Squaring theory with practice in RNA design

Ribonucleic acid (RNA) design offers unique opportunities for engineering genetic networks and nanostructures that self-assemble within living cells. Recent years have seen the creation of increasingly complex RNA devices, including proof-of-concept applications for in vivo three-dimensional scaffolding, imaging, computing, and control of biological behaviors. Expert intuition and simple design rules — the stability of double helices, the modularity of noncanonical RNA motifs, and geometric closure — have enabled these successful applications. Going beyond heuristics, emerging algorithms may enable automated design of RNAs with nucleotide-level accuracy but, as illustrated on a recent RNA square design, are not yet fully predictive. Looking ahead, technological advances in RNA synthesis and interrogation are poised to radically accelerate the discovery and stringent testing of design methods.

► Simple heuristics for RNA design are yielding switches, amplifiers, circuits, and polyhedra.
► Automated RNA design tools are being developed but are not yet well benchmarked.
► The gap between theory and practice is illustrated with a recent RNA square design.
► Modeling RNA atomic-level structures and thermodynamic behaviors remains difficult.
► Massively parallel synthesis and structure mapping may elicit missing RNA design rules.