Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements.

ABSTRACT: The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin i

SUBMITTER: Fernandez-Chamorro J 

PROVIDER: S-EPMC4823658 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature