AMPLIFICATION; GENE DELETION; GENE INSERTION; HUMAN; METHODOLOGY; MUTAGENESIS; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL;

EID: 0029869449     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0049     Document Type: Article

References (68)

1. Abdul-Mashi, M. T. & Bessman, M. J. (1986). Biochemical studies on the mutagen 6-N-hydroxylaminopurine. J. Biol. Chem. 261, 2020-2026.
2. Anand N. N., Brown, D. M. & Salisbury, S. A. (1987). The stability of oligodeoxynucleotide duplexes containing degenerate bases. Nucl. Acids Res. 15, 8167-8176.
3. Berek, C. & Milstein, C. (1987). Mutation drift and repertoire shift in the maturation of the immune response. Immunol. Rev. 96, 23-41.
4. Boosalis, M. S., Petruska, J. & Goodman, M. F. (1987). DNA polymerase insertion fidelity. J. Biol. Chem. 262, 14689-14696.
5. Brown, D. M., Hewlins, M. J. E. & Schell, P. (1968). The tautomeric state of N(4)-hydroxy- and N(4)-aminocytosine derivatives. J. Chem. Soc. C 1925-1929.
6. Cadwell, R. C. & Joyce, G. F. (1992). Randomization of genes by PCR mutagenesis. PCR Methods Applic. 2, 28-33.
7. Cheng, K. C., Cahill, D. S., Kasai, H., Nishimuta, S. & Loeb, L. A. (1992). 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G to T and A to C substitutions. J. Biol. Chem. 267, 166-172.
8. Cunningham, B. C. & Wells, J. A. (1987). Improvement in the alkaline stability of subtilisin using an efficient random mutagenesis and screening procedure. Protein Eng. 1, 319-325.
9. Dower, W. J., Miller, J. F. & Ragsdale, C. W. (1988). High efficiency transformation of E. coli by high voltage electroporation. Nucl. Acids Res. 16, 6127-6145.
10. 6-methylguanine. Nature, 308, 201-203.
11. Eckert, K. A. & Kunkel, T. A. (1990). High fidelity DNA synthesis by the Thermus acquaticus DNA polymerase. Nucl. Acids Res. 18, 3739-3744.
12. Eisenthal, R. & Cornish-Bowden, A. (1974). The direct linear plot. A new graphical procedure for estimating enzyme kinetic parameters. Biochem. J. 139, 715-720.
13. Estell, D. A., Graycar, T. P. & Wells, J. A. (1985). Engineering an enzyme by site-directed mutagenesis to be resistant to chemical oxidation. J. Biol. Chem. 260, 6518-6521.
14. Flavell, R. A., Sabo, D., Bandle, E. & Weissman, C. (1974). Site-directed mutagenesis: generation of an extracistronic mutation in bacteriophage Qβ. J. Mol. Biol. 89, 255-272.
15. Gillam, S. & Smith, M. (1979a). Site-specific mutagenesis using synthetic oligonucleotide primers: I. Optimum conditions and minimum oligodeoxy ribonucleotide length. Gene, 8, 81-97.
16. Gillam, S. & Smith, M. (1979b). Site-specific mutagenesis using synthetic oligonucleotide primers: II. In vitro selection of mutant DNA. Gene, 8, 99-106.
17. Gram, H., Marconi, L. A., Barbas III, C. F., Collet, T. A., Lerner, R. A. & Kang, A. S. (1992). In vitro selection and affinity maturation of antibodies from naive combinatorial immunoglobulin libraries. Proc. Natl Acad. Sci. USA, 89, 3576-3580.
18. Griffiths, A. D., Williams, S. C. Hartley, O., Tomlinson, I. M., Waterhouse, P., Crosby W. L., Kontermann, R. E., Jones, P. T., Low, N. M., Allison, T. J., Prospero, T. D., Hoogenboom, H. R., Nissim, A., Cox, J. P. L., Harrison, J. L., Zaccolo, M., Gherardi, E. & Winter, G. (1994). Isolation of high-affinity human antibodies directly from large synthetic repertoires. EMBO J. 13, 3245-3260.
19. Grossberger, D. & Clough, W. (1981). Incorporation into DNA of the base analogue 2-aminopurine by Epstein Barr virus induced DNA polymerase in vivo and in vitro. Proc. Natl Acad. Sci. USA, 78, 7271-7275.
20. Hawkins, R. E., Russell, S. J. & Winter, G. (1992). Selection of phage antibodies by binding affinity. Mimicking affinity maturation. J. Mol. Biol. 226, 889-896.
21. Hutchinson, C. A., Phillips, S., Edgell, M. N. Gillam, S. Jahnke, P. & Smith, M. (1978). Mutagenesis at a specific position in a DNA sequence. J. Biol. Chem. 253, 6551-6560.
22. Ikeda, M., Hamano, K. & Shibata, T. (1992). Epitope mapping of anti-recA protein IgGs by region specified polymerase chain reaction mutagenesis. J. Biol. Chem. 267, 6291-6296.
23. Innis, M. A., Myambo, K. B., Gelfand, D. H. & Brow M. A. D. (1988). DNA sequencing with Thermus aquations DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc. Natl Acad. Sci. USA, 85, 9436-9440.
24. Jones, P. T., Dear, R. H., Foote, J., Neuberger, M. S. & Winter, G. (1986). Replacing the complementary-determining regions in human antibody with those from a mouse. Nature, 321, 522-525.
25. Kabat, E. A., Wu, T. T., Perry, H. M. Gottesman, K., S. & Foeller, C. (1991). Sequences of Proteins of Immunological Interest, 5th edit., U. S. Department of Health and Human Services, Public Health Services National Institute of Health.
26. Kamiya, H., Murata-Kamiya, N., Kong Thoo Lin, P., Brown, D. M. & Ohtsuka, E. (1994). Nucleotide incorporation opposite degenerate bases by Taq polymerase. Nucleosides Nucleotides, 13, 1483-1492.
27. Kaartinen, M., Griffiths, G. M., Markham, A. F. & Milstein, C. (1983). mRNA sequences define an unusually restricted IgG response to 2-phenyl-oxazolone and its early diversification. Nature, 304, 320-325.
28. Komiyama, N. H., Miyazaki, G., Tame, J. & Nagai, K. (1995). Transplanting a unique, allosteric effect from crocodile into human haemoglobin. Nature, 373, 244-246.
29. Kong, H., Kucera, R. B. & Jack, W. E. (1993). Characterisation of a DNA polymerase from the Hyperthermophile Archea Thermococcus litoralis. J. Biol. Chem. 268, 1965-1975.
30. Kong Thoo Lin, P. & Brown, D. M. (1989). Synthesis and duplex stability of oligonucleotides containing cytosine-thymine analogues. Nucl. Acids Res. 17, 10373-10383.
31. Kouchakdjian, M., Bodepudi, V., Shibutani, S., Eisenberg, M., Johnson, F., Grollman, A. P. & Patel, D. J. (1991). NMR structural studies of the ionizing radiation adduct 7-hydro-8-oxodeoxyguanosine (8-oxo-7H-dG) opposite deoxyadenosine in a DNA duplex. 8-oxo-7H-dG(syn).dA(anti) alignment at lesion site. Biochemistry, 30, 1403-1412.
32. Lehtovaara, P. M., Koivula, A. K., Bamford, J. & Knowles, J. K. C. (1988). A new method for random mutagenesis of complete genes: enzymatic generation of mutant libraries in vitro. Protein Eng. 2, 63-68.
33. Leung, D. W., Chen, E. & Goeddel, D. V. (1989). A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction. Techniques, 1, 11-15.
34. Lim, W. A. & Sauer, R. T. (1991). The role of internal packing interactions in determining the structure and stability of a protein. J. Mol. Biol. 219, 359-376.
35. Looker, D., Abbott-Brown, D., Cozart, P., Durfee, S., Hoffman, S., Mathews, A. J., Miller-Roerich, J., Shoemaker, S., Trimble, T., Fermi, G., Komiyama, N. H., Nagai, K. & Steuer, G. L. (1992). A human recombinant haemoglobin designed for use as a blood substitute. Nature, 356, 258-260.
36. Ludwig, J. (1981). A new route to nucleoside 5′-triphosphates (1981). Acta Biochim. Biophys. Acad. Sci. Hung. 16, 131-133.
37. Maki, A. & Sekiguchi, M. (1992). MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature, 355, 273-275.
38. 4-aminodeoxycytidine 5′-triphosphate into DNA of phage M13mp2. Mutat. Res. 268, 59-64.
39. Mo, J. Y., Maki, H. & Sekiguchi, M. (1992). Hydrolytic elimination of a mutagenic nucleotide, 8-oxodGTP, by human 18-kilodalton protein: sanitization of the nucleotide pool. Proc. Natl Acad. Sci. USA, 89, 11021-11025.
40. Moore, M. H., van Meervelt, L., Salisbury S. A., Kong Thoo Lin, P. & Brown, D. M. (1995). Direct observation of two base-pairing modes of a cytosine-thymine analogue with guanine in a DNA Z-form duplex; Significance for base analogue mutagenesis. J. Mol. Biol. 251, 665-673.
41. Mott, J. E., van Arsdell, J. & Platt, T. (1984). Targeted mutagenesis in vitro: lac repressor mutations generated using AMV reverse transcriptase and dBrUTP. Nucl. Acids Res. 12, 4139-4152.
42. Morozov, Y. V, Savin, F. A., Chechov, V. O., Budowsky E. I. & Yakovlev, D. Y (1982). Photochemistry of N6-methoxyadenosine and of N4-hydroxycytidine and its methyl derivatives. J. Photochem. 20, 229-252.
43. Müller, W., Weber, H., Meyer, F. & Weissman, C. (1978). Site-directed mutagenesis in DNA: Generation of point mutations in cloned β globin complementary DNA at the positions corresponding to amino acids 121 to 123. J. Mol. Biol. 124, 343-358.
44. 1H nuclear magnetic resonance studies of oli gonucleotide duplexes containing base-modified cytosine residues. J. Mol. Biol. 230, 1068-1076.
45. Negishi, K., Takahashi, M., Yamashita, Y., Nishizawa M. & Hayatsu, H. (1985). Mutagenesis by N4-aminocytidine: induction of AT to GC transition and its molecular mechanism. Biochemistry, 24, 7273-7278.
46. Neuberger, M. S., Williams, G. T. & Fox, R. O. (1984). Recombinant antibodies possessing novel effector functions. Nature, 312, 604-608.
47. Oda, Y., Uesugi, H., Ikehara, M., Nishimura, S., Kawase, Y., Ishikawa, H., Inoue, H. & Ohtsuka, E. (1991). NMR studies of a DNA containing 8-hydroxydeoxyguanosine. Nucl. Acids Res. 19, 1407-1412.
48. Ohtsuka, E., Shigeru, M., Ikehara, M., Takahashi, Y. & Matsubara, K. (1985). An alternative approach to deoxyoligonucleotides as hybridisation probes by insertion of deoxyinosine at ambiguous positions. J. Biol. Chem. 260, 2605-2608.
49. Pavlov, Y. I., Minnik, D. T., Izuta, S. & Kunkel, T. A. (1994). DNA replication fidelity with 8-oxodeoxyguanosine triphosphate. Biochemistry, 33, 4695-4701.
50. Purmal, A. A., Wah Kow Y. & Wallace S. S. (1994). 5-Hydroxypyrimidine deoxynucleoside triphosphates are more efficiently incorporated into DNA by exonuclease-free Klenow fragment than 8-oxopurine deoxynucleoside triphosphates. Nucl. Acids Res. 22, 3930-3935.
51. Reeves, S. T. & Beattie, K. L. (1985). Base-pairing properties of N4-methoxydeoxycytidine 5′-triphosphate during DNA synthesis on natural templates, catalysed by DNA polymerase I of Escherichia coli. Biochemistry, 24, 2262-2268.
52. Rennell, D., Bouvier, S. E., Hardy L. W. & Poteete, A. R. (1991) Systematic mutation of bacteriophage T4 lysozyme. J. Mol. Biol. 222, 67-87.
53. Sanger, F., Niklen, S. & Coulson, A. R. (1977). DNA sequencing with chain terminating inhibitors. Proc. Natl Acad. Sci. USA, 74, 5463-5466.
54. Sharon, J. (1990). Structural correlates of high antibody affinity: three engineered aminoacid substitutions can increase the affinity of an anti p-axophenylarsonate antibody 200 fold. Proc. Natl Acad. Sci. USA, 87, 4814-4817.
55. Shibutani, S., Takeshita, M. & Grollman, A. P. (1991) Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature, 349, 431-434.
56. Shugar, D., Huber, C. P. & Birnbaum, G. I. (1976). Mechanism of hydroxylamine mutagenesis. Crystal structure and conformation of 1,5-dimethyl-N4-hydroxycytosine. Biochim. Biophys. Acta, 447, 274-284.
57. 4-Methoxydeoxycytidine triphosphate is in the imino tautomeric form and substitutes for deoxythymidine triphosphate in primed poly d[A-T] synthesis with E. coli DNA polymerase I. Nucl. Acids Res. 12, 4609-4619.
58. 4-isopropylthymidine 5′-triphosphates as analogues of thymidine 5′-triphosphate: kinetics of incorporation by Escherichia coli DNA polymerase I. Biochemistry, 25, 1201-1205.
59. 4-methyldeoxythymidine triphosphate. Biochemistry, 28, 1478-1483.
60. Smith G. P. (1985). Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science, 228, 1315-1317.
61. Smith, J. M. & Thomas, D. J. (1990). Quantitative analysis of one-dimensional gel electrophoresis profiles. CABIOS, 6, 93-99.
62. 6-methyldeoxyguanosine monophosphate during in vitro DNA synthesis. Biochemistry, 23, 4289-4294.
63. Spee, J. H., de Vos, W. M. & Kuipers, O. P. (1993). Efficient random mutagenesis method with adjustable mutation frequency by use of PCR and dITP. Nucl. Acids Res. 21, 777-778.
64. Stemmer, W. P. C. (1994a). DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Nacl Acad. Sci. USA, 91, 10747-10751.
65. Stemmer, W. P. C. (1994b). Rapid evolution of a protein in vitro by DNA shuffling. Nature, 370, 389-391.
66. 1H nuclear magnetic resonance studies of base-modified oligodeoxynucleotides. J. Mol. Biol. 222, 711-723.
67. Tindall, K. R. & Kunkel, T. A. (1988). Fidelity of DNA synthesis by the Thermus acquaticus DNA polymerase. Biochemistry, 27, 6008-6013.
68. Winter, G., Fersht, A. R., Wilkinson, A. J., Zoller, M. & Smith, M. (1982). Redesigning enzyme structure by site-directed mutagenesis: tyrosyl tRNA synthetase and ATP binding. Nature, 299, 756-758.