Part I. Point Mutagenesis (i) Random Mutagenesis Methods 1. Error-Prone PCR and Effective Generation of Gene Variant Libraries for Directed Evolution Janine N. Copp, Paulina Hanson-Manful, David F. Ackerley, and Wayne M. Patrick 2. Error-Prone Rolling Circle Amplification Greatly Simplifies Random Mutagenesis Ryota Fujii, Motomitsu Kitaoka, and Kiyoshi Hayashi 3. Random Mutagenesis by Error-Prone Pol Plasmid Replication in Escherichia coli David L. Alexander, Joshua Lilly, Jaime Hernandez, Jillian Romsdahl, Christopher J. Troll, and Manel Camps 4. The Sequence Saturation Mutagenesis (SeSaM) Method Anna Joelle Ruff, Tsvetan Kardashliev, Alexander Dennig, and Ulrich Schwaneberg 5. Generation of Effective Libraries by Neutral Drift Miriam Kaltenbach and Nobuhiko Tokuriki (ii) Saturation Mutagenesis Methods 6. Site Saturation Mutagenesis Elsie M. Williams, Janine N. Copp, and David F. Ackerley 7. Iterative Saturation Mutagenesis (ISM): A Powerful Approach to Engineer Proteins by Systematically Simulating Darwinian Evolution Carlos G. Acevedo-Rocha, Sabrina Killeand, and Manfred T. Reetz 8. Generating Targeted Libraries by the Combinatorial Incorporation of Synthetic Oligonucleotides During Gene Shuffling (ISOR) Liat Rockah-Shmuel, Dan S Tawfik, and Moshe Goldsmith 9. Omni Change: Simultaneous Site-Saturation of up to Five Codons Alexander Dennig, Jan Marienhagen, Anna Joelle Ruff, and Ulrich Schwaneberg (iii) Insertional/Deletional Methods 10. Random Insertional-Deletional Strand Exchange Mutagenesis (RAISE): A Simple Method for Generating Random Insertion and Deletion Mutations Ryota Fujii, Motomitsu Kitaoka, and Kiyoshi Hayashi 11. Transposon-Based Approaches for Generating Novel Molecular Diversity during Directed Evolution Dafydd Jones, James A.J. Arpino, Amy J. Baldwin, and Matthew C. Edmundson Part II. Recombinatorial Methods (i)Homology-Dependent Methods 12. Restriction Enzyme-Mediated DNA Family Shuffling James B.Y.H. Behrendorff, Wayne A. Johnston, and Elizabeth M. J. Gillam 13. Assembly of Designed Oligonucleotides (ADO): A Useful Tool in Synthetic Biology for Creating High Quality Combinatorial DNA Libraries Carlos G. Acevedo-Rocha and Manfred T. Reetz 14. One-Pot, Simple Methodology for Cassette Randomization and Recombination for Focused Directed Evolution (OSCARR) Aurelio Hidalgo Anna Schliessmann, and Uwe T. Bornscheuer 15. USER Friendly DNA Recombination (USERec): Gene Library Construction Requiring Minimal Sequence Homology Benoit Villiers and Florian Hollfelder (ii) Homology-Independent Methods 16. ITCHY: Incremental Truncation for the Creation of Hybrid Enzymes Wayne M. Patrick and Monica L. Gerth 17. Generating Random Circular Permutation Libraries Stefan Lutz, Ashley B. Daugherty, Ying Yu, and Zhen Qian Part III. Structure Guided Methods and Computational Tools for the Design and Analysis of Mutant Libraries 18. Probabilistic Methods in Directed Evolution: Library Size, Mutation Rate, and Diversity Yuval Nov 19. The Mutagenesis Assistant Program Rajni Verma, Tuck Seng Wong, Ulrich Schwaneberg, and Danilo Roccatano 20. Computational Tools for Designing Smart Libraries Eva Sebestova, Jaroslav Bendl, Jan Brezovsky, and Jiri Damborsky 21. Computational Tools for Directed Evolution: A Comparison of Prospective and Retrospective Strategies Julian Zaugg, Yosephine Gumulya, Elizabeth M.J. Gillam, and Mikael Boden 22. Designing Libraries of Chimeric Proteins Using SCHEMA Recombination and RASPP Matthew A. Smith & Frances H. Arnold 23. Non-Contiguous SCHEMA Protein Recombination Matthew A. Smith and Frances H. Arnold 24. Engineering Proteins by Reconstructing Evolutionary Adaptive Paths Vanessa E. Cox and Eric A. Gaucher
