title: Structure-inhibition analysis of RNA aptamers that bind to HCV IRES.
abstract: The translation of HCV starts at the internal ribosomal entry site (IRES) within the 5' untranslated region and IRES is well-conserved in HCV strains. We developed a novel selection strategy using biotinylated oligonucleotide probe and obtained RNA aptamers that bind HCV IRES domain II and domain III-IV, respectively. Selected aptamers specifically bound to target sequence via RNA-RNA interactions. These aptamers inhibited IRES-depend translation in vitro. Especially, 3-07 aptamer, which bound domain IIId, showed strong inhibition. Structure/function relationship of these aptamers was analyzed by mutagenesis, RNase mapping and binding kinetics.
mesh_terms: D001483:Base Sequence; D018076:DNA, Complementary; D016174:Hepacivirus / Q000378:metabolism*; D012313:RNA / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D012270:Ribosomes / Q000378:metabolism*; D013329:Structure-Activity Relationship; D020349:Surface Plasmon Resonance
chemical_list: D018076:DNA, Complementary; D012313:RNA