Advisor: 

Corey Wilson, Ph.D. (Chemical & Biomolecular Engineering, Georgia Institute of Technology) 

Committee:  

Ravi Kane, Ph.D. (School of Chemical & Biomolecular Engineering, Georgia Institute of Technology) 

Manu Platt, Ph.D. (School of Biomedical Engineering, Georgia Institute of Technology) 

Matthew Realff, Ph.D. (School of Chemical & Biomolecular Engineering, Georgia Institute of Technology) 

Eric Vogel, Ph.D. (School of Materials Science & Engineering, Georgia Institute of Technology) 

Next-Generation Genetic Memory for Synthetic Biology Applications 

Synthetic biology seeks to mine engineerable components from complex natural biological systems and reapply them in a way that is amenable to predictive design and other engineering approaches, eventually developing new, useful applications. A significant gap in this approach is an ability to perform biological memory operations (genetic manipulations that permanently store the results of biological information-processing operations) efficiently and controllably. Site-specific recombinases are enzymes that catalyze permanent DNA rearrangements at specific DNA sequences, making them prime targets for use in biological memory circuits. However, these enzymes can be difficult to employ because only a small number of traditional genetic regulatory parts can effectively regulate their expression. We hypothesize that using DNA-binding transcription factors (TFs) to sterically block the function of recombinases at their target DNA sequences will enable finer control over recombinase activity, a novel strategy we term “interception”. To investigate this hypothesis, we will build and test genetic memory circuits that apply interception to fluorescent reporter genes in E. coli. Aim 1 will demonstrate the feasibility and efficacy of this approach on single-input deletion circuits. Aim 2 will develop multi-input memory information processing. Aim 3 will exploit a characteristic of recombinase-binding DNA sequences to generate up to six independent memory operations per recombinase, culminating in the development of a novel one-recombinase, seven-input memory array. Interception will enable stronger control over recombinase expression, reduced metabolic burden from their use, and the creation of more complex genetic memory operations.