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HCV RNA MICROARRAYS: AN IN VITRO APPROACH TO SCREEN FOR HIGH AFFINITY SIRNA INTERACTIONS WITH THE HCV GENOMIC RNA
SM Sagan, JP Pezacki
Hepatitis C virus (HCV) is the leading cause of liver disease and affects more than 120 million people worldwide. The HCV genome is a positive-sense, single-stranded RNA that functions as the template for both translation of the viral proteins and for replication of genomic RNA, making it an attractive target for antiviral therapy using short-interfering RNA (siRNA). The use of siRNA is common in functional genomics to specifically silence the expression of target genes by creating complementary siRNAs to the gene(s) of interest. siRNAs have been demonstrated to efficiently silence the expression of both cellular and viral RNAs in vitro and in vivo in a number of cell types and animal models. In accordance with this, siRNAs have been used to effectively silence HCV gene expression and replication. However, efficient siRNA knockdown is hampered by target site accessibility. Thus, there is a need for an in vitro screening approach to identify high affinity siRNA interactions. Herein, we use a high-throughput, microarray-based approach to screen for high affinity siRNA interactions using arrayed HCV RNA. We demonstrate that microarrayed HCV RNA can be used to predict the “in vivo” potency of siRNAs directed against the HCV genome. This result suggests that an array-based approach can be used to screen for highly potent siRNAs that can be applied to functional genomics or as novel therapeutics for both viral and cellular target RNAs.