Protein Engineering Protocols - Mycobacteriology research center

Protein Library Design and Screening 153Montréal, Canada), Sabine C. Stebel (Universität Freiburg, Germany), and theeditors Katja M. Arndt and Kristian M. Müller (Universität Freiburg, Germany)for their valuable comments.This work was supported by National Sciences and Engineering ResearchCouncil grants 227853-02 (J. N. Pelletier) and 227838-00 (M. Denault).References1. Arnold, F. H. and Georgiou, G. (2003) Directed Evolution Library Creation Methodsand Protocols. Methods in Molecular Biology 231, Humana Press, Totowa, NJ.2. Arnold, F. H. and Georgiou, G. (2003) Directed Enzyme Evolution Screeningand Selection Methods. Methods in Molecular Biology 230, Humana Press,Totowa, NJ.3. Moore, J. C., Jin, H. M., Kuchner, O., and Arnold, F. H. (1997) Strategies for thein vitro evolution of protein function—enzyme evolution by random recombinationof improved sequences. J. Mol. Biol. 272, 336–347.4. Moore, G. L. and Maranas, C. D. (2000) Modeling DNA mutation and recombinationfor directed evolution experiments. J. Theor. Biol. 205, 483–503.5. Moore, G. L., Maranas, C. D., Lutz, S., and Benkovic, S. J. (2001) Predictingcrossover generation in DNA shuffling. Proc. Natl. Acad. Sci. USA 98, 3226–3231.6. Moore, G. L. and Maranas, C. D. (2002) Predicting out-of-sequence reassembly inDNA shuffling. J. Theor. Biol. 219, 9–17.7. Sun, F. (1999) Modeling DNA shuffling. J. Comput. Biol. 6, 77–90.8. Patrick, W. M., Firth, A. E., and Blackburn, J. M. (2003) User-friendly algorithmsfor estimating completeness and diversity in randomized protein-encodinglibraries. Protein Eng. 16, 451–457.9. Bittker, J. A., Le, B. V., Liu, J. M., and Liu, D. R. (2004) Directed evolution of proteinenzymes using nonhomologous random recombination. Proc. Natl. Acad. Sci.USA 101, 7011–7016.10. Gribskov, M., Devereux, J., and Burgess, R. R. (1984) The codon preference plot:graphic analysis of protein coding sequences and prediction of gene expression.Nucleic Acids Res. 12, 539–549.11. Virnekas, B., Ge, L., Plückthun, A., Schneider, K. C., Wellnhofer, G., andMoroney, S. E. (1994) Trinucleotide phosphoramidites: ideal reagents for thesynthesis of mixed oligonucleotides for random mutagenesis. Nucleic AcidsRes. 22, 5600–5607.12. Pelletier, J. N., Arndt, K. M., Plückthun, A., and Michnick, S. W. (1999) An in vivolibrary-versus-library selection of optimized protein-protein interactions. NatureBiotechnol. 17, 683–690.13. Braunagel, M. and Little, M. (1997) Construction of a semisynthetic antibodylibrary using trinucleotide oligos. Nucleic Acids Res. 25, 4690, 4691.14. Gaytan, P., Yanez, J., Sanchez, F., and Soberon, X. (2001) Orthogonal combinatorialmutagenesis: a codon-level combinatorial mutagenesis method useful for lowmultiplicity and amino acid-scanning protocols. Nucleic Acids Res. 29, E9.