Directed Evolution Library Creation
Methods and Protocols
(Sprache: Englisch)
Directed Evolution Library Creation: Methods and Protocols, Second Edition presents user-friendly protocols for both proven strategies and cutting-edge approaches for the creation of mutant gene libraries for directed evolution. As well as experimental...
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Directed Evolution Library Creation: Methods and Protocols, Second Edition presents user-friendly protocols for both proven strategies and cutting-edge approaches for the creation of mutant gene libraries for directed evolution. As well as experimental methods, information on current computational approaches is provided in a user-friendly format that will allow researchers to make informed choices without needing to comprehend the full technical details of each algorithm. Directed evolution has become a fundamental approach for engineering proteins to enhance activity and explore structure-function relationships, and has supported the rapid development of the field of synthetic biology over the last decade. Divided into three convenient sections, topics include point mutagenesis strategies, recombinatorial methods wherein genetic diversity is sourced from multiple parental genes that are combined via either homology-dependent or -independent techniques and a variety of computational methods to guide the design and analysis of mutant libraries. Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols and notes on troubleshooting and avoiding known pitfalls.Authoritative and easily accessible, Directed Evolution Library Creation: Methods and Protocols, Second Edition will serve as a reliable manual for both novice and experienced protein engineers and synthetic biologists and will enable further technical innovation and the exploitation of directed evolution for a deeper understanding of protein design and function.
Inhaltsverzeichnis zu „Directed Evolution Library Creation “
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 Joëlle 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. OmniChange: 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
... mehr
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 Bodén
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
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 Bodén
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
... weniger
Bibliographische Angaben
- 2014, 2. Aufl., XI, 369 Seiten, 19 farbige Abbildungen, Masse: 18,3 x 26 cm, Gebunden, Englisch
- Herausgegeben: Elizabeth M.J. Gillam, Janine N. Copp, David Ackerley
- Verlag: Springer, Berlin
- ISBN-10: 1493910523
- ISBN-13: 9781493910526
- Erscheinungsdatum: 24.07.2014
Sprache:
Englisch
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