1. ¹Howard Hughes Medical Institute, Yale University, New Haven, CT, USA
2. ²Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
3. ³Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA

Correspondence: Dr RR Breaker, Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520-8103, USA. E-mail: ronald.breaker@yale.edu

Received 9 September 2008; Revised 4 March 2009; Accepted 5 March 2009; Published online 9 July 2009.

Abstract

In the last two decades, remarkable advances have been made in the development of technologies used to engineer new aptamers and ribozymes. This has encouraged interest among researchers who seek to create new types of gene-control systems that can be made to respond specifically to small-molecule signals. Validation of the fact that RNA molecules can exhibit the characteristics needed to serve as precision genetic switches has come from the discovery of numerous classes of natural ligand-sensing RNAs called riboswitches. Although a great deal of progress has been made toward engineering useful designer riboswitches, considerable advances are needed before the performance characteristics of these RNAs match those of protein systems that have been co-opted to regulate gene expression. In this review, we will evaluate the potential for engineered RNAs to regulate gene expression and lay out possible paths to designer riboswitches based on currently available technologies. Furthermore, we will discuss some technical advances that would empower RNA engineers who seek to make routine the production of designer riboswitches that can function in eukaryotes.