My name is Shawn Jin (SAR ’15), and I am doing research as part of Professor Douglas Densmore‘s Cross-Disciplinary Integration of Design Automation Research (CIDAR) Group. My research is in the field of synthetic biology, which involves the design, manipulation and transfer of DNA into living organisms in order to engineer and characterize novel biological behaviors that could range from gene therapeutics to bioremediation.
I started working in the CIDAR lab as a member of the BU team in the synthetic biology competition, iGEM (International Genetically Engineered Machines) in the summer of 2012. Together with a teammate, we were able to use a newly published DNA assembly technique called Modular Cloning (Weber et al, 2011) to create basic parts such as promoters, RBSs, genes and terminators with unique fusion sites and Typer IIS restriction sites which will allow the ligation of up to six of these parts together in a one pot reaction. This can then be used to create constructs, which include multiple transcriptional units and inverters, in an easy and time-effective fashion. The uniqueness of the CIDAR lab is that it has both a wet lab and computational arm which allows wet lab user members such as myself to use a synthetic biology software called Clotho, which contains a spectrum of powerful applications that enhance the synthetic biology experience.
Currently, I am working on creating special fusion proteins that involves a gene of interest linking with a reporter gene such as the green or red fluorescent protein (GFP and RFP respectively). This includes designing specialized primers and performing PCR to link together genes of interest and reporter genes. Clotho is integrated into the workflow by allowing me to store and extract DNA information, find various features such as fusion and cut sites within sequences, and generate possible combinations of fusion proteins using a language called Eugene.
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