Chapter 19
Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): A Versatile Tool for Generating Targeted Libraries
Asael Herman,
Dan S. Tawfik,
Asael Herman
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Department of Pathology, University of Washington School of Medicine, HSB K-058, BOX 357 705, Seattle, WA 98195-7705, USA
Search for more papers by this authorDan S. Tawfik
Department of Biological Chemistry, Weizmann Institute of Science, Ullmann Bldg, Room 201a, PO BOX 26, Rehovot 76100, Israel
Search for more papers by this authorAsael Herman,
Dan S. Tawfik,
Asael Herman
Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
Department of Pathology, University of Washington School of Medicine, HSB K-058, BOX 357 705, Seattle, WA 98195-7705, USA
Search for more papers by this authorDan S. Tawfik
Department of Biological Chemistry, Weizmann Institute of Science, Ullmann Bldg, Room 201a, PO BOX 26, Rehovot 76100, Israel
Search for more papers by this authorBook Editor(s):Prof. Dr. Stefan Lutz,
Prof. Dr. Uwe T. Bornscheuer,
Prof. Dr. Stefan Lutz
Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA
Search for more papers by this authorProf. Dr. Uwe T. Bornscheuer
Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
Search for more papers by this authorFirst published: 12 November 2008
Summary
This chapter contains sections titled:
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Introduction
-
Materials
-
Methods
-
Notes
-
Acknowledgments
-
References
References
- Stemmer, W.P. (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proceedings of the National Academy of Sciences of the United States of America, 91 (22), 10747–51.
- Stutzman-Engwall, K., Conlon, S., Fedechko, R., McArthur, H., Pekrun, K., Chen, Y., Jenne, S., La, C., Trinh, N., Kim, S., Zhang, Y.X., Fox, R., Gustafsson, C. and Krebber, A. (2005) Semi-synthetic DNA shuffling of aveC leads to improved industrial scale production of doramectin by Streptomyces avermitilis. Metabolic Engineering, 7 (1), 27–37.
- van den Beucken, T., van Neer, N., Sablon, E., Desmet, J., Celis, L., Hoogenboom, H.R. and Hufton, S.E. (2001) Building novel binding ligands to B7.1 and B7.2 based on human antibody single variable light chain domains. Journal of Molecular Biology, 310 (3), 591–601.
- Herman, A. and Tawfik, D.S. (2007) incorporating synthetic oligonucleotides via gene reassembly (ISOR): a versatile tool for generating targeted libraries. Protein Engineering, Design and Selection, 20 (5), 219–26.
- Chica, R.A., Doucet, N. and Pelletier, J.N. (2005) Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. Current Opinion in Biotechnology, 16 (4), 378–84.
- Minshull, J., Govindarajan, S., Cox, T., Ness, J.E. and Gustafsson, C. (2004) Engineered protein function by selective amino acid diversification. Methods, 32 (4), 416–27.
- Patrick, W.M. and Firth, A.E. (2005) Strategies and computational tools for improving randomized protein libraries. Biomolecular Engineering, 22 (4), 105–12.
- Santoro, S.W. and Schultz, P.G. (2002) Directed evolution of the site specificity of Cre recombinase. Proceedings of the National Academy of Sciences of the United States of America, 99 (7), 4185–90.
- Rui, L., Cao, L., Chen, W., Reardon, K.F. and Wood, T.K. (2004) Active site engineering of the epoxide hydrolase from Agrobacterium radiobacter AD1 to enhance aerobic mineralization of cis-1,2-dichloroethylene in cells expressing an evolved toluene ortho-monooxygenase. Journal of Biological Chemistry, 279 (45), 46810–17.
- Park, S., Morley, K.L., Horsman, G.P., Holmquist, M., Hult, K. and Kazlauskas, R.J. (2005) Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations. Chemistry and Biology, 12 (1), 45–54.
- Reetz, M.T., Bocola, M., Carballeira, J.D., Zha, D. and Vogel, A. (2005) Expanding the range of substrate acceptance of enzymes: combinatorial active-site saturation test. Angewandte Chemie – International Edition in English, 44 (27), 4192–6.
- Mena, M.A., Treynor, T.P., Mayo, S.L. and Daugherty, P.S. (2006) Blue fluorescent proteins with enhanced brightness and photostability from a structurally targeted library. Nature Biotechnology, 24 (12), 1569–71.
- Hayes, R.J., Bentzien, J., Ary, M.L., Hwang, M.Y., Jacinto, J.M., Vielmetter, J., Kundu, A. and Dahiyat, B.I. (2002) Combining computational and experimental screening for rapid optimization of protein properties. Proceedings of the National Academy of Sciences of the United States of America, 99 (25), 15926–31.
- Dwyer, M.A., Looger, L.L. and Hellinga, H.W. (2004) Computational design of a biologically active enzyme. Science, 304 (5679), 1967–71.
- Voigt, C.A., Martinez, C., Wang, Z.G., Mayo, S.L. and Arnold, F.H. (2002) Protein building blocks preserved by recombination. Nature Structural and Molecular Biology, 9 (7), 553–8.
- Fox, R.J., Davis, S.C., Mundorff, E.C., Newman, L.M., Gavrilovic, V., Ma, S.K., Chung, L.M., Ching, C., Tam, S., Muley, S., Grate, J., Gruber, J., Whitman, J.C., Sheldon, R.A. and Huisman, G.W. (2007) Improving catalytic function by ProSAR-driven enzyme evolution. Nature Biotechnology, 25 (3), 338–44.
- Antikainen, N.M., Hergenrother, P.J., Harris, M.M., Corbett, W. and Martin, S.F. (2003) Altering substrate specificity of phosphatidylcholine-preferring phospholipase C of Bacillus cereus by random mutagenesis of the headgroup binding site. Biochemistry, 42 (6), 1603–10.
- Reetz, M.T. (2004) Controlling the enantioselectivity of enzymes by directed evolution: practical and theoretical ramifications. Proceedings of the National Academy of Sciences of the United States of America, 101 (16), 5716–22.
-
Reetz, M.T.,
Wilensek, S.,
Zha, D. and
Jaeger, K.E.
(2001)
Directed evolution of an enantioselective enzyme through combinatorial multiple-cassette mutagenesis.
Angewandte Chemie – International Edition in English,
40
(19),
3589–91.
10.1002/1521-3773(20011001)40:19<3589::AID-ANIE3589>3.0.CO;2-X CAS PubMed Web of Science® Google Scholar
- Balint, R.F. and Larrick, J.W. (1993) Antibody engineering by parsimonious mutagenesis. Gene, 137 (1), 109–18.
- Zha, D., Eipper, A. and Reetz, M.T. (2003) Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution. Chembiochem, 4 (1), 34–9.
- Ness, J.E., Kim, S., Gottman, A., Pak, R., Krebber, A., Borchert, T.V., Govindarajan, S., Mundorff, E.C. and Minshull, J. (2002) Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nature Biotechnology, 20 (12), 1251–5.
- Miller, O.J., Bernath, K., Agresti, J.J., Amitai, G., Kelly, B.T., Mastrobattista, E., Taly, V., Magdassi, S., Tawfik, D.S. and Griffiths, A.D. (2006) Directed evolution by in vitro compartmentalization. Nature Methods, 3 (7), 561–70.
- Aharoni, A., Amitai, G., Bernath, K., Magdassi, S. and Tawfik, D.S. (2005) High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. Chemistry and Biology, 12 (12), 1281–9.
- Zhao, H. and Arnold, F.H. (1997) Optimization of DNA shuffling for high fidelity recombination. Nucleic Acids Research, 25 (6), 1307–8.
