Category: Automation and High-Throughput Technologies

1023-D - Automating DNA Assembly: Optimizing Pipeline Development and Implementation Process

Tuesday, February 6, 2018
5:00 PM - 6:00 PM

Due to a lack of standardized methods and metrics, researchers have struggled with forming a well-informed plan of execution among the different automation-friendly, DNA-based cloning methodologies available. The goal of our synthetic biology automation project is to develop protocols, hardware, and software to investigate and optimize DNA assembly through quantifiable metrics. First, we performed a parameter sensitivity analysis of DNA assembly in order to develop a standardized Modular Cloning protocol, suitable to be used at the bench and in liquid-handling robots. Next, we identified key metrics (number of colonies, percent correctly assembled colonies, and our new “Q”-metrics) for measuring success of automated DNA assembly. These metrics were used to describe the success of the automation method (versus manual), regarding parameters a researcher would care most about: output, cost and time. Finally, a novel software tool called Puppeteer was developed to help define the assembly design and provide both human and robot instructions. These techniques and metrics proved to be effective in indicating the parameters that are most impactful to the experiments. For instance, while DNA concentration and plating volume do not have a strong impact on efficiency, cloning reaction efficiency was decreased when the number of parts increased. The Q-metrics were instrumental in indicating when automation is warranted such as the fact that as the scale of an experiment increases, automation saves money and hands-on time. In summary, we have developed and quantitatively evaluated the benefits of standardized pipelines and metrics for DNA cloning by automating the process in a robust and efficient way.

Marilene Pavan

DAMP Lab (
Boston, MA - I am currently part of CIDAR (Cross-disciplinary Integration of Design Automation Research) lab as part of the research staff at Boston University, working on synthetic biology projects, mainly in the Living Computing Project ( My main roles / expertises are related but not limited to: automation of genetic circuits assemblies, cell free systems, synthetic biology tools evaluation and implementation, microfluidics, science outreach programs (, IGEM mentorship, lab management, and training of new students. Previously, I've gained expertise in molecular and synthetic biology, metabolic engineering, patent writing, and leadership, as part of the research staff in leader companies like Monsanto S.A. and Braskem S.A., both in Brazil, and also at JBEI (, CA. I am also specialist in Strategic Management of Technological Innovation.