Synthetic biological devices hold great potential for many biotechnological applications. However, the functional complexity of synthetic devices has been limited by the available design tools. An advance is presented in a paper that demonstrates a computer-aided approach for designing RNA-based devices with predictable functional properties in Escherichia coli.

Carothers et al. designed expression devices based on two naturally occurring control systems: ribozymes and aptazymes (aptazymes are ribozymes that are controlled by the binding of a ligand). A ribozyme or aptazyme can be engineered to be transcribed in the mRNA of a gene of interest, where it catalyses self-cleavage of the transcript and thus variably regulates expression. The design process used biochemical and biophysical modelling to take into account the many variables — such as rates of RNA folding or catalysis — that can alter the functional output of the device. Importantly, the authors showed that devices that achieved a wide range of expression levels could be obtained by tuning just a few of the design variables.

The authors tested the predicted output from their designed devices by using them to control the production of red fluorescent protein in E. coli; the predicted and observed expression levels were closely matched. They went on to show the use of the designed devices in controlling the metabolic flux of a chemical that is a precursor for bioactive compounds: namely, 2-p-aminophenylalanine.

These approaches for design and experimental testing could be extended to develop systems that control large numbers of genes, or they could be used to explore natural RNA activities.