title: Isolation of RNA aptamers specific for the 3' X tail of HCV.
abstract: The 3' end of the HCV genome, designated as the 3' X tail, comprises an almost invariant 98-nucleotide sequence containing three highly conserved stem-loop structures (3' SL1, 3' SL2, and 3' SL3). Since these sequences are all critical for the initiation of negative-strand synthesis and essential for viral replication, they are attractive targets for novel anti-HCV drugs. To obtain effective RNA aptamers specific for the 3' X tail, and with the aim of developing novel inhibitors of HCV replication, we performed in vitro selection of aptamers with specificity for the 3' X tail. In vitro selection, namely SELEX (systematic evolution of ligands by exponential enrichment) is a useful strategy for isolating nucleic acid sequences from a randomized oligonucleotide pool that have a high affinity for a target molecule. After four selection cycles, a pool of the 3' X tail-specific RNA aptamers were obtained. This RNA pool included 39 clones that could be divided into three main classes (cSL1, cSL2, and cSL3) which harbor complementary sequences to the apical loops of 3' SL1, 3' SL2, and 3' SL3, respectively. Biochemical analyses are in progress to evaluate whether these RNA aptamers have the potential to block HCV replication.
authors.affiliation: Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan. kotaro.f@sci.kj.yamagata-u.ac.jp
authors.forename: Kotaro
authors.initials: K
authors.lastname: Fukuda
authors.forename: Yohei
authors.initials: Y
authors.lastname: Toyokawa
authors.forename: Kunio
authors.initials: K
authors.lastname: Kikuchi
authors.forename: Keisuke
authors.initials: K
authors.lastname: Konno
authors.forename: Rie
authors.initials: R
authors.lastname: Ishihara
authors.forename: Chisato
authors.initials: C
authors.lastname: Fukazawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nishikawa
authors.forename: Tsunemi
authors.initials: T
authors.lastname: Hasegawa
mesh_terms: D020413:3' Untranslated Regions / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000302:isolation & purification; D001483:Base Sequence; D016174:Hepacivirus / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D038621:Regulatory Sequences, Ribonucleic Acid; D052156:SELEX Aptamer Technique; D017423:Sequence Analysis, RNA
chemical_list: D020413:3' Untranslated Regions; D052157:Aptamers, Nucleotide; D012367:RNA, Viral; D038621:Regulatory Sequences, Ribonucleic Acid