End-to-end automated microfluidic platform for synthetic biology: from design to functional analysis

Abstract

BackgroundSynthetic biology aims to engineer biological systems for desired behaviors. The construction of these systems can be complex, often requiring genetic reprogramming, extensive de novo DNA synthesis, and functional screening.ResultsHerein, we present a programmable, multipurpose microfluidic platform and associated software and apply the platform to major steps of the synthetic biology research cycle: design, construction, testing, and analysis. We show the platform’s capabilities for multiple automated DNA assembly methods, including a new method for Isothermal Hierarchical DNA Construction, and for Escherichia coli and Saccharomyces cerevisiae transformation. The platform enables the automated control of cellular growth, gene expression induction, and proteogenic and metabolic output analysis.ConclusionsTaken together, we demonstrate the microfluidic platform’s potential to provide end-to-end solutions for synthetic biology research, from design to functional analysis.Electronic supplementary materialThe online version of this article (doi:10.1186/s13036-016-0024-5) contains supplementary material, which is available to authorized users.

From DNA Nanotechnology to Material Systems Engineering

“…This “big data” can be used, in a “data‐driven science” approach, to gain new insights into complex processes that are not accessible by experiment or simulation. At the moment, intensive work is being conducted on the development of end‐to‐end automated platforms for synthetic organic chemistry and synthetic biology as well as for biocatalysis and materials research . Taking into account that i) DNA‐templated synthesis has emerged as an almost routine tool for materials discovery and ii) DNA nanotechnology is intrinsically tied to data sciences (Section ),[57,58c] it is the next logical step to develop technical platforms that can be used for the automated development of customized DNA‐based material systems.…”

Open-source, community-driven microfluidics with Metafluidics

“…Synthetic biologists have used microfluidics to miniaturize DNA assembly (for oligonucleotides 6 , genes 7 , and genetic circuits 8 ), to purify DNA 9 , to clone DNA 10 , and to transform 11 and transfect 12 cells. Multipurpose platforms have been developed that integrate several processes 8,13 . Despite their utility, microfluidic devices are not widely used by synthetic biologists.…”

A data model for biopart datasheets

“…This is despite clear evidence that the use of automation in the execution of synthetic biology experiments can lead to significant improvements in throughput of repetitive processes [19]. This situation is now changing with the opening of DNA foundries around the world [20,21]; the increased disclosures by companies like Amyris [22] or Gingko [23]; and the development of automated platforms (such as the microfluidics platform by Linshiz et al [24]). …”