Structure and function of a small RNA that selectively inhibits internal ribosome entry site-mediated translation

Arun Venkatesan, Saumitra Das, Asim Dasgupta

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


A 60 nt long RNA termed IRNA, isolated from the yeast Saccharomyces cerevesiae, was previously shown to selectively block internal ribosome entry site (IRES)-mediated translation without interfering with cap-dependent translation of cellular mRNAs both in vivo and in vitro. IRNA specifically bound cellular proteins believed to be important for IRES-mediated translation. We demonstrate here that a complementary copy of IRNA (cIRNA) is also active in blocking IRES-mediated translation and that it binds many of the same cellular proteins that IRNA does. We have probed the secondary structure of both IRNA and cIRNA using single-strand- and double-strand-specific nucleases as well as using oligonucleotide hybridization followed by RNase H digestion. Both IRNA and cIRNA share secondary structural homology, although distinct differences do exist between the two structures. Mutational analysis of IRNA shows that sequences that form both the main stem and one loop are critical for its translation inhibitory activity. Maintenance of the established secondary structure appears to be required for both IRNA's ability to bind cellular trans-acting proteins believed to be required for IRES-mediated translation and its ability to block IRES-mediated translation.

Original languageEnglish (US)
Pages (from-to)562-572
Number of pages11
JournalNucleic acids research
Issue number2
StatePublished - Jan 15 1999
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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