Selectively binding complementary oligonucleotides (SBC ODN's) are oligomers which are synthesized as paired complements or as a single self-complementary hairpin. Due to the presence of modified base pairs, these ODN's don't hybridize to each other but are able to strand invade and hybridize to both strands of a short DNA or RNA duplex. The extensive secondary structure in a typical mRNA transcript suggested to us that SBC ODN's should have a significant advantage over traditional ODNs as antisense agents. I preliminary cell experiments with Leishmania amazonensis amastigotes we have shown this to be true. A partially complementary pair of SBC ODN's targeted to both sides of a putative hairpin present in the spliced leader of every transcript in this protozoan exhibited potent antisense activity relative to a standard antisense ODN. Here we propose to more thoroughly investigate the antisencse potential of paired and self-complementary SBC ODNs. SBC and traditional ODNs targeted to different RNA sequences will be evaluated for their ability to kill L. amazonensis amastigotes in murine macrophages and to inhibit expression of luciferase in Hela X1/5 cells. In vitro studies of the self-association , hybridization, and strand invasion properties of selected SBC ODNs will augment the cell culture work.
The ability of SBC ODNs to freely hybridize to regions of secondary structure, such as found in mRNA, should make them particularly efficacious antisense agents, diagnostic probes, and primers. SBC ODNs with PNA, 2'-O-alkyl, or phosphormidate backbones represent ideal antisense agents.
