Designing and implementing algorithmic DNA assembly pipelines for multi-gene systems

Szu Yi Hsu; Michael J. Smanski

doi:10.1007/978-1-4939-7295-1_9

Designing and implementing algorithmic DNA assembly pipelines for multi-gene systems

Szu Yi Hsu, Michael J. Smanski

Research output: Chapter in Book/Report/Conference proceeding › Chapter

4 Scopus citations

Abstract

Advances in DNA synthesis and assembly technology allow for the high-throughput fabrication of hundreds to thousands of multi-part genetic constructs in a short time. This allows for rapid hypothesis-testing and genetic optimization in multi-gene biological systems. Here, we discuss key considerations to design and implement an algorithmic DNA assembly pipeline that provides the freedom to change nearly any design variable in a multi-gene system. In addition to considerations for pipeline design, we describe protocols for three useful molecular biology techniques in plasmid construction.

Original language	English (US)
Title of host publication	Methods in Molecular Biology
Publisher	Humana Press Inc.
Pages	131-147
Number of pages	17
DOIs	https://doi.org/10.1007/978-1-4939-7295-1_9
State	Published - 2018

Publication series

Name	Methods in Molecular Biology
Volume	1671
ISSN (Print)	1064-3745

Bibliographical note

Funding Information:
S-Y. H. is supported by Biocatalysis Grant from the University of Minnesota BioTechnology Institute.

Publisher Copyright:
© 2018, Springer Science+Business Media, LLC.

Keywords

BioDesign automation
DNA assembly
Genetic refactoring
Golden Gate assembly
Isothermal assembly
PCR-ligation

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10.1007/978-1-4939-7295-1_9

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AU - Smanski, Michael J.

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AB - Advances in DNA synthesis and assembly technology allow for the high-throughput fabrication of hundreds to thousands of multi-part genetic constructs in a short time. This allows for rapid hypothesis-testing and genetic optimization in multi-gene biological systems. Here, we discuss key considerations to design and implement an algorithmic DNA assembly pipeline that provides the freedom to change nearly any design variable in a multi-gene system. In addition to considerations for pipeline design, we describe protocols for three useful molecular biology techniques in plasmid construction.

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KW - Genetic refactoring

KW - Golden Gate assembly

KW - Isothermal assembly

KW - PCR-ligation

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BT - Methods in Molecular Biology

PB - Humana Press Inc.

ER -

Designing and implementing algorithmic DNA assembly pipelines for multi-gene systems

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