Design and assembly of DNA molecules using multi-objective optimization

Angelo Gaeta, Valentin Zulkower, Giovanni Stracquadanio

Research output: Contribution to journalArticlepeer-review


Rapid engineering of biological systems is currently hindered by limited integration of manufacturing constraints into the design process, ultimately reducing the yield of many synthetic biology workflows. Here we tackle DNA engineering as a multi-objective optimization problem aiming at finding the best tradeoff between design requirements and manufacturing constraints. We developed a new open-source algorithm for DNA engineering, called Multi-Objective Optimisation algorithm for DNA Design and Assembly, available as a Python and Anaconda package, as well as a Docker image. Experimental results show that our method provides near-optimal constructs and scales linearly with design complexity, effectively paving the way to rational engineering of DNA molecules from genes to genomes.

Original languageEnglish
Article numberysab026
Number of pages9
JournalSynthetic Biology
Issue number1
Publication statusPublished - 11 Oct 2021


  • biodesign
  • optimization
  • combinatorial assembly
  • computer-aided design
  • multi-objective optimization


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