A new frontier in synthetic biology: automated design of small RNA devices in bacteria

• RNA is readily amendable to computer-based design due to its energy model-based structural predictability and functional modularity.
• A completely automated design methodology can be developed to engineer synthetic riboregulatory circuits in bacteria.
• The objective function for RNA design automation can be approached as the sum of the interaction and activation energies and several terms of constraint.
• 3D structure models could be required for improving the predictability of the systems.

RNA devices provide synthetic biologists with tools for manipulating post-transcriptional regulation and conditional detection of cellular biomolecules. The use of computational methods to design RNA devices has improved to the stage where it is now possible to automate the entire design process. These methods utilize structure prediction tools that optimize nucleotide sequences, together with fragments of known independent functionalities. Recently, this approach has been used to create an automated method for the de novo design of riboregulators. Here, we describe how it is possible to obtain riboregulatory circuits in prokaryotes by capturing the relevant interactions of RNAs inside the cytoplasm using a physicochemical model. We focus on the regulation of protein expression mediated by intra- or intermolecular interactions of small RNAs (sRNAs), and discuss the design of riboregulators for other functions. The automated design of RNA devices opens new possibilities for engineering fully synthetic regulatory systems that program new functions or reprogram dysfunctions in living cells.