In vitro constructive approaches to the origin of coding sequences

Journal of Biochemistry and Molecular Biology

Volumn 31, Issue 3, 1998, Pages 209-220

  Shiba, Kiyotaka ^a,b  

^a JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^b CANCER INSTITUTE   (Japan)

Author keywords

Evolutionary molecular engineering; Ex vivo evolution; Microgene polymerization reaction (MPR); Molecular diversity; Periodic structure

Indexed keywords

EID: 0032393115     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (130)

1. Agterberg, M., Adriaanse, H., van Bruggen, A., Karperien, M., and Tommassen, J. (1990) Outer-membrane PhoE protein of Escherichia coli K-12 as an exposure vector: possibilities and limitations. Gene 88, 37-45.
2. Aita, T. and Husimi, Y. (1996) Fitness spectrum among random mutants on Mt. Fuji-type fitness landscape. J. Theor. Biol. 182, 469-485
3. Auld, D. S. and Schimmel, P. (1995) Switching recognition of two tRNA synthetases with an amino acid swap in a designed peptide. Science 267, 1994-1996.
4. Ball, P. (1994) Polymers made to measure. Nature 367, 323-324.
5. Barbas, C. F. and Burton, D. R. (1996) Selection and evolution of high-affinity human anti-viral antibodies. Trends Biotech. 14, 230-234.
6. Bartel, D. P. and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences. Science 261, 1411-1418.
7. Bass, S., Greene, R., and Wells, J. A. (1990) Hormone phage - an enrichment method for variant proteins with altered binding properties. Proteins Struct. Funct. Genet. 8, 309-314.
8. Benkovic, S. J. (1992) Catalytic antibodies. Annu. Rev. Biochem. 61, 29-54.
9. Biebricher, C. K. and Gardiner, W. C. (1997) Molecular evolution of RNA in vitro. Biophys. Chem. 66, 179-192.
10. Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H., and Toole, J. J. (1992) Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 355, 564-566.
11. Boder, E. T. and Wittrup, K. D. (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nature Biotech. 15, 553-557.
12. Breaker, R. R. and Joyce, G. F. (1994) A DNA enzyme that cleaves RNA. Chem. Biol. 1, 223-229.
13. Brenner, S. and Lerner, R. A. (1992) Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA 89, 5381-5383.
14. Brown, S. (1997) Metal-recognition by repeating polypeptides. Nature Biotech. 15, 269-272.
15. Brown, J. R. and Doolittle, W. F. (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 92, 2441-2445.
16. Cadwell, R. C. and Joyce, G. F. (1992) Randomization of genes by PCR mutagenesis. PCR Methods Applic. 2, 28-33.
17. Crameri, A., Raillard, S. A., Bermudez, E., and Stemmer, W. P. C. (1998) DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391, 288-291.
18. Cwirla, S. E., Peters, E. A., Barrett, R. W., and Dower, W. J. (1990) Peptides on phage - a vast library of peptides for identifying ligands. Proc. Natl. Acad. Sci. USA 87, 6378-6382.
19. Davidson, A. R. and Sauer, R. T. (1994) Folded proteins occur frequently in libraries of random amino acid sequences. Proc. Natl. Acad. Sci. USA 91, 2146-2150.
20. Davidson, A. R., Lumb, K. J., and Sauer, R. T. (1995) Cooperatively folded proteins in random sequence libraries. Nature Struct. Biol. 2, 856-864.
21. Devlin, J. J., Panganiban, L. C., and Devlin, P. E. (1990) Random peptide libraries - a source of specific protein binding molecules. Science 249, 404-406.
22. Ecker, D. J. and Crooke, S. T. (1995) Combinatorial drug discovery: which methods will produce the greatest value? Bio/Technology 13, 351-360.
23. Eigen, M. (1992) Steps Towards Life: A Perspective on Evolution, Oxford University Press, Oxford.
24. Ekland, E. H., Szostak, J. W., and Bartel, D. P. (1995) Structurally complex and highly active RNA ligases derived from random RNA sequences. Science 269, 364-370.
25. Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822.
26. Ellington, A. D. and Conrad, R. (1995) Aptamers as potential nucleic acid pharmaceuticals. Biotech. Annu. Rev. 1, 185-214.
27. Ferris, J. P., Hill, A. R., Liu, R. H., and Orgel, L. E. (1996) Synthesis of long prebiotic oligomers on mineral surfaces. Nature 381, 59-61.
28. Fisch, I., Kontermann, R. E., Finnern, R., Hartley, O., Solergonzalez, A. S., Griffiths, A. D., and Winter, G. (1996) A strategy of exon shuffling for making large peptide repertoires displayed on filamentous bacteriophage. Proc. Natl. Acad. Sci. USA 93, 7761-7766.
29. Fitch, W. M. and Upper, K. (1987) The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Symp. Quant. Biol. 52, 759-737.
30. Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, J. L., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T. R., Saudek, D. M., Phillips, C. A., Merrick, J. M., Tomb, J. F., Dougherty, B. A., Bott, K. F., Hu, P. C., Lucier, T. S., Peterson, S. N., Smith, H. O., Hutchison, C. A., and Venter, J. C. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270, 397-403.
31. Gallop, M. A., Barrett, R. W., Dower, W. J., Fodor, S. P. A., and Gordon, E. M. (1994) Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J. Med. Chem. 37, 1233-1251.
32. Georgiou, G., Stephens, D. L., Stathopoulos, C., Poetschke, H. L., Mendenhall, J., and Earhart, C. F. (1996) Display of β-lactamase on the Escherichia coli surface: Outer membrane phenotypes conferred by Lpp′-OmpA′-β-lactamase fusions. Protein Engng. 9, 239-247.
33. Geysen, H. M., Houghten, R. A., Kauffman, S., Lebl, M., Moos, M. H., Pavia, M. R., and Szostak, J. W. (1995) Molecular diversity comes of age! Mol. Divers. 1, 1-3.
34. Gilbert, W. (1987) The exon theory of genes. Cold Spring Harbor Symp. Quant. Biol. 52, 901-905.
35. Glaser, S. M., Yelton, D. E., and Huse, W. D. (1992) Antibody engineering by codon-based mutagenesis in a filamentous phage vector system. J. Immunol. 149, 3903-3913.
36. Goffeau, A., Barrell, B. G., Bussey, H., Davis, R. W., Dujon, B., Feldmann, H., Galibert, F., Hoheisel, J. D., Jacq, C., Johnston, M., Louis, E. J., Mewes, H. W., Murakami, Y., Philippsen, P., Tettelin, H., and Oliver, S. G. (1996) Life with 6000 genes. Science 274, 546.
37. Gold, L. (1995) Oligonucleotides as research, diagnostic, and therapeutic agents. J. Biol. Chem. 270, 13581-13584.
38. Gold, L., Polisky, B., Uhlenbeck, O., and Yarus, M. (1995) Diversity of oligonucleotide functions. Annu. Rev. Biochem. 64, 763-797.
39. Gordon, E. M., Barrett, R. W., Dower, W. J., Fodor, S. P. A., and Gallop, M. A. (1994) Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J. Med. Chem. 37, 1385-1401.
40. Hanes, J. and Pluckthun, A. (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl. Acad. Sci. USA 94, 4937-4942.
41. Hawkins, R. E., Russell, S. J., and Winter, G. (1992) Selection of phage antibodies by binding affinity - mimicking affinity maturation. J. Mol. Biol. 226, 889-896.
42. Hoogenboom, H. R. (1997) Designing and optimizing library selection strategies for generating high-affinity antibodies. Trends Biotech. 15, 62-70.
43. Houghten, R. A., Pinilla, C., Blondelle, S. E., Appel, J. R., Dooley, C. T., and Cuervo, J. H. (1991) Generating and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 354, 84-86.
44. Huse, W. D., Sastry, L., Iverson, S. A., Kang, A. S., Alting-Mees, M., Burton, D. R., Benkovic, S. J., and Lerner, R. A. (1989) Generation of a large combinatorial library of the immunoglobulin repertoire in phage λ. Science 246, 1275-1281.
45. Illangasekare, M., Sanchez, G., Nickles, T., and Yarus, M. (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267, 643-647.
46. Janda, K. D., Lo, C.-H. L., Li, T., Barbas III, C. F., Wirshing, P., and Lerner, R. A. (1994) Direct selection for a catalytic mechanism from combinatorial antibody libraries. Proc. Natl. Acad. Sci. USA 91, 2532-2536.
47. Janda, K. D., Lo, L. C., Lo, C. H. L., Sim, M. M., Wang, R., Wong, C. H., and Lerner, R. A. (1997) Chemical selection for catalysis in combinatorial antibody libraries. Science 275, 945-948.
48. Jencks, W. P. (1969) Catalysis in Chemistry and Enzymology, McGraw-Hill, New York.
49. Jiang, F., Kumar, R.A., Jones, R.A., and Patel, D.J. (1996) Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382, 183-186.
50. Joyce, G. F. (1989) Amplification, mutation and selection of catalytic RNA. Gene 82, 83-87.
51. Joyce, G. F. (1997) Evolutionary chemistry: getting there from here. Science 276, 1658-1659.
52. Kamtekar, S., Schiffer, J. M., Xiong, H., Babik, J. M., and Hecht, M. H. (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680-1685.
53. Kauffman, S. (1993) The Origins of Order. Oxford University Press, Oxford.
54. Kobe, B. (1996) Leucines on a roll. Nature Struct. Biol. 3, 977-980.
55. Korotkov, E. V. and Korotkova, M. A. (1995) Latent periodicity of DNA sequences from some human gene regions. DNA Seq. 5, 353-358.
56. Kozlovska, T. M., Cielens, I., Vasiljeva, I., Strelnikova, A., Kazaks, A., Dislers, A., Dreilina, D., Ose, V., Gusars, I., and Pumpens, P. (1996) RNA phage Qβ coat protein as a carrier for foreign epitopes. Intervirology 39, 9-15.
57. Kramer, F. R., Mills, D. R., Cole, P. E., Nishihara, T., and Spiegelman, S. (1974) Evolution in vitro: sequence and phenotype of a mutant RNA resistant to ethidium bromide. J. Mol. Biol. 89, 719-736.
58. Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E., and Cech, T. R. (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31, 147-157.
59. Kumar, P. K. R., Nishikawa, S., and Nakamura, Y. (1995) Evolutionary molecular engineering in Japan. Mol. Diversity 1, 135-137.
60. Lam, K. S., Salmon, S. E., Hersh, E. M., Hruby, V. J., Kazmierski, W. M., and Knapp, R. J. (1991) A new type of synthetic peptide library for identifying ligand-binding activity. Nature 354, 82-84.
61. Lee, D. H., Granja, J. R., Martinez, J. A., Severin, K., and Ghadiri, M. R. (1996) A self-replicating peptide. Nature 382, 525-528.
62. Lerner, R. A., Benkovic, S. J., and Schultz, P. G. (1991) At the crossroads of chemistry and immunology: catalytic antibodies. Science 252, 659-667.
63. Lerner, R. A., Kang, A. S., Bain, J. D., Burton, D. R., and Barbas III, C. F. (1992) Antibodies without immunization. Science 258, 1313-1314.
64. Li, T. and Nicolaou, K. C. (1994) Chemical self-replication of palindromic duplex DNA. Nature 369, 218-221.
65. Lorsch, J. R. and Szostak, J. W. (1994) In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature 371, 31-36.
66. Lu, Z., Murray, K. S., Cleave, V. V., LaVallie, E. R., Stahl, M. L., and McCoy, J. M. (1995) Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin: a system designed for exploring protein-protein interactions. Bio/Technology 13, 366-372.
67. Marks, J. D., Hoogenboom, H. R., Griffiths, A. D., and Winter, G. (1992) Molecular evolution of proteins on filamentous phage - mimicking the strategy of the immune system. J. Biol. Chem. 267, 16007-16010.
68. Matteucci, M. D. and Heyneker, H. L. (1983) Targeted random mutagenesis: the use of ambiguously synthesized oligonucleotides to mutagenize sequences immediately 5′ of an ATG initiation codon. Nucleic Acids Res. 11, 3113-3121.
69. Mattheakis, L. C., Bhatt, R. R., and Dower, W. J. (1994) An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl. Acad. Sci. USA 91, 9022-9026.
70. McCafferty, J., Jackson, R. H., and Chiswell, D. J. (1991) Phage-enzymes: expression and affinity chromatography of functional alkaline phosphatase on the surface of bacteriophage. Protein Engng. 4, 955-961.
71. Mikawa, Y. G., Maruyama, I. N., and Brenner, S. (1996) Surface display of proteins on bacteriophage lambda heads. J. Mol. Biol. 262, 21-30.
72. Mikheeva, S. and Jarrell, K. A. (1996) Use of engineered ribozymes to catalyze chimeric gene assembly. Proc. Natl. Acad. Sci. USA 93, 7486-7490.
73. Miller, S. L. (1953) A production of amino acids under possible primitive Earth conditions. Science 117, 528-530.
74. Milligan, J. F., Groebe, D. R., Witherell, G. W., and Uhlenbeck, O. C. (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798.
75. Mills, D. R., Peterson, R. L., and Spiegelman, S. (1967) An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc. Natl. Acad. Sci. USA 58, 217-224.
76. Mottershead, D., van der Linden, I., von Bonsdorff, C. H., Keinanen, K., and OkerBlom, C. (1997) Baculoviral display of the green fluorescent protein and rubella virus envelope proteins. Biochem. Biophys. Res. Commun. 238, 717-722.
77. Myers, P. L. (1997) Will combinatorial chemistry deliver real medicines? Curr. Opin. Biotechnol. 8, 701-707.
78. Needels, M. C., Jones, D. G., Tate, E. H., Heinkel, G. L., Kochersperger, L. M., Dower, W. J., Barrett, R. W., and Gallop, M. A. (1993) Generation and screening of an oligonucleotide-encoded synthetic peptide library. Proc. Natl. Acad. Sci. USA 90, 10700-10704.
79. Nemoto, N., Miyamoto-Sato, E., Husimi, Y., and Yanagawa, H. (1997) In vitro virus: bonding of mRNA bearing puromycin at the 3′-terminal end to the C-terminal end of its encoded protein on the ribosome in vitro. FEBS Lett. 414, 405-408.
80. Nord, K., Nilsson, J., Nilsson, B., Uhlén, M., and Nygren, P. A. (1995) A combinatorial library of an alpha-helical bacterial receptor domain. Protein Engng. 8, 601-608.
81. Nord, K., Gunneriusson, E., Ringdahl, J., Stahl, S., Uhlén, M., and Nygren, P.A. (1997) Binding proteins selected from combinatorial libraries of an α helical bacterial receptor domain. Nature Biotech. 15, 772-777.
82. Ohlmeyer, M. H., Swanson, R. N., Dillard, L. W., Reader, J. C., Asouline, G., Kobayashi, R., Wigler, M., and Still, W. C. (1993) Complex synthetic chemical libraries indexed with molecular tags. Proc. Natl. Acad. Sci. USA 90, 10922-10926.
83. Ohno, S. (1981) Original domain for the serum albumin family arose from repeated sequences. Proc. Natl. Acad. Sci. USA 78, 7657-7661.
84. Ohno, S. (1987) Evolution from primordial oligomeric repeats to modern coding sequences. J. Mol. Evol. 25, 325-329.
85. Ohno, S. (1989) Modern coding sequences are in the periodic-to-chaotic transition. Hamatol. Bluttransfus. 32, 512-519.
86. Ohno, S. (1992) Of palindromes and peptides. Hum. Genet. 90, 342-345.
87. Ohno, S. (1994) The cardinal principle of like attracting like generates many ubiquitous oligopeptides shared by divergent proteins. Animal Genet. 25s, 5-11.
88. Ohno, S. and Matsunaga, T. (1982) The 48-base-long primordial building block of immunoglobulin light-chain variable regions is complementary to the primordial building block of heavy-chain variable regions. Proc. Natl. Acad. Sci. USA 79, 2338-2341.
89. Ohno, S. and Epplen, J. T. (1983) The primitive code and repeats of base oligomers as the primordial protein-encoding sequence. Proc. Natl. Acad. Sci. USA 80, 3391-3395.
90. Oparin, A. I. (1938) The Origin of Life, MacMillan, New York.
91. Palmer, J. D. and Logsdon, J. J. M. (1991) The recent origins of introns. Curr. Opin. Genet. Develop. 1, 470-477.
92. Pauling, L. (1948) Chemical achievement and hope for the future. Am. Sci. 36, 51.
93. Pollack, S. J., Jacobs, J. W., and Schultz, P. G. (1986) Selective chemical catalysis by an antibody. Science 234, 1570-1573.
94. Prijambada, I. D., Yomo, T., Tanaka, F., Kawama, T., Yamamoto, K., Hasegawa, A., Shima, Y., Negoro, S., and Urabe, I. (1996) Solubility of artificial proteins with random sequences. FEBS Lett. 382, 21-25.
95. Rebar, E. J. and Pabo, C. O. (1994) Zinc finger phage - affinity selection of fingers with new DNA-binding specificities. Science 263, 671-673.
96. Roberts, B. L., Markland, W., Ley, A. C., Kent, R. B., White, D. W., Guterman, S. K., and Ladner, R. C. (1992) Directed evolution of a protein - selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage. Proc. Natl. Acad. Sci. USA 89, 2429-2433.
97. Roberts, R. W. and Szostak, J. W. (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc. Natl. Acad. Sci. USA 94, 12297-12302.
98. Robertson, D. L. and Joyce, G. F. (1990) Selection in vitro of an RNA enzyme that specifically cleaves single stranded DNA. Nature 344, 467-468.
99. Rojas, N. R. L., Kamtekar, S., Simons, C. T., McLean, J. E., Vogel, K. M., Spiro, T. G., Farid, R. S., and Hecht, M. H. (1997) De novo heme proteins from designed combinatorial libraries. Protein Sci. 6, 2512-2524.
100. Saiki, R. K., Gelfand, D. H., Stoffel, S., Scharf, S. J., Higuchi, R., Horn, G. T., Mullis, K. B., and Erlich, H. A. (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 29, 487-491.
101. Schultz, J. S. and Schultz, J. S. (1996) The combinatorial library: a multifunctional resource. Biotechnol. Progr. 12, 729-743.
102. Scott, J. K. and Smith, G. P. (1990) Searching for peptide ligands with an epitope library. Science 249, 386-390.
103. Seidel, H. M., Pompliano, D. L., and Knowles, J. R. (1992) Exons as microgenes? Science 257, 1489-1490
104. Shiba, K. (1995) Dissection of an enzyme into two fragments at intron-exon boundaries; in Tracing Biological Evolution in Protein and Gene Structures, Go, M. and Schimmel, P. (eds.), pp. 11-21, Elsevier Science Publishers, Amsterdam.
105. Shiba, K. (1997) Creation of genes (Japanese). KAGAKU 67, 938-947.
106. Shiba, K. and Schimmel, P. (1992a) Functional assembly of a randomly cleaved protein. Proc. Natl. Acad. Sci. USA 89, 1880-1884.
107. Shiba, K. and Schimmel, P. (1992b) Tripartite functional assembly of a large class I aminoacyl tRNA synthetase. J. Biol. Chem. 267, 22703-22706.
108. Shiba, K., Hatada, T., and Noda, T. (1996) Combinatorial assembly of microgenes. Protein Engng. 9, 813-814.
109. Shiba, K., Motegi, H., and Schimmel, P. (1997) Maintaining genetic code through adaptations of tRNA synthetases to taxonomic domains. Trends Biochem. Sci. 22, 453-157.
110. Shiba, K., Takahashi, T., and Noda, T. (1997) Creation of libraries with long open reading frames by polymerization of a microgene. Proc. Natl. Acad. Sci. USA 94, 3805-3810.
111. Smith, G. P. (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315-1317.
112. Solovyev, V. V. (1993) Fractal graphical representation and analysis of DNA and protein sequences. BioSystems 30, 137-160.
113. Stemmer, W. P. C. (1994a) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370, 389-391.
114. Stemmer, W. P. C. (1994b) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91, 10747-10751.
115. Stemmer, W. P. C. (1995) Searching sequence space - using recombination to search more efficiently and thoroughly instead of making bigger combinatorial libraries. Bio/ Technology 13, 549-553.
116. Sternberg, N. and Hoess, R. H. (1995) Display of peptides and proteins on the surface of bacteriophage λ. Proc. Natl. Acad. Sci. USA 92, 1609-1613.
117. Szostak, J. W. (1992) In vitro genetics. Trends Biochem. Sci. 17, 89-93.
118. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997) A genomic perspective on protein families. Science 278, 631-637.
119. Tramontano, A., Janda, K. D., and Lerner, R. D. (1986) Catalytic antibodies. Science 234, 1566-1570.
120. Tirrell, D. A., Fournier, M. J., and Mason, T. L. (1991) Protein engineering for materials applications. Curr. Opin. Struct. Biol. 1, 638-641.
121. Tsonis, A. A. and Tsonis, P. A. (1997). Simplicity and complexity in gene evolution Complexity 2(5), 23-30.
122. Tsonis, A. A., Elsner, J. B., and Tsonis, P. (1991) Periodicity in DNA coding sequences: implications in gene evolution. J. Theor. Biol. 151, 323-331.
123. Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment - RNA ligands to bacteriophage-T4 DNA polymerase. Science 249, 505-510.
124. White, S. H. and Jacobs, R. E. (1993) The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern protein sequences. J. Mol. Evol. 36, 79-95.
125. Wilson, C. and Szostak, J. W. (1995) In vitro evolution of a self-alkylating ribozyme. Nature 374, 777-782.
126. Wolfe, K. H. and Shields, D. C. (1997) Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.
127. Yamauchi, A., Yomo, T., Tanaka, F., Prijambada, I. D., Ohhashi, S., Yamamoto, K., Shima, Y., Ogasahara, K., Yutani, K., Kataoka, M., and Urabe, I. (1998) Characterization of soluble artificial proteins with random sequences. FEBS Lett. 421, 147-151.
128. Yura, K., Tomoda, S., and Go, M. (1993) Repeat of α helix-turn-helix module in DNA-binding proteins. Protein Engng. 6, 621-628.
129. Zhang, J. H., Dawes, G., and Stemmer, W. P. C. (1997) Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc. Natl. Acad. Sci. USA 94, 4504-4509.
130. Zoller, M. J. and Smith, M. (1982) Oligonucleotide-directed mutagenesis using M13-derived vectors: an efficient and general procedure for the production of point mutations in any fragment of DNA. Nucleic Acids Res. 10, 6487-6500.