title: Computational Design of a Circular RNA with Prionlike Behavior.
abstract: RNA molecules engineered to fold into predefined conformations have enabled the design of a multitude of functional RNA devices in the field of synthetic biology and nanotechnology. More complex designs require efficient computational methods, which need to consider not only equilibrium thermodynamics but also the kinetics of structure formation. Here we present a novel type of RNA design that mimics the behavior of prions, that is, sequences capable of interaction-triggered autocatalytic replication of conformations. Our design was computed with the ViennaRNA package and is based on circular RNA that embeds domains amenable to intermolecular kissing interactions.
authors.forename: Stefan
authors.initials: S
authors.lastname: Badelt
authors.forename: Christoph
authors.initials: C
authors.lastname: Flamm
authors.affiliation: University of Vienna.
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
mesh_terms: D019295:Computational Biology; D007700:Kinetics; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D012984:Software; D013816:Thermodynamics
chemical_list: D012313:RNA
keywords: RNA structure; folding kinetics; self-replication; sequence design