title: Single-molecule observations of RNA-RNA kissing interactions in a DNA nanostructure.
abstract: RNA molecules uniquely form a complex through specific hairpin loops, called a kissing complex. The kissing complex is widely investigated and used for the construction of RNA nanostructures. Molecular switches have also been created by combining a kissing loop and a ligand-binding aptamer to control the interactions of RNA molecules. In this study, we incorporated two kinds of RNA molecules into a DNA origami structure and used atomic force microscopy to observe their ligand-responsive interactions at the single-molecule level. We used a designed RNA aptamer called GTPswitch, which has a guanosine triphosphate (GTP) responsive domain and can bind to the target RNA hairpin named Aptakiss in the presence of GTP. We observed shape changes of the DNA/RNA strands in the DNA origami, which are induced by the GTPswitch, into two different shapes in the absence and presence of GTP, respectively. We also found that the switching function in the nanospace could be improved by using a cover strand over the kissing loop of the GTPswitch or by deleting one base from this kissing loop. These newly designed ligand-responsive aptamers can be used for the controlled assembly of the various DNA and RNA nanostructures.
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
authors.forename: Yosuke
authors.initials: Y
authors.lastname: Takeuchi
authors.affiliation: Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan. endo@kuchem.kyoto-u.ac.jp hs@kuchem.kyoto-u.ac.jp.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Endo
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan.
authors.forename: Kumi
authors.initials: K
authors.lastname: Hidaka
authors.affiliation: ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. jean-jacques.toulme@inserm.fr and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Durand
authors.affiliation: ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. jean-jacques.toulme@inserm.fr and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Dausse
authors.affiliation: ARNA laboratory, University of Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France. jean-jacques.toulme@inserm.fr and Inserm U869, 146 rue Léo Saignat, 33076 Bordeaux, France.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Toulmé
authors.affiliation: Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan. endo@kuchem.kyoto-u.ac.jp hs@kuchem.kyoto-u.ac.jp.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sugiyama
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D020029:Base Pairing; D015374:Biosensing Techniques; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006160:Guanosine Triphosphate / Q000737:chemistry*; D008024:Ligands; D049329:Nanostructures; D036103:Nanotechnology; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000378:metabolism
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D012313:RNA; D006160:Guanosine Triphosphate; D004247:DNA