Isolation and characterization of RNA aptamers specific for the HCV minus-IRES domain I

The minus-IRES ((-)IRES), corresponding to the 3'-terminal end of the negative strand of hepatitis C virus (HCV) RNA, is well conserved among HCV subtypes. The higher order structure of (-)IRES is essential for HCV replication, because the viral RNA dependent RNA polymerase, NS5B, recognizes it as the initiation site for plus-strand synthesis of the HCV genome. To inhibit the "de novo" synthesis of plus-strand RNA molecules, we performed an in vitro selection procedure for RNA aptamers that are specific for (-)IRES domain I. Among the selected aptamers, one RNA aptamer had two binding sites for the (-)IRES domain I. We found that this aptamer inhibited plus-strand synthesis by about 50%, suggesting that both binding sites are important for binding to its target within the (-)IRES domain I.