title: Investigation of de novo totally random biosequences, Part III: RNA Foster: A novel assay to investigate RNA folding structural properties.
abstract: Fold is essential to RNA properties, and, in particular, its thermodynamic stability can be used to monitor RNA-protein or RNA-ligand interactions, and to engineer RNA with novel or improved properties. While clearly valuable, experimental determination of RNA folding stability by traditional biophysical techniques requires substantial amounts of pure sample and rather expensive equipment. In this paper, we report a new, simple approach to the determination of RNA folding stability by coupling enzymatic digestion and temperature denaturation. The assay, named RNA folding stability Test (RNA Foster), is designed to probe the fraction of folded RNA (f(fold)) in an equilibrium mixture of folded and unfolded ones as a function of temperature. The simplicity of RNA Foster suggests that it can easily be scaled up for high-throughput studies of RNA folding stability both in basic and applied research.
authors.affiliation: Department of Biology, University of Roma TRE, Viale G. Marconi 446, IT-00146 Rome.
authors.forename: Davide
authors.initials: D
authors.lastname: De Lucrezia
authors.forename: Marco
authors.initials: M
authors.lastname: Franchi
authors.forename: Cristiano
authors.initials: C
authors.lastname: Chiarabelli
authors.forename: Enzo
authors.initials: E
authors.lastname: Gallori
authors.forename: Pier Luigi
authors.initials: PL
authors.lastname: Luisi
mesh_terms: D001483:Base Sequence; D002384:Catalysis; D030561:Databases, Nucleic Acid; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D020871:RNA Stability; D013696:Temperature
chemical_list: D012313:RNA