Synthetic biology hinges on the ability to build biological systems from the bottom up using biological parts. Plasmid design is crucial and with so many parts to choose from, assembling compatible parts can be a bottleneck in Syn Bio workflows. To address this, Explora Biotech have recently launched Double Helix Technologies (DOULIXTM) – a toolkit to design, validate and synthesise custom constructs for synthetic biology.
This is a 3-step process:
1. Design. Using their free online design platform, users can design a custom plasmid from their library of parts (‘biomodules’) or from your own custom sequence to assemble into a vector of choice.
2. Validation. The software guides you through a design validation to avoid common design flaws.
3. Synthesis. You can order ready-to-use full length constructs, or order individual Biomodules to assemble yourself.
It looks good on paper, so we got in touch with Davide De Lucrezia from DOULIX to find out more.
Q. What do you think are the current bottlenecks of synthetic biology projects?
We feel that the lack of in vivo standardization of standard biological parts is the main bottleneck. Without reliable in vivo data, any simulation will run on wobbling data and will inevitably be of little help to experimental synthetic biologists.
Q. How does DOULIX aim to circumvent these issues?
We started a challenging project to measure in vivo activity of most commonly used standard biological parts called DOULIX GrandChallenge. Together with the LIAR EU project (http://livingarchitecture-h2020.eu/) we aim to provide the SB community with rock-solid in vivo data to be used for simulation and model refinement. These data will be available through DOULIX’s database and used by our multiscale simulation platform to be released in 2018. Together with our synthesis platform, we hope to provide the SB community with a comprehensive toolkit that allows them to move seamlessly from design to fabrication.
Q. What is the average turn-around time for de novo constructs from DOULIX?
Individual dsDNA can be delivered in as little as 5 working days and full-length circular constructs of up to 10 kbp are usually delivered in 15 working days.
Q. Are the Biomodules all optimised for E. coli, or are other (and if so which?) expression systems catered for?
To date, most of our Biomodules are optimised for E.coli chassis. However, we are glad to announce to EUSynBioS a new partnership with Agilent that will tremendously expand our Biomodule collection to include parts optimised for Yeast and mammalian cells.
Q. What is the advantage of DOULIX over designing constructs ourselves?
With DOULIX you can finally use in vivo validated Biomodules so you can focus on construct/circuit design rather than part validation. I think that DOULIX is a substantial step ahead toward abstraction and decoupling in SB, something we really need if we want to unlock the full potential of SB.
Q. How do you see DOULIX expanding to serve the Synthetic Biology community in the future?
The next big thing is our DOULIX simulator, an integrated simulation platform for multiscale modelling using in vivo data. We expect it to have a big impact on the SB workflow. Yesterday we used the old genetic engineering approach of trial-and-error, today we are using the Synthetic Biology approach of design-build-test. But as for tomorrow we envision a time when we will confidently simulate before we built, saving time, money and delivering safer drugs, greener products and greater knowledge. Tomorrow, we envision the dawn of constructive biology.