Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots

The advancement of synthetic biology requires the ability to create new DNA sequences to produce unique behaviors in biological systems. Automation is increasingly employed to carry out well-established assembly methods of DNA fragments in a multiplexed, high-throughput fashion, allowing many differ...

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Bibliographic Details
Published in:SLAS technology 2019-06, Vol.24 (3), p.282-290
Main Authors: Walsh, David I., Pavan, Marilene, Ortiz, Luis, Wick, Scott, Bobrow, Johanna, Guido, Nicholas J., Leinicke, Sarah, Fu, Dany, Pandit, Shreya, Qin, Lucy, Carr, Peter A., Densmore, Douglas
Format: Article
Language:English
Subjects:
Automation, Laboratory - methods
Cloning, Molecular - methods
DNA - genetics
Genetic Engineering - methods
Genetic Engineering - standards
Practice Guidelines as Topic
Robotics - methods
Synthetic Biology - methods
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Summary:The advancement of synthetic biology requires the ability to create new DNA sequences to produce unique behaviors in biological systems. Automation is increasingly employed to carry out well-established assembly methods of DNA fragments in a multiplexed, high-throughput fashion, allowing many different configurations to be tested simultaneously. However, metrics are required to determine when automation is warranted based on factors such as assembly methodology, protocol details, and number of samples. The goal of our synthetic biology automation work is to develop and test protocols, hardware, and software to investigate and optimize DNA assembly through quantifiable metrics. We performed a parameter analysis of DNA assembly to develop a standardized, highly efficient, and reproducible MoClo protocol, suitable to be used both manually and with liquid-handling robots. We created a key DNA assembly metric (Q-metric) to characterize a given automation method’s advantages over conventional manual manipulations with regard to researchers’ highest-priority parameters: output, cost, and time. A software tool called Puppeteer was developed to formally capture these metrics, help define the assembly design, and provide human and robotic liquid-handling instructions. Altogether, we contribute to a growing foundation of standardizing practices, metrics, and protocols for automating DNA assembly.
ISSN:2472-6303
2472-6311
2472-6311
DOI:10.1177/2472630318825335