A linear programming-based strategy to save pipette tips in automated DNA assembly
File(s)
Published version
Author(s)
Sechkar, Kirill
Tuza, Zoltan A
Stan, Guy-Bart
Type
Journal Article
Abstract
Laboratory automation and mathematical optimization are key to improving the efficiency of synthetic biology research.
While there are algorithms optimizing the construct designs and synthesis strategies for DNA assembly, the optimization
of how DNA assembly reaction mixes are prepared remains largely unexplored. Here, we focus on reducing the pipette
tip consumption of a liquid-handling robot as it delivers DNA parts across a multi-well plate where several constructs
are being assembled in parallel. We propose a linear programming formulation of this problem based on the capacitated
vehicle routing problem, as well as an algorithm which applies a linear programming solver to our formulation, hence
providing a strategy to prepare a given set of DNA assembly mixes using fewer pipette tips. The algorithm performed
well in randomly generated and real-life scenarios concerning several modular DNA assembly standards, proving capable
of reducing the pipette tip consumption by up to 59% in large-scale cases. Combining automatic process optimization
and robotic liquid-handling, our strategy promises to greatly improve the efficiency of DNA assembly, either used alone
or combined with other algorithmic DNA assembly optimization methods.
While there are algorithms optimizing the construct designs and synthesis strategies for DNA assembly, the optimization
of how DNA assembly reaction mixes are prepared remains largely unexplored. Here, we focus on reducing the pipette
tip consumption of a liquid-handling robot as it delivers DNA parts across a multi-well plate where several constructs
are being assembled in parallel. We propose a linear programming formulation of this problem based on the capacitated
vehicle routing problem, as well as an algorithm which applies a linear programming solver to our formulation, hence
providing a strategy to prepare a given set of DNA assembly mixes using fewer pipette tips. The algorithm performed
well in randomly generated and real-life scenarios concerning several modular DNA assembly standards, proving capable
of reducing the pipette tip consumption by up to 59% in large-scale cases. Combining automatic process optimization
and robotic liquid-handling, our strategy promises to greatly improve the efficiency of DNA assembly, either used alone
or combined with other algorithmic DNA assembly optimization methods.
Date Issued
2022-04-11
Date Acceptance
2022-03-18
Citation
Synthetic Biology, 2022, 7 (1), pp.1-8
ISSN
2397-7000
Publisher
Oxford University Press
Start Page
1
End Page
8
Journal / Book Title
Synthetic Biology
Volume
7
Issue
1
Copyright Statement
© The Author(s) 2022. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
https://academic.oup.com/synbio/article/7/1/ysac004/6552983
Publication Status
Published
Date Publish Online
2022-04-11