Our strategy builds upon existing biological mechanisms. We are fortunate that the natural world exhibits mechanisms similar to those a good engineer would design. By using a modified version of these naturally occurring mechanisms we avoid potentially very challenging issues of engineering complex protein-DNA interactions, allowing us to build interesting structures with a mix and match approach, combined with limited modification.
Here we show the feasibility of building a family of logic gates where the signals are represented by concentrations of naturally-occurring DNA-binding proteins, and where the nonlinear amplification is implemented by in vivo DNA-directed protein synthesis. We first review the essential aspects of protein manufacturing in the cell.