Directed evolution library creation : methods and protocols / edited by Elizabeth M.J. Gillam, Janine N. Copp, David F. Ackerley.

Contributor(s): Gillam, Elizabeth M [editor] | Copp, Janine N [editor] | Ackerley, David F [editor]
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): v. 1179.Publisher: New York : Humana Press, [2014]Copyright date: ©2014Edition: Second editionDescription: 1 online resource (xi, 369 pages) : illustrations (some color)Content type: text Media type: computer Carrier type: online resourceISBN: 9781493910533; 1493910531Subject(s): Gene libraries -- Laboratory manuals | Genetic engineering -- Laboratory manuals | Molecular evolution -- Laboratory manuals | Microbial mutation -- Laboratory manuals | Combinatorial chemistry -- Laboratory manuals | Genetic recombination -- Laboratory manuals | Directed Molecular Evolution | Combinatorial Chemistry Techniques | Gene Library | Gene libraries | Genetic engineering | Molecular evolution | Microbial mutation | Combinatorial chemistry | Genetic recombination | Biology -- Laboratory manuals | evolutie | evolution | biomedische wetenschappen | biomedicine | genetische modificatie | genetic engineering | humane genetica | human genetics | Medicine (General) | Geneeskunde (algemeen)Genre/Form: Laboratory Manual. Additional physical formats: Print version:: Directed evolution library creation.DDC classification: 576.5 LOC classification: QH442.4 | .D57 2014Online resources: Click here to access online
Contents:
POINT MUTAGENESIS -- 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 -- Error-Prone Rolling Circle Amplification Greatly Simplifies Random Mutagenesis / Ryota Fujii, Motomitsu Kitaoka, and Kiyoshi Hayashi -- 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 -- The Sequence Saturation Mutagenesis (SeSaM) Method / Anna Joëlle Ruff, Tsvetan Kardashliev, Alexander Dennig, and Ulrich Schwaneberg -- Generation of Effective Libraries by Neutral Drift / Miriam Kaltenbach and Nobuhiko Tokuriki -- Site-Saturation Mutagenesis by Overlap Extension PCR / Elsie M. Williams, Janine N. Copp, and David F. Ackerley -- Iterative Saturation Mutagenesis: A Powerful Approach to Engineer Proteins by Systematically Simulating Darwinian Evolution / Carlos G. Acevedo-Rocha, Sabrina Hoebenreich, and Manfred T. Reetz -- Generating Targeted Libraries by the Combinatorial Incorporation of Synthetic Oligonucleotides During Gene Shuffling (ISOR) / Liat Rockah-Shmuel, Dan S. Tawfik, and Moshe Goldsmith -- OmniChange: Simultaneous Site Saturation of Up to Five Codons / Alexander Dennig, Jan Marienhagen, Anna Joëlle Ruff, and Ulrich Schwaneberg -- Random Insertional-Deletional Strand Exchange Mutagenesis (RAISE): A Simple Method for Generating Random Insertion and Deletion Mutations / Rota Fujii, Motomitsu Kitaoka, and Kiyoshi Hayashi -- Transposon-Based Approaches for Generating Novel Molecular Diversity During Directed Evolution / D. Dafydd Jones, James A.J. Arpino, Amy J. Baldwin, and Matthew C. Edmundson.
RECOMBINATORIAL METHODS -- Restriction Enzyme-Mediated DNA Family Shuffling / James B.Y.H. Behrendorff, Wayne A. Johnston, and Elizabeth M.J. Gillam -- Assembly of Designed Oligonucleotides: A Useful Tool in Synthetic Biology for Creating High-Quality Combinatorial DNA Libraries / Carlos G. Acevedo-Rocha and Manfred T. Reetz -- One-Pot Simple Methodology for Cassette Randomization and Recombination for Focused Directed Evolution (OSCARR) / Aurelio Hidalgo, Anna Schließmann, and Uwe T. Bornscheuer -- USER Friendly DNA Recombination (USERec): Gene Library Construction Requiring Minimal Sequence Homology / Benoit Villiers and Florian Hollfelder -- ITCHY: Incremental Truncation for the Creation of Hybrid Enzymes / Wayne M. Patrick and Monica L. Gerth -- Generating Random Circular Permutation Libraries / Stefan Lutz, Ashley B. Daugherty, Ying Yu, and Zhen Qian.
STRUCTURE-GUIDED METHODS AND COMPUTATIONAL TOOLS FOR THE DESIGN AND ANALYSIS OF MUTANT LIBRARIES -- Probabilistic Methods in Directed Evolution: Library Size, Mutation Rate, and Diversity / Yuval Nov -- The Mutagenesis Assistant Program / Rajni Verma, Tuck Seng Wong, Ulrich Schwaneberg, and Danilo Roccatano -- Computational Tools for Designing Smart Libraries / Eva Sebestova, Jaroslav Bendl, Jan Brezovsky, and Jiri Damborsky -- Computational Tools for Directed Evolution: A Comparison of Prospective and Retrospective Strategies / Julian Zaugg, Yosephine Gumulya, Elizabeth M.J. Gillam, and Mikael Bodén -- Designing Libraries of Chimeric Proteins Using SCHEMA Recombination and RASPP / Matthew A. Smith and Frances H. Arnold -- Noncontiguous SCHEMA Protein Recombination / Matthew A. Smith and Frances H. Arnold -- Engineering Proteins by Reconstructing Evolutionary Adaptive Paths / Vanessa E. Cox and Eric A. Gaucher.
Abstract: 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.Abstract: 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.Abstract: 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.Abstract: 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.Abstract: 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.Abstract: 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.
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Includes bibliographical references and index.

PART I. POINT MUTAGENESIS -- 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 -- 6. Site-Saturation Mutagenesis by Overlap Extension PCR / Elsie M. Williams, Janine N. Copp, and David F. Ackerley -- 7. Iterative Saturation Mutagenesis: A Powerful Approach to Engineer Proteins by Systematically Simulating Darwinian Evolution / Carlos G. Acevedo-Rocha, Sabrina Hoebenreich, 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 Joëlle Ruff, and Ulrich Schwaneberg -- 10. Random Insertional-Deletional Strand Exchange Mutagenesis (RAISE): A Simple Method for Generating Random Insertion and Deletion Mutations / Rota Fujii, Motomitsu Kitaoka, and Kiyoshi Hayashi -- 11. Transposon-Based Approaches for Generating Novel Molecular Diversity During Directed Evolution / D. Dafydd Jones, James A.J. Arpino, Amy J. Baldwin, and Matthew C. Edmundson.

PART II. RECOMBINATORIAL 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: 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 -- 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 and Frances H. Arnold -- 23. Noncontiguous 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.

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.

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