Shifted Reverse PAGE: a novel approach based on structure switching for the discovery of riboswitches and aptamers

Abstract

Riboswitches are regulatory sequences composed of an aptamer domain capable of binding a ligand and an expression platform that allows the control of the downstream gene expression based on a conformational change. Current bioinformatic methods for their discovery have various limitations. To circumvent this, we developed an experimental technique to discover new riboswitches called SR-PAGE (Shifted Reverse Polyacrylamide Gel Electrophoresis). A ligand-based regulatory molecule is recognized by exploiting the conformational change of the sequence following binding with the ligand within a native polyacrylamide gel. Known riboswitches were tested with their corresponding ligands to validate our method. SR-PAGE was imbricated within an SELEX to enrich switching RNAs from a TPP riboswitch-based degenerate library to change its binding preference from TPP to thiamine. The SR-PAGE technique allows performing a large screening for riboswitches, search in several organisms and test more than one ligand simultaneously.