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Synthetic DNA

Methods and Protocols

  • Book
  • © 2017

Overview

Editors:
  1. Randall A. Hughes

    1. Applied Research Laboratories, The University of Texas at Austin, AUSTIN, USA

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  • 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 1472)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xiii
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  2. Computational Tools for Design and Assembly of Synthetic DNA

    1. Front Matter

      Pages 1-1
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    2. A Guide to Using STITCHER for Overlapping Assembly PCR Applications

      • Damien M. O’Halloran
      Pages 3-11

    3. Synthetic Gene Design Using Codon Optimization On-Line (COOL)

      • Kai Yu, Kok Siong Ang, Dong-Yup Lee
      Pages 13-34

    4. Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering

      • John N. Milligan, Daniel J. Garry
      Pages 35-45

  3. DNA Synthesis, Assembly, and Cloning

    1. Front Matter

      Pages 47-47
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    2. Simple Cloning by Prolonged Overlap Extension-PCR with Application to the Preparation of Large-Size Random Gene Mutagenesis Library in Escherichia coli

      • Chao Zhong, Chun You, Ping Wei, Yi-Heng Percival Zhang
      Pages 49-61

    3. SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Synthetic Protein Libraries for Directed Evolution

      • Andrew Currin, Neil Swainston, Philip J. Day, Douglas B. Kell
      Pages 63-78

    4. BASIC: A Simple and Accurate Modular DNA Assembly Method

      • Marko Storch, Arturo Casini, Ben Mackrow, Tom Ellis, Geoff S. Baldwin
      Pages 79-91

    5. Enzymatic Synthesis of Single-Stranded Clonal Pure Oligonucleotides

      • Cosimo Ducani, Björn Högberg
      Pages 93-103

    6. Rapid Assembly of DNA via Ligase Cycling Reaction (LCR)

      • Sunil Chandran
      Pages 105-110

    7. PaperClip: A Simple Method for Flexible Multi-Part DNA Assembly

      • Maryia Trubitsyna, Chao-Kuo Liu, Alejandro Salinas, Alistair Elfick, Christopher E. French
      Pages 111-128

    8. The Polymerase Step Reaction (PSR) Method for Gene and Library Synthesis

      • Brian S. DeDecker
      Pages 129-138

    9. Clonetegration Using OSIP Plasmids: One-Step DNA Assembly and Site-Specific Genomic Integration in Bacteria

      • Lun Cui, Keith E. Shearwin
      Pages 139-155

    10. Generation of DNA Constructs Using the Golden GATEway Cloning Method

      • Stephan Kirchmaier, Katharina Lust, Jochen Wittbrodt
      Pages 157-168

    11. Gene Deletion by Synthesis in Yeast

      • Jinsil Kim, Dong-Uk Kim, Kwang-Lae Hoe
      Pages 169-185

    12. Efficient Assembly of DNA Using Yeast Homologous Recombination (YHR)

      • Sunil Chandran, Elaine Shapland
      Pages 187-192

    13. Simultaneous Removal of Multiple DNA Segments by Polymerase Chain Reactions

      • Vishnu Krishnamurthy, Kai Zhang
      Pages 193-203

    14. Rapid Construction of Recombinant Plasmids by QuickStep-Cloning

      • Pawel Jajesniak, Tuck Seng Wong
      Pages 205-214

  4. Reducing Error in Synthetic DNA

    1. Front Matter

      Pages 215-215
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Keywords

About this book

This volume presents state-of-the art methods for the synthesis, design, assembly, post synthesis processing, and application of synthetic DNA to modern biotechnology.  Chapters are divided into three general sections focusing on protocols for the computational design of synthetic DNA sequences, the synthesis, assembly and cloning of synthetic DNA, and post-synthesis error reduction strategies.  Written in the highly 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 laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 

Authoritative and cutting-edge, Synthetic DNA: Methods and Protocols aims to help researchers further their research on manipulate DNA sequences.

Editors and Affiliations

  • Applied Research Laboratories, The University of Texas at Austin, AUSTIN, USA

    Randall A. Hughes

Bibliographic Information

  • Book Title: Synthetic DNA

  • Book Subtitle: Methods and Protocols

  • Editors: Randall A. Hughes

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-6343-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2017

  • Hardcover ISBN: 978-1-4939-6341-6Published: 27 September 2016

  • Softcover ISBN: 978-1-4939-8170-0Published: 27 June 2018

  • eBook ISBN: 978-1-4939-6343-0Published: 26 September 2016

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 248

  • Number of Illustrations: 14 b/w illustrations, 60 illustrations in colour

  • Topics: Human Genetics

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