Programmable ligand-controlled riboregulators of eukaryotic gene expression

Recent studies have demonstrated the importance of noncoding RNA elements in regulating gene expression networks(1,2). We describe the design of a class of small trans-acting RNAs that directly regulate gene expression in a ligand-dependent manner. These allosteric riboregulators, which we call antiswitches, are made fully tunable and modular by rational design. They offer flexible control strategies by adopting active or inactive forms in response to ligand binding, depending on their design. They can be tailor-made to regulate the expression of target transcripts in response to different cellular effectors. Coupled with in vitro selection technologies for generating nucleic acid ligand-binding species(3,4), antiswitches present a platform for programming cellular behavior and genetic networks with respect to cellular state and environmental stimuli.