The reading assignments listed below show what you should read before coming to class. You are expected to come to class prepared to discuss the assigned articles.

1 Introduction  
2 Library generation by point mutation

Cadwell, R. C., and G. F. Joyce. "Randomization of Genes by PCR Mutagenesis." PCR Methods Applic 2 (1992): 28-33.

Kegler-Ebo, D. M., C. M. Docktor, and D. DiMaio. "Codon Cassette Mutagenesis: A General Method to Insert or Replace Individual Codons by using Universal Mutagenic Cassettes." Nuc Acids Res 22 (1994): 1593-1599.

3 Library generation by recombination

Zhao, H., L. Giver, A. Shao, J. A. Affholter, and F. A. Arnold. "Molecular Evolution by Staggered Extension Process (StEP) in vitro Recombination." Nature Biotechnol 16 (1998): 258-261.

Stemmer, W. P. C. "Rapid Evolution of a Protein in vitro by DNA Shuffling." Nature 370 (1994): 389-391.

4 Alternative methods for library generation

Lai, Y.-P, J. Huang, L.-F. Wang, J. Li, and Z.-J. Wu. "A New Approach to Random Mutagenesis in vitro." Biotech Bioeng 86 (2004): 622-627.

Coia, G., A. Ayres, G. G. Lilley, P. J. Hudson, and R. A. Irving. "Use of Mutator Cells as a Means for Increasing Production Levels of a Recombinant Antibody Directed Against Hepatitis B." Gene 201 (1997): 203-209.

5 Enzyme evolution by genetic complementation

Yano, T., S. Oue, and H. Kagamiyama. "Directed Evolution of an Aspartate Aminotransferase with New Substrate Specificities." PNAS 95 (1998): 5511-5515.

Otten, L. G., C. F. Sio, J. Vrielink, R. H. Cool, and W. J. Quax. "Altering the Substrate Specificity of Cephalosporin Acylase by Directed Evolution of the β-Subunit." J Biol Chem 277 (2002): 42121-42127.

6 Enzyme evolution by chemical complementation

Baker, K., C. Bleczinski, H. Lin, G. Salazar-Jimenez, D. Sengupta, S. Krane, and V. W. Cornish. "Chemical Complementation: A Reaction-independent Genetic Assay for Enzyme Catalysis." PNAS 99 (2002): 16537-16542.

Azizi, B., E. I. Chang, and D. F. Doyle. "Chemical Complementation: Small-Molecule-Based Genetic Selection in Yeast." Biochem Biophys Res Commun 306 (2003): 774-780.

Lin, H., H. Tao, and V. W. Cornish. "Directed Evolution of a Glycosynthase via Chemical Complementation." J Am Chem Soc 126 (2004): 15051-15059.

7 Enzyme evolution using phage display

Smith, G. P. "Filamentous Fusion Phage: Novel Expression Vectors that Display Cloned Antigens on the Virion Surface." Science 228 (1985): 1315-1317.

Ponsard, I., M. Galleni, P. Soumillion, and J. Fastrez. "Selection of Metalloenzymes by Catalytic Activity using Phage Display and Catalytic Elution." Chembiochem 2 (2001): 253-259.

8 Enzyme evolution using phage display (cont.)

Strobel, H., D. Ladant, and J. L. Jestin. "In vitro Selection for Enzymatic Activity: A Model Study using Adenylate Cyclase." J Mol Biol 332 (2003): 1-7.

Pedersen, H., S. Holder, D. P. Sutherlin, U. Schwitter, D. S. King, and P. G. Schultz. "A Method for the Directed Evolution and Functional Cloning of Enzymes." Proc Natl Acad Sci USA 95 (1998): 10523-10528.

9 Enzyme evolution using bacterial cell surface display

Olsen, M. J., D. Stephens, D. Griffiths, P. Daughtery, G. Georgiou, and B. L. Iverson. "Function-Based Isolation of Novel Enzymes from a Large Library." Nat Biotechnol 18 (2000): 1071-1074.

Kim, Y.-S., H.-C. Jung, and J.-G. Pan. "Bacterial Cell Surface Display of an Enzyme Library for Selective Screening of Improved Cellulose Variants." App Environ Microbiol 66 (2000): 788-793.

10 Enzyme evolution using yeast surface display

Boder, E. T., and K. D. Wittrup. "Yeast Surface Display for Screening Combinatorial Polypeptide Libraries." Nat Biotechnol 15 (1997): 553-557.

Shiraga, S., M. Kawakami, M. Ishiguro, and M. Ueda. "Enhanced Reactivity of Rhizopus Oryzae Lipase Displayed on Yeast Cell Surfaces in Organic Solvents: Potential as a Whole-cell Biocatalyst in Organic Solvents." App Environ Microbiol 71 (2005): 4335-4338.

11 Enzyme evolution using ribosome display

Amstutz, P., J. N. Pelletier, A. Guggisberg, L. Jermutus, S. Cesaro-Tadic, C. Zahnd, and A. Pluckthun. "In vitro Selection for Catalytic Activity with Ribosome Display." JACS 124 (2002): 9396-9403.

Takahashi, F., H. Funabashi, M. Mie, Y. Endo, T. Sawasaki, M. Aizawa, and E. Kobatake. "Activity-based in vitro Selection of T4 DNA Ligase." Biochem Biophys Res Commun 336 (2005): 987-993.

12 Enzyme evolution by in vitro compartmentalization

Tawfik, D. S., and A. D. Griffiths. "Man-Made Cell-like Compartments for Molecular Evolution." Nat Biotechnol 16 (1998): 652-656.

———. "Directed Evolution of an Extremely Fast Phosphotriesterase by in vitro Compartmentalization." EMBO J 22 (2003): 24-35.

13 Alternative methods for enzyme/catalyst design

Hill, C. M., W.-S. Li, J. B. Thoden, H. M. Holden, and F. M. Raushel. "Enhanced Degradation of Chemical Warfare Agents through Molecular Engineering of the Phosphotriesterase Active Site." JACS 125 (2003): 8990-8991.

Williams, G. J., T. Woodhall, A. Nelson, and A. Berry. "Structure-guided Saturation of N-Acetylneuraminic Acid Lyase for the Synthesis of Sialic Acid Mimetics." Prot Eng Des Select 18 (2005): 239-246.

Reetz, M. T., M. Bocola, J. D. Carballeira, D. Zha, and A. Vogel. "Expanding the Range of Substrate Acceptance of Enzymes: Combinatorial Active-Site Saturation Test." Angew Chem Int Ed 44 (2005): 4192-4196.

14 Student presentations