Developing RNA tools for engineered regulatory systems.

RNA has been shown recently to playa prominent role in regulating gene expression in a wide variety of organisms. Natural examples of RNA-dependent gene regulation include modulation of transcription (Wassarman and Storz, 2000; Winkler et al., 2002), translation (Moller-Jensen et al., 200 I; Moller et al., 2002; Bartel, 2004), and the temporal stability of mRNA (Masse et al., 2003; Meister and Tuschl, 2004; Winkler et al., 2004). Environmental perturbations, such as temperature (Hoe and Goguen, 1993; Johansson et al., 2002), osmolarity (Andersen et al., 1987; Chen et al., 2004), oxidative stress (Altuvia et al., 1997), and chemistry (such as the presence of metabolites or toxins, reviewed in MandaI and Breaker, 2004) can all trigger RNA-mediated changes in gene expression. In parallel, researchers have begun to use engineered RNAs as regulatory molecules for artificial genetic circuits. The same mechanisms (base-pairing and ligand-induced conformational change) that make RNA a 'natural' choice for gene regulation are also amenable to rational engineering or directed evolution efforts. Nonetheless, the clever machines that nature has crafted have accelerated the use of artificial regulatory RNAs. Therefore, we will initially consider the natural RNA tools and mechanisms that are available to researchers, then examine how these tools are being applied in artificial genetic circuits. Ultimately, though, both the adapta­ tion of natural, and the de novo development of artificial, RNA-based regulatory mechanisms should foment the production of much more complex artificial genetic circuits, potentially including 'smart' nucleic acid drugs that regulate their own production and release.