Design of transcription regulating riboswitches

Abstract

In this chapter, we review both computational and experimental aspects of de novo RNA sequence design. We give an overview of currently available design software and their limitations, and discuss the necessary setup to experimentally validate proper function in vitro and in vivo. We focus on transcription-regulating riboswitches, a task that has just recently lead to first successful designs of such RNA elements.

Keywords: Inverse folding; Multi-state design; RNA design; Riboswitch; Transcription regulation.