PT  - JOURNAL ARTICLE
AU  - Tai-Yin Chiu
AU  - Jie-Hong R. Jiang
TI  - Logic Synthesis of Recombinase-Based Genetic Circuits
AID  - 10.1101/088930
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 088930
4099  - http://biorxiv.org/content/early/2016/11/21/088930.short
4100  - http://biorxiv.org/content/early/2016/11/21/088930.full
AB  - A synthetic approach to biology is a promising technique for various applications. Recent advancements have demonstrated the feasibility of constructing synthetic two-input logic gates in Escherichia coli cells with long-term memory based on DNA inversion induced by recombinases. On the other hand, recent evidences indicate that DNA inversion mediated by genome editing tools is possible; powerful genome editing technologies, such as CRISPR-Cas9 systems, have great potential to be exploited to implement large-scale recombinase-based circuits. What remains unclear is how to construct arbitrary Boolean functions based on these emerging technologies. In this paper, we lay the theoretical foundation formalizing the connection between recombinase-based genetic circuits and Boolean functions. It enables systematic construction of any given Boolean function using recombinase-based logic gates. We further develop a methodology leveraging existing electronic design automation (EDA) tools to automate the synthesis of complex recombinase-based genetic circuits with respect to area and delay optimization. Experimental results demonstrate the feasibility of our proposed method.