Faster, Scarless Assemblies

By Aaron Krol 

 

October 22, 2013 | There are plenty of plaudits for organizations in the life sciences that change the industry’s conceptions of what is possible, but one purpose of the Bio-IT World Best Practices Awards is to highlight those who refine those achievements until the merely possible becomes truly practical. That is why Bio-IT World was pleased to award an honorable mention at the 2013 Best Practices Awards to TeselaGen Biotechnology, a startup that spun out from the Berkeley Lab’s Joint BioEnergy Institute (JBEI) in 2011, and Amgen for the development of TeselaGen: j5, an automated platform for designing DNA assembly protocols. This new, cloud-based platform allows even small institutions to quickly find the most cost-effective protocols for assembling scarless, multipart DNA.

 

While DNA assembly has become a standard laboratory function in recent years, used in biologics, synthetic genomes and a variety of other applications, researchers struggle to move through the process efficiently. Traditional cloning can be hugely time-consuming for any substantial assortment of DNA constructs, delaying a project’s completion by months. Direct oligonucleotide synthesis is faster, but the price, while falling, is likely to be many times higher than cloning for complex tasks. For even moderately-ambitious projects, like creating a combinatorial DNA library, the time and cost constraints imposed by these methods quickly exceed the means of smaller laboratories.

 

The middle ground is to design protocols for assembling large strands of DNA out of shorter sequences, but existing platforms have significant drawbacks. The popular BioBrick assembly method leaves “scars” of several non-coding base pairs between the pieces being assembled, and only allows two pieces to be combined at a time. A few more recent methods, like SLIC and Golden Gate, allow scarless, multipart assembly, but their design protocols cannot be easily optimized: users might spend hours working on a protocol that produces the desired sequence, only to find that molecular constraints make it unworkable in practice, or that the assembly will actually be more expensive than outsourcing direct synthesis.

 

The purpose of j5 is to leverage the power of these assembly methods, while automating the tedious work of finding the optimal design protocol. TeselaGen believed they could create an algorithm that would quickly generate possible protocols, eliminate unpromising avenues, and compare costs between those protocols that arrive at functional assemblies. Users simply upload to j5 the DNA pieces they want combined, choose an assembly method like Golden Gate that the program will design for, and specify any additional constraints they wish their protocol to follow—for instance, that two given parts must always appear together and in a specified order. From these specifications, j5 will not only provide a functional protocol for assembling the parts, but will also determine, for each part, whether DNA synthesis, PCR, or oligo embedding will be most cost-effective.

 

TeselaGen began testing j5 with Amgen in 2012, and released a commercial version in early 2013. The software’s success was immediately apparent: in a test run, a medium-sized DNA library of around 250 constructs was assembled with j5 almost eight times as quickly as with traditional cloning, and at an eighteenth the cost of direct DNA synthesis—without wasting researchers’ time on dead ends. “For our customers, time is the biggest consideration,” Michael Fero, the CEO of TeselaGen, told Bio-IT World. “We are taking timelines that would otherwise extend out to the horizon and are bringing them down to the scale of a few weeks. The software is truly enabling.”

 

At the Bio-IT World Conference & Expo in Boston this April, the design team behind j5 received an honorable mention in the Best Practices Awards in recognition of the program’s massive cost-saving potential and the simplified workflow it offers genetic researchers. Fero was pleased to receive recognition for this major technical achievement. “There are not many venues for getting recognized for this type of hard-core informatics work,” he said. “Bio-IT World stands pretty much alone in that regard… I think that Nathan's insight [Nathan Hillson, the team leader at JBEI] was that the informatics behind the assembly challenge was getting ignored or trivialized.”

 

Since receiving the award, TeselaGen has revamped j5 with a new, more streamlined interface for browsers and tablets. Users can also store their DNA libraries in the j5 cloud, powered by Amazon. “The primary factor for the core software was that it could do the job correctly,” says Fero, but moving forward ease of use will be an equally key focus. TeselaGen is also developing a system for direct integration with automation hardware, allowing j5’s design protocols to be immediately implemented.

 

The 2014 Bio-IT World Best Practices Awards will be opening their call for entries this month. For more information, see www.bio-itworld.com/bestpractices.