EFFECT OF RNA SECONDARY STRUCTURE AND MODIFIED BASES ON THE INHIBITION OF TRYPANOSOMATID PROTEIN-SYNTHESIS IN CELL-FREE-EXTRACTS BY ANTISENSE OLIGODEOXYNUCLEOTIDES

Every messenger RNA from leishmanias and trypanosomes has at its 5′ end a conserved region termed the mini-exon sequence which, however, varies from species to species. In a systematic study mRNAs from Trypanosoma brucei, Trypanosoma vivax, and Leishmania enriettii were translated in cell-free extracts in the presence of oligodeoxynucleotides complementary to part of the mini-exon sequence. The affinity of the same oligonucleotides for target and non-target mRNAs was determined by thermal elution of filterbound complexes showing that the critical temperatureof half-dissociation of the complexes was linearly related to log(l+x), where l is the length of the oligomer and x its G + C content. A few oligomers exhibited alower Tc value than expected which was ascribed tothe presence of modified RNA bases or to the existence of a hairpin structure in the L. enriettii mini-exon. Inmost cases the efficiency of translation inhibition bythe oligonucleotides was clearly correlated to their affinity for the target RNA. The modified bases weakened the inhibition of protein synthesis byoligonucleotides complementary to these regions. © 1990 Oxford University Press.