Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA

Abstract

Switches and sensors play important roles in our everyday lives. The chemical properties of RNA make it amenable for use as a switch or sensor, both artificially and in nature. This review focuses on recent advances in artificial RNA switches and sensors. Researchers have been applying classical biochemical principles such as allostery in elegant ways that are influencing the development of biosensors and other applications. Particular attention is given here to allosteric ribozymes (aptazymes) that are regulated by small organic molecules, by proteins, or by oligonucleotides. Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies.

FIGURE 1.

In vitro selection of ligand-binding aptamers with fluorescence detection. The green pathway shows a relatively conventional two-step strategy of (1) selecting an aptamer responsive to a given ligand such as ATP, followed by (2) appending a fluorescent chromophore that renders the aptamer useful for signaling (Jhaveri et al. 2000b). The blue pathway shows an alternate one-step strategy in which fluorescent aptamers are selected directly by incorporation of one or more fluorescently labeled mononucleotides during the selection process (Jhaveri et al. 2000a).

FIGURE 2.

(A) General strategy for creation of an allosteric ribozyme (aptazyme), depicting the aptamer, communication, and ribozyme modules. The order of events starting with ligand binding is numbered. (B) Specific example of an allosteric ribozyme that is sensitive to flavin mononucleotide (FMN; Soukup and Breaker 1999b). (C) The general communication module of Kertsburg and Soukup (2002).

FIGURE 3.

Allosteric (A) and inhibitor (B) control strategies for protein-mediated modulation of ribozyme activity, illustrated with the hammerhead ribozyme. In the classification proposed here, the inhibitor control strategies are not truly “allosteric” in that they do not involve a communication module. Instead, the inhibitor oligonucleotide strand binds in direct competition with the ribozyme’s substrate. In principle, small molecules could also function as the inhibitor (see text). (C) The TRAP strategy of Burke et al. (2002). (D) The expansive regulation strategy of Sen and coworkers (Wang and Sen 2001; Wang et al. 2002a).