Abstract
Synthetic biology employs the mathematical models to capture the gene expression of engineered biological systems and implements the designed synthetic gene circuits in living cells for a variety of applications. In this study, robust biological filters with an external control to match a desired input/output (I/O) response are engineered based on the well-characterized promoter-RBS libraries and a cascade gene circuit topology. In the synthetic biological field, the biological filter system serves as a powerful detector or sensor that can sense different molecular signals and produces a specific output response only if the concentration of the input molecular signal is higher or lower than a specified threshold. Here the design approach of robust biological filters is summarized to three steps. Firstly, several well-characterized promoter-RBS libraries are established by identifying and collecting the quantitative and qualitative characteristics of three kinds of promoter-RBS components via nonlinear parameter estimation method. Secondly, the synthetic gene circuit functioned as the biological filter is decomposed into three cascade gene regulatory modules, and an adequate promoter-RBS component is selected for each module from the corresponding promoter-RBS library. Finally, based on the proposed systematic method, a robust externally tunable biological filter is engineered by searching the promoter-RBS component libraries and a control inducer concentration library to achieve the optimal matching with the specified I/O filtering response. The biological filters design in this study might be applicable to detect the residual of different metallic ions. In addition, the designed biological filters can be integrated into higher-order systems with the concept of modularity for a wide range of biological applications in synthetic biology.