title: 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.
authors.affiliation: Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiß
authors.affiliation: Institute for Biochemistry, University of Leipzig, Leipzig, Germany.
authors.forename: Manja
authors.initials: M
authors.lastname: Wachsmuth
authors.affiliation: Institute for Biochemistry, University of Leipzig, Leipzig, Germany. Electronic address: moerl@uni-leipzig.de.
authors.forename: Mario
authors.initials: M
authors.lastname: Mörl
authors.affiliation: Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Leipzig, Germany; Center for RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark; Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, New Mexico, USA.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D001483:Base Sequence / Q000235:genetics / Q000502:physiology; D012313:RNA / Q000737:chemistry / Q000235:genetics; D059370:RNA Folding; D058928:Riboswitch / Q000235:genetics / Q000502:physiology*
chemical_list: D058928:Riboswitch; D012313:RNA
keywords: Inverse folding; Multi-state design; RNA design; Riboswitch; Transcription regulation