Antisense oligonucleotides containing modified bases inhibit in vitro translation of Leishmania amazonensis mRNAs by invading the mini-exon hairpin

Complementary oligodeoxynucleotides (ODNs) that contain 2-aminoadenine and 2-thiothymine interact weakly with each other but form stable hybrids with unmodified complements, These selectively binding complementary (SBC) agents can invade duplex DNA and hybridize to each strand (Kutyavin, I. V., Rhinehart, R, L,, Lukhtanov, E, A, Gorn, V, V,, Meyer, R, B,, and Camper, H. B, (1996) Biochemistry 35, 11170-11176), Antisense ODNs with similar properties should be less encumbered by RNA secondary structure. Here we show that SEC ODNs strand invade a hairpin in the mini-exon RNA of Leishmania amazonensis and that the resulting heteroduplexes are substrates for Escherichia coli RNase H. SEC ODNs either with phosphodiester or phosphorothioate backbones form more stable hybrids with RNA than normal base (NB) ODNs, Optimal binding was observed when the entire hairpin sequence was targeted. Translation of L, amazonensis mRNA in a cell-free extract was more efficiently inhibited by SEC ODNs complementary to the mini-exon hairpin than by the corresponding NE ODNs, Nonspecific protein binding in the cell-free extract by phosphorothioate SEC ODNs rendered them ineffective as antisense agents in vitro. SEC phosphorothioate ODNs displayed a modest but significant improvement of leishmanicidal properties compared with NE phosphorothioate ODNs.