Synthetic DNA: Methods and Protocols

ISBN-13: 9781493963416 / Angielski / Twarda / 2016 / 248 str.

Randall Hughes

Opis

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.

Spis treści

Part I: Computational Tools for Design and Assembly of Synthetic DNA

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

Damien M. O’Halloran

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

Kai Yu, Kok Siong Ang, and Dong-Yup Lee

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

John N. Milligan and Daniel J. Garry

Part II:  DNA Synthesis, Assembly, and Cloning

4.  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, and Yi-Heng Percival Zhang

5.  SpeedyGenes: Exploiting an Improved Gene Synthesis Method for the Efficient Production of Error-corrected, Synthetic Protein Libraries for Directed Evolution

Andrew Currin, Neil Swainston, Philip J. Day, and Douglas Kell

6. BASIC – A Simple and Accurate Modular DNA Assembly Method

Marko Storch, Arturo Casini, Ben Mackrow, Tom Ellis, and Geoff Baldwin

7.  Enzymatic Synthesis of Single Stranded Clonal Pure Oligonucleotides

Cosimo Ducani and Bjorn Hogberg

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

Sunil Chandran

9. PaperClip: A Simple Method for Flexible Multi-part DNA Assembly

Maryia Trubitsyna, Chao-Kuo Liu, Alejandro Salinas, Alistair Elfick, and Christopher French

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

Brian DeDecker

11.  Clonetegration Using OSIP Plasmids – One Step DNA Assembly and Site Specific Genomic Integration in Bacteria

Lun Cui and Keith Sherwin

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

Stephan Kirchmaier, Katharin Lust, and Jochen Wittbrodt

13. Gene Deletion by Synthesis in Yeast

Jinsil Kim, Dong-uk Kim, and Kawang-Lae Hoe

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

Sunil Chandran and Elaine Shapland

 

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

Vishnu Krishnamurthy and Kai Zhang

16. Rapid Construction of Recombinant Plasmids by QuickStep-Cloning

Pawel Jajesniak and Tuck Seng Wong

Part III: Reducing Error in Synthetic DNA

17.  Immobilized MutS-mediated Error Removal of Microchip-synthesized DNA

Wen Wan, Dongmei Wang, Xiaolian Gao, and Jiong Hong

18.  Selection of Error-less Synthetic Genes in Yeast

Hisashi Hoshida, Tohru Yarimizu, and Rinji Akada