A Scalable Cellular Logic Technology Using Zinc-Finger Proteins

Simple cellular logic circuits have been built by engineering the DNA of host cells. Similar to systems found in nature, these circuits use repressor protein concentrations as logic signals; a gate’s input repressors interact with the cell’s DNA to influence the production of the gate’s output repressors. A limitation in building these circuits is the number of unique repressor proteins available to use as logic signals, and previous designs have consisted of only a few gates. In this paper, we propose a scalable cellular logic technology with zinc-finger proteins acting as the unique repressor logic signals. A zinc-finger protein binds to DNA at a specific target site determined by the nucleotide sequence, and zinc-finger proteins can readily be engineered to target almost any sequence. Our proposed technology uses engineered zinc-finger proteins and target DNA sequences as a scalable solution to implementing independent logic gates. The technology additionally attaches dimerization domains to the zinc-finger proteins to enable cooperativity and provide logic gates with nonlinear gain. We analyze our proposed cellular logic technology, including the interference caused by interactions between gates, and conclude that building robust circuits with hundreds and even thousands of gates seems feasible.