Leveraging Resource Competition for Part Characterization in Cell-Free Extracts

The rational design of complex biocircuits requires well-characterized genetic parts. Unfortunately, the behavior of these parts depends on their cellular context. One major source of context-dependence is competition for shared cellular resources, introducing coupling among virtually all components of a genetic circuit. By explicitly accounting for the scarcity of these resources, here we demonstrate how the resulting coupling phenomenon can be leveraged to characterize non-fluorescent parts by monitoring the expression of fluorescent probes. In particular, we develop a protocol that combines fluorescent measurements with mathematical modeling to extract information about the expression of non-fluorescent parts based on the loading on fluorescent probes due to competition effects. Furthermore, by quantifying the information content of candidate experiments, both experimental conditions and fluorescent probe parts can be optimized to minimize parameter uncertainty, thus leading to sharp parameter estimates. To validate our results, we demonstrate that the developed method can be successfully used for indirect part characterization considering in vitro data.