Synthetic Biology

Current Projects

One of the major tenets of synthetic biology is the ability to assemble genetic devices from standardized biological parts. While new formats and methodologies for DNA assembly are emerging rapidly, the availability of well-characterized component parts that conform to these formats is low, leading many researchers to use less efficient methods that offer a wider selection of pre-existing parts.

MoClo is a relatively new assembly method utilizing Type IIs restriction enzymes that allows the ligation of up to six DNA fragments together at one time using small, oligo-derived fusion sites. Our wetlab team has adapted the MoClo methodology to reduce thermocycler reaction time and reaction volume, thereby lowering labor and reagent costs. Using this modified protocol, we have constructed a library of well-characterized, reliable MoClo parts for use in the assembly of biological devices in E. coli. This library includes many part types that are essential to the construction of basic genetic circuits, including promoters, ribosome binding sites, reporter genes, and transcriptional terminators.

The CIDAR MoClo Library is the first bacterial DNA part library compatible with a multipart assembly standard. CIDAR MoClo allows for the rapid assembly of interchangeable DNA parts. While many DNA assembly standards have been published in recent years, only the Modular Cloning standard, or MoClo, has the advantage of providing publicly available part libraries for use in plant, yeast, mammalian systems, and now E. coli.

This library is publicly available as part of the Hummingbird project and is intended to facilitate the adoption of the MoClo format as a viable alternative to both the BioBrick standard and less-modular scarless assembly methods, such as Gibson Assembly.

MoClo-Hummingbird-Logo

 

 

Computational Synthetic Biology for Engineers (ENG EC500D1) presents the field of computational synthetic biology through the lens of four distinct activities: Specification, Design, Assembly, and Test. Engineering students of all backgrounds are provided an introduction to synthetic biology and then exposed to core challenges and approaches in each of these four areas. Homework assignments are provided which allow the students to use existing computational software to explore each of these themes. In addition, advanced concepts are presented around data management, design algorithms, standardization, and simulation challenges in the field. The course culminates in a group project in which the students apply computational design methods to an experimentally created system (working with graduate students in the Biological Design Center).

Course Website : https://www.compsynbio.org/