Isolation 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 that is specific for the (-)IRES domain I. After confirming the binding convergence in the ninth RNA pool, 42 RNA clones were sequenced and analyzed. Of these, 25 clones (Family-I) had the consensus sequence, 5'-UGGAUC-3', which is complementary to the apical loop of SL-E1, an important region for NS5B recognition. Another 13 clones (Family-II) had the consensus sequence, 5'-GAGUAC-3', which is complementary to the apical loop of SL-D1. Biochemical analyses are in progress to evaluate whether these RNA aptamers have the ability to inhibit HCV replication.