title: Loop swapping in an antisense RNA/target RNA pair changes directionality of helix progression.
abstract: The binding pathway of the natural antisense RNA CopA to its target CopT proceeds through a hierarchical order of steps. It initiates by reversible loop-loop contacts followed by unidirectional helix progression into the upper stems. This involves extensive breakage of intramolecular base pairs and the subsequent formation of two intermolecular helices, B and B'. Based on the known tRNA anticodon loop structure and on results from the Sok/Hok antisense/target RNA system, it had been suggested that a U-turn (or pi-turn) in the loop of CopT might determine the directionality of helix progression. Data presented here show that the putative U-turn is one of the structural elements of antisense/target RNA pairs required to achieve fast binding kinetics. Swapping of the hypothetical U-turn structure from the target RNA to the antisense RNA retained regulatory performance in vivo and binding rates in vitro but altered the binding pathway by changing the direction in which the initiating helix was extended. In addition, our data indicate that a helical stem immediately adjacent to the target loop sequence is required to provide a scaffold for the U-turn.
authors.affiliation: Institute of Cell and Molecular Biology, Department of Microbiology, Biomedical Center, Uppsala University, Box 596, Husargatan 3, S-75124 Uppsala, Sweden.
authors.forename: Jacoba G
authors.initials: JG
authors.lastname: Slagter-Jäger
authors.forename: E Gerhart H
authors.initials: EG
authors.lastname: Wagner
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D020755:Coat Protein Complex I / Q000235:genetics; D017931:DNA Primers; D007700:Kinetics; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016372:RNA, Antisense / Q000737:chemistry* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D020755:Coat Protein Complex I; C071263:CopA protein, Bacteria; C073592:CopT protein, Plasmid R1; D017931:DNA Primers; D016372:RNA, Antisense