Open AccessA linear programming-based strategy to save pipette tips in automated DNA assembly
Author(s) -
Kirill Sechkar,
Zoltán A. Tuza,
Guy-Bart Stan
Publication year - 2022
Publication title -
synthetic biology
Language(s) - English
Resource type - Journals
ISSN - 2397-7000
DOI - 10.1093/synbio/ysac004
Subject(s) - pipette , computer science , modular design , linear programming , automation , solver , synthetic biology , robot , algorithm , mathematical optimization , artificial intelligence , engineering , mathematics , bioinformatics , programming language , chemistry , mechanical engineering , biology
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 to be 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. Graphical Abstract