title: A hepatitis C virus (HCV) internal ribosome entry site (IRES) domain III-IV-targeted aptamer inhibits translation by binding to an apical loop of domain IIId.
abstract: The hepatitis C virus (HCV) has a positive single-stranded RNA genome, and translation starts within the internal ribosome entry site (IRES) in a cap-independent manner. The IRES is well conserved among HCV subtypes and has a unique structure consisting of four domains. We used an in vitro selection procedure to isolate RNA aptamers capable of binding to the IRES domains III-IV. The aptamers that were obtained shared the consensus sequence ACCCA, which is complementary to the apical loop of domain IIId that is known to be a critical region of IRES-dependent translation. This convergence suggests that domain IIId is preferentially selected in an RNA-RNA interaction. Mutation analysis showed that the aptamer binding was sequence and structure dependent. One of the aptamers inhibited translation both in vitro and in vivo. Our results indicate that domain IIId is a suitable target site for HCV blockage and that rationally designed RNA aptamers have great potential as anti-HCV drugs.
authors.affiliation: Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
authors.forename: Kunio
authors.initials: K
authors.lastname: Kikuchi
authors.forename: Takuya
authors.initials: T
authors.lastname: Umehara
authors.forename: Kotaro
authors.initials: K
authors.lastname: Fukuda
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kuno
authors.forename: Tsunemi
authors.initials: T
authors.lastname: Hasegawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Nishikawa
mesh_terms: D020121:5' Untranslated Regions; D000998:Antiviral Agents / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D001483:Base Sequence; D001665:Binding Sites; D004252:DNA Mutational Analysis; D006367:HeLa Cells; D016174:Hepacivirus / Q000187:drug effects* / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D014176:Protein Biosynthesis / Q000187:drug effects*; D012367:RNA, Viral / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA
chemical_list: D020121:5' Untranslated Regions; D000998:Antiviral Agents; D009843:Oligoribonucleotides; D012367:RNA, Viral