Electrical engineering is a strong contender for the central analogy of synthetic biology. Synthetic biologists often think of electrical circuits when designing gene networks, and logic gates are central to the metaphor.
Biological logic gates can be difficult to design from scratch, however, and they can’t just be bought at Radio Shack, even before it declared bankruptcy. To fill this void, a new paper from Harbin Medical University in China describes a new database: SynBioLGDB (Synthetic Biology Logic Gates DataBase): a manually curated repository of genetic logic gates from the literature.
SynBIoLGDB has 189 bio-logic gates, including AND, OR, NOR, NOT, NAND, XOR, and others. No matter what you’re building, there’s likely a gate for you; the database includes circuits combining protein inputs, promoter inputs, and other signals, like small molecules. Currently, the gates all come from three species – E. coli, Bacillus clausii, and that standout model of an organism, human.
Engineering analogies notwithstanding, biology tends to be a bit squishier than silicon, and the LGDB tends to give that complexity short shrift. Bio-logic gates are not binary, so a bit more information on how the gates behave in the wild would be useful. For example, what is the dynamic range (“on” level vs “off”) of the output? How sharp is the transition from “on” to “off”? How much input is needed to change the output? Fortunately, each entry comes with a Pubmed link for users who want to dig deeper.
While the LGDB still doesn’t make biological logic gates a plug-and-play proposition, it does provide a useful starting point for anyone who has, say, the all-too-common problem of needing a ribozyme-based NOR gate in B. clausii, and isn’t quite sure where to start. To make the database even better, the authors plan to continually add gates from new papers, and scientists can submit their own entries. As this database develops, it could become a go-to resource for bio-logic.