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Synthetic DNA

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Cover of 'Synthetic DNA'

Table of Contents

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    Book Overview
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    Chapter 1 A Guide to Using STITCHER for Overlapping Assembly PCR Applications.
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    Chapter 2 Synthetic Gene Design Using Codon Optimization On-Line (COOL).
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    Chapter 3 Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering.
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    Chapter 4 Simple Cloning by Prolonged Overlap Extension-PCR with Application to the Preparation of Large-Size Random Gene Mutagenesis Library in Escherichia coli.
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    Chapter 5 Synthetic DNA
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    Chapter 6 BASIC: A Simple and Accurate Modular DNA Assembly Method.
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    Chapter 7 Enzymatic Synthesis of Single-Stranded Clonal Pure Oligonucleotides.
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    Chapter 8 Rapid Assembly of DNA via Ligase Cycling Reaction (LCR).
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    Chapter 9 PaperClip: A Simple Method for Flexible Multi-Part DNA Assembly.
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    Chapter 10 The Polymerase Step Reaction (PSR) Method for Gene and Library Synthesis.
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    Chapter 11 Clonetegration Using OSIP Plasmids: One-Step DNA Assembly and Site-Specific Genomic Integration in Bacteria.
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    Chapter 12 Generation of DNA Constructs Using the Golden GATEway Cloning Method.
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    Chapter 13 Synthetic DNA
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    Chapter 14 Efficient Assembly of DNA Using Yeast Homologous Recombination (YHR).
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    Chapter 15 Simultaneous Removal of Multiple DNA Segments by Polymerase Chain Reactions.
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    Chapter 16 Synthetic DNA
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    Chapter 17 Immobilized MutS-Mediated Error Removal of Microchip-Synthesized DNA.
  19. Altmetric Badge
    Chapter 18 Selection of Error-Less Synthetic Genes in Yeast.
Attention for Chapter 3: Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering.
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Chapter title
Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering.
Chapter number 3
Book title
Synthetic DNA
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-6343-0_3
Pubmed ID
Book ISBNs
978-1-4939-6341-6, 978-1-4939-6343-0
Authors

John N. Milligan, Daniel J. Garry

Editors

Randall A. Hughes

Abstract

DNA shuffling is a powerful tool to develop libraries of variants for protein engineering. Here, we present a protocol to use our freely available and easy-to-use computer program, Shuffle Optimizer. Shuffle Optimizer is written in the Python computer language and increases the nucleotide homology between two pieces of DNA desired to be shuffled together without changing the amino acid sequence. In addition we also include sections on optimal primer design for DNA shuffling and library construction, a small-volume ultrasonicator method to create sheared DNA, and finally a method to reassemble the sheared fragments and recover and clone the library. The Shuffle Optimizer program and these protocols will be useful to anyone desiring to perform any of the nucleotide homology-dependent shuffling methods.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 19 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 5%
China 1 5%
Unknown 17 89%

Demographic breakdown

Readers by professional status Count As %
Researcher 4 21%
Student > Ph. D. Student 4 21%
Student > Bachelor 2 11%
Other 1 5%
Librarian 1 5%
Other 3 16%
Unknown 4 21%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 7 37%
Agricultural and Biological Sciences 4 21%
Computer Science 2 11%
Arts and Humanities 1 5%
Chemical Engineering 1 5%
Other 0 0%
Unknown 4 21%