title: Isolation and characterization of RNA aptamers specific for the HCV minus-IRES domain I.
abstract: 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.
authors.affiliation: Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Konno
authors.forename: Syusuke
authors.initials: S
authors.lastname: Fujita
authors.forename: Mana
authors.initials: M
authors.lastname: Iizuka
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nishikawa
authors.forename: Tsunemi
authors.initials: T
authors.lastname: Hasegawa
authors.forename: Kotaro
authors.initials: K
authors.lastname: Fukuda
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000302:isolation & purification / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D016174:Hepacivirus / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000096:biosynthesis; D012367:RNA, Viral / Q000737:chemistry* / Q000378:metabolism
chemical_list: C541631:AP30 aptamer; D052157:Aptamers, Nucleotide; D012367:RNA, Viral; D012313:RNA