April 8, 2015

Rapid Prototyping in Biology With Synbiota

Synbiota
DNA Tinker Studio. Source: Synbiota

LEGO blocks are a great comparison for genetic parts when the modular nature of synthetic biology is concerned. Just as LEGOs can fit into various arrangements to build different structures, genetic parts can be theoretically assembled into a variety of circuits. These circuits in turn enable synthetic organisms to glow, detect toxins, or produce valuable chemicals.
Undergraduates and high school students all over the world are able to practice this type of engineering now thanks to The Registry of Standard Parts and the iGEM competition. However, it is still very technical and inaccessible to most individuals.

Synbiota, a rapid DNA prototyping company based out of Canada, aims to lower the technicality and make genetic engineering more accessible to the general public with their DNA Tinker Studio kit.

Build your own living app

The first program that anyone learning to code writes is “Hello world”. That is also what the simplest of kits from Synbiota does. Using this kit, one can learn to design genetic constructs on Synbiota’s software platform and to deliver plasmids into bacteria. It allows the workhorse bacteria of molecular biology, E. coli, to be engineered to glow red. Success! Level one completed and all for the reasonable price  of $45.

The next level, the Rainbow Factory, has more genes and more colours. Genetic circuits can be designed with genes coding for red, blue, and yellow fluorescent proteins. Different combinations of the constructs give rise to different colours. The next level is as useful as it is beautiful. The kit sells at $395, with a classroom version or one that allows more trials, priced  at $595.

Why not produce something that is also beneficial in addition to having an aesthetic value? The Violacein Factory kit allows you to engineer a certain metabolic pathway and get E. coli to produce violacein. The purple-coloured product is being researched for anti-cancer activity and current costs of production are well above $350,000 per gram.

What is their next step for biohacking? A kit that allows you to design your own project. The kit includes a variety of parts that can be assembled in various configurations to build sophisticated genetic circuits. Other than the parts included in the kit, imagination is the limit. It is aimed at the advanced biohacker and can be used by iGEM teams to accelerate their research. Synbiota is currently hosting a crowdfunding campaign on Indiegogo to begin production on their newest kit, the DNA Tinker Studio.

Involving people in biotech

Synbiota’s platform allows  independent researchers as well as those from universities  and hackerspaces to collaborate on projects. They can use its in-built DNA design feature, GENtle, to design gene circuits. Every construct starts with an anchor, ends with a cap, and has the genes of interest in between. Protocols can also be shared, and subsequently built upon, in the form of lab notes. Anyone with access to a public project can contribute to it, thus opening biotech research even to individual citizens.

The most remarkable proof of Synbiota’s talent for building this has been the #sciencehack campaign. Violacein factory kits were distributed to researchers, biohackers, and enthusiasts. To come up with the genetic circuit that would  make E. coli efficiently produce violacein would take lots of trial-and-error. The campaign distributed the onus onto different teams that worked side by side to come up with an optimum construct. Each team sent back their results, which were then assembled in a large, virtual notebook. Synbiota’s promotion and effort paid off when one biohacker reportedly produced violacein worth $90,000 in a single tube.

Violacein produced using the violacein factory kit. (Source: Synbiota)

Violacein produced using the violacein factory kit. (Source: Synbiota)

The #sciencehack was announced and most of the biohacking was done at the SXSW accelerator in 2014. Synbiota went on to win the Innovative World Technologies award. Fast forward to SXSW 2015, Synbiota hosted a panel on synthetic biology. During the program, it taught genetic engineering to absolute beginners using its rapid prototyping kits and thus released the DNA Tinker studio.

Rapid prototypes in biology

Synthetic biology is powered primarily by the fall in DNA sequencing and synthesis costs. How far could the price drop for DNA synthesis? Connor Dickie, CEO and one of the co-founders of Synbiota, believes that within a decade or so, it could become practically free. After all, cells, all around and within us, replicate their DNA constantly. If the Carlson curve for sequencing costs continues to be replicated in synthesis costs, his projected outcome could be correct!

In hackathons, people team up over a few days and build a product, usually an app. Such rapid prototyping isn’t generally possible in biotechnology. Hopefully, that will change. The DNA Tinker Studio is still expensive at $995 per kit, but it is vastly less expensive than the cost of engineering a microbe just a few years ago.