Rational design of artificial riboswitches

Abstract

A riboswitch is a cis-regulatory RNA element that controls gene expression in response to a specific ligand. This functional RNA is composed of two domains, an aptamer and an expression platform. A ligand binds to the former to induce the latter's conformational change or alternative folding, which turns on or off the expression of the downstream (or upstream in some cases) gene. Although natural riboswitches are limited in terms of the variation of their ligands, an in vitro-selected aptamer enables us to construct an artificial riboswitch responsive to a user-defined ligand molecule. However, it is difficult to functionally couple such an in vitro-selected aptamer with an expression platform for their efficient communication, which generally requires ligand-dependent hybridization switches of RNA duplexes over a wide range of mRNA. Nonetheless, we have thus far developed several rational methods for designing artificial riboswitches that function in bacterial or eukaryotic translation systems. The methods are described herein in historical order.