Suppression of Hepatitis C Virus Genome Replication in Cells with RNA-Cleaving DNA Enzymes and Short-Hairpin RNA

A class of antisense oligodeoxyribozymes, known as the 10-23 DNA enzymes (DNAzyme), has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. Herein we have utilized a strategy to identify accessible cleavage sites for DNAzyme in the target RNA, the hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of randomized DNAzyme library. The screening procedure identified 18 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA cleavage in vitro. Using positively charged dendrimer nanoparticles, the target RNA-cleaving DNAzymes that are 31-mer oliogonucleotides are delivered into the human hepatoma cells harboring the HCV subgenomic replicon RNA. DNAzymes introduced into the cells efficiently inhibited HCV RNA replication by reducing the expression of HCV NS3. In addition, we designed short-hairpin RNA (shRNA) that targets the same cleavage site for the selected DNAzyme and confirmed that the shRNA also inhibited HCV NS3 gene expression in the HCV replicon cells. These selected DNAzyme and shRNA may be a viable therapeutic intervention to inhibit HCV replication in hepatic cells. We suggest that the method used in this study can be applicable for identification of available sites in any target RNA for antisense oligonucleotides and siRNAs.