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 inter

SUBMITTER: Ohuchi SP 

PROVIDER: S-EPMC2441787 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature