Core specific antisense phosphorothioate oligodeoxynucleotides as potent and specific inhibitors of hepatitis C viral translation

Antisense phosphorothioate oligodeoxynucleotides (S-ODN) complementary to sequence stretches in the 5′ non coding region (NCR) of the hepatitis C virus (HCV) have recently been shown to effectively inhibit viral gene expression. In order to further delineate the optimum target region in the highly conserved 5′ end of the viral RNA, S-ODN complementary to HCV core coding sequences were analysed in the present study. In a rabbit reticulocyte lysate (RRL) in vitro translation assay S-ODN 5, complementary to the HCV-RNA nucleotides 340–353, and S-ODN-6, complementary to nucleotides 348–365, resulted in an inhibition of viral translation of 90.4± 1.3% and 93.7± 5.1%, respectively at a concentration of 4.14 µM. S-ODN 7, complementary to nucleotides 371–388, was relatively inefficient and showed a maximal inhibition of 42.4± 12.2% It has been suggested that in living cells an inhibition by S-ODN is mainly mediated by the action of RNAse H. In RRL the RNAseH content is very low; therefore, to simulate the situation in living cells inhibition experiments in RRL enriched with RNAse H were performed. Under these conditions S-ODN 5, 6 and 7 inhibited viral translation by 45.6± 6.3%, 80.3± 2.8% and 70.9± 5.7% at concentrations as low as 0.2 µM. At this concentration no inhibition was observed in the standard RRL assay. In cell culture S-ODN 7 was by far the most efficient inhibitor of viral translation, resulting in a specific inhibition of 89.4± 3.6% at a concentration of 0.3 µM. Taken together with the results of our previous study, nucleotides 326–348 comprising the 3′ end of the NCR and nucleotides 371–388, located entirely in the core coding region of the HCV RNA, are effective targets for S-ODN mediated inhibition of viral translation.