title: Selection of a novel class of RNA-RNA interaction motifs based on the ligase ribozyme with defined modular architecture.
abstract: To develop molecular tools for the detection and control of RNA molecules whose functions rely on their 3D structures, we have devised a selection system to isolate novel RNA motifs that interact with a target RNA structure within a given structural context. In this system, a GAAA tetraloop and its specific receptor motif (11-ntR) from an artificial RNA ligase ribozyme with modular architecture (the DSL ribozyme) were replaced with a target structure and random sequence, respectively. Motifs recognizing the target structure can be identified by in vitro selection based on ribozyme activity. A model selection targeting GAAA-loop successfully identified motifs previously known as GAAA-loop receptors. In addition, a new selection targeting a C-loop motif also generated novel motifs that interact with this structure. Biochemical analysis of one of the C-loop receptor motifs revealed that it could also function as an independent structural unit.
authors.affiliation: Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Shoji P
authors.initials: SP
authors.lastname: Ohuchi
authors.forename: Yoshiya
authors.initials: Y
authors.lastname: Ikawa
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Nakamura
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D005818:Genetic Engineering / Q000379:methods*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011130:RNA Ligase (ATP) / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry*
chemical_list: D016337:RNA, Catalytic; D011130:RNA Ligase (ATP)