Selection of a novel class of RNA-RNA interaction motifs based on the ligase ribozyme with defined modular architecture.
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.
Ohuchi
Shoji P
SP
Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
Ikawa
Yoshiya
Y
Nakamura
Yoshikazu
Y
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*
D016337:RNA, Catalytic; D011130:RNA Ligase (ATP)