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

Szu Yi Hsu, Michael J. Smanski

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations


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 languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages17
StatePublished - 2018

Publication series

NameMethods in Molecular Biology
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.


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


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