Figure 4.

XOR gates designed by our algorithm (Marchisio and Stelling, 2011). The schemes here shown have the lowest S both in POS (A) and SOP (B) configuration. Our algorithm is based on rather strict assumptions: POS solutions accept, as inputs, only corepressor chemicals able to switch off aptamers or activate repressor proteins; SOP solutions demand inducer chemicals that activate either aptamers or activator proteins. The input layer contains, both in POS and SOP, either YES or NOT gates. (A) The two corepressor inputs a and b act directly on riboswitches/ribozymes whereas their negated signals are a unique active repressor (R^a). (B) The two inputs are inducers that activate their riboswitch/rybozyme target and their negated signals are an active activator (A^a) for a and a key (k, an sRNA that induces translation) for b. Here, moreover, the two NOT gates are made of two genes. The internal layer of POS solutions is made of NOR gates (whenever a gate takes a single input, it becomes a NOT gate); AND gates (YES for a single input) are present in SOP schemes instead. NOR gates require transcription and/or translation repression; AND gates transcription/translation activation. Both circuits in figure belong to what we called single-gate class of solutions since their final layer is made of only one gate: NOR in POS, OR in SOP. Single-gate configurations are, generally, the least complex ones but not necessarily the most efficient. Every gate is here represented by its Parts (the terminator is always omitted) together with its electronic symbol.