Cartoons of <i>cis</i>-Regulatory Constructs Emerging from Our In Silico Design of Transcriptional Logic Gates

<p>The boxes indicate the TF binding sites; green indicates that a TF acts as an activator, red that it acts as a repressor, and brown that the action of the TF depends upon the concentrations of the two TFs. Weak binding sites (<i>K</i>_D > 2 × 10³ nM) have a light color, strong ones are dark. Yellow connections between TFs signify cooperative interactions. The designs show that the logic gates are constructed as overlapping arrays of cooperative binding sites. Each layer acts as a module, either activating or repressing transcription. Signals are integrated via the interplay between intramodular cooperativity and intermodular competition.