Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system.

ABSTRACT: Many well-characterized examples of antisense RNAs from prokaryotic systems involve hybridization of the looped regions of stem-loop RNAs, presumably due to the high thermodynamic stability of the resulting loop-loop and loop-linear interactions. In this study, the identification of RNA stem-loops that inhibit U1A protein binding to the hpII RNA through RNA-RNA interactions was attempted using a bacterial reporter system based on phage lambda N-mediated antitermination. As a result, loop sequences possessing 7-8 base complementarity to the 5' region of the boxA element important for functional antitermination complex formation, but not the U1 hpII loop, were identified. In vitro and in vivo mutational analysis strongly suggested that the selected loop sequences were binding to the boxA reg

SUBMITTER: Yano A 

PROVIDER: S-EPMC2879510 | biostudies-literature | 2010 Jun

REPOSITORIES: biostudies-literature