A linear programming-based strategy to save pipette tips in automated DNA assembly.

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.

SUBMITTER: Sechkar K 

PROVIDER: S-EPMC9074407 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature