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Directed Evolution Library Creation

Methods and Protocols

  • Book
  • © 2014

Overview

Editors:
  1. Elizabeth M.J. Gillam

    1. Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Australia

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    You can also search for this editor in PubMed   Google Scholar

  2. Janine N. Copp

    1. Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

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    You can also search for this editor in PubMed   Google Scholar

  3. David Ackerley

    1. School of Biological Sciences, Victoria University, Wellington, New Zealand

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1179)

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Table of contents (24 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Point Mutagenesis

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Error-Prone PCR and Effective Generation of Gene Variant Libraries for Directed Evolution

      • Janine N. Copp, Paulina Hanson-Manful, David F. Ackerley, Wayne M. Patrick
      Pages 3-22

    3. Error-Prone Rolling Circle Amplification Greatly Simplifies Random Mutagenesis

      • Ryota Fujii, Motomitsu Kitaoka, Kiyoshi Hayashi
      Pages 23-29

    4. Random Mutagenesis by Error-Prone Pol Plasmid Replication in Escherichia coli

      • David L. Alexander, Joshua Lilly, Jaime Hernandez, Jillian Romsdahl, Christopher J. Troll, Manel Camps
      Pages 31-44

    5. The Sequence Saturation Mutagenesis (SeSaM) Method

      • Anna Joëlle Ruff, Tsvetan Kardashliev, Alexander Dennig, Ulrich Schwaneberg
      Pages 45-68

    6. Generation of Effective Libraries by Neutral Drift

      • Miriam Kaltenbach, Nobuhiko Tokuriki
      Pages 69-81

    7. Site-Saturation Mutagenesis by Overlap Extension PCR

      • Elsie M. Williams, Janine N. Copp, David F. Ackerley
      Pages 83-101

    8. Iterative Saturation Mutagenesis: A Powerful Approach to Engineer Proteins by Systematically Simulating Darwinian Evolution

      • Carlos G. Acevedo-Rocha, Sabrina Hoebenreich, Manfred T. Reetz
      Pages 103-128

    9. Generating Targeted Libraries by the Combinatorial Incorporation of Synthetic Oligonucleotides During Gene Shuffling (ISOR)

      • Liat Rockah-Shmuel, Dan S. Tawfik, Moshe Goldsmith
      Pages 129-137

    10. OmniChange: Simultaneous Site Saturation of Up to Five Codons

      • Alexander Dennig, Jan Marienhagen, Anna Joëlle Ruff, Ulrich Schwaneberg
      Pages 139-149

    11. Random Insertional–Deletional Strand Exchange Mutagenesis (RAISE): A Simple Method for Generating Random Insertion and Deletion Mutations

      • Ryota Fujii, Motomitsu Kitaoka, Kiyoshi Hayashi
      Pages 151-158

    12. Transposon-Based Approaches for Generating Novel Molecular Diversity During Directed Evolution

      • D. Dafydd Jones, James A. J. Arpino, Amy J. Baldwin, Matthew C. Edmundson
      Pages 159-172

  3. Recombinatorial Methods

    1. Front Matter

      Pages 173-173
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    2. Restriction Enzyme-Mediated DNA Family Shuffling

      • James B. Y. H. Behrendorff, Wayne A. Johnston, Elizabeth M. J. Gillam
      Pages 175-187

    3. Assembly of Designed Oligonucleotides: A Useful Tool in Synthetic Biology for Creating High-Quality Combinatorial DNA Libraries

      • Carlos G. Acevedo-Rocha, Manfred T. Reetz
      Pages 189-206

    4. One-Pot Simple Methodology for Cassette Randomization and Recombination for Focused Directed Evolution (OSCARR)

      • Aurelio Hidalgo, Anna Schließmann, Uwe T. Bornscheuer
      Pages 207-212

    5. USER Friendly DNA Recombination (USERec): Gene Library Construction Requiring Minimal Sequence Homology

      • Benoit Villiers, Florian Hollfelder
      Pages 213-224

    6. ITCHY: Incremental Truncation for the Creation of Hybrid Enzymes

      • Wayne M. Patrick, Monica L. Gerth
      Pages 225-244

    7. Generating Random Circular Permutation Libraries

      • Stefan Lutz, Ashley B. Daugherty, Ying Yu, Zhen Qian
      Pages 245-258
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Keywords

About this book

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.

Editors and Affiliations

  • Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane, Australia

    Elizabeth M.J. Gillam

  • Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

    Janine N. Copp

  • School of Biological Sciences, Victoria University, Wellington, New Zealand

    David Ackerley

Bibliographic Information

  • Book Title: Directed Evolution Library Creation

  • Book Subtitle: Methods and Protocols

  • Editors: Elizabeth M.J. Gillam, Janine N. Copp, David Ackerley

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-1053-3

  • Publisher: Springer New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2014

  • Hardcover ISBN: 978-1-4939-1052-6Published: 24 July 2014

  • Softcover ISBN: 978-1-4939-5329-5Published: 17 September 2016

  • eBook ISBN: 978-1-4939-1053-3Published: 23 July 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XI, 369

  • Number of Illustrations: 44 b/w illustrations, 19 illustrations in colour

  • Topics: Human Genetics, Evolutionary Biology, Genetic Engineering

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