title: RNA aptamers targeted to domain II of hepatitis C virus IRES that bind to its apical loop region.
abstract: The internal ribosome entry site (IRES) is important for translation of hepatitis C virus (HCV) mRNA and has a unique RNA structure containing conserved domains I to IV. To investigate the function of domain II, we selected RNA aptamers that bind to domain II of HCV IRES by applying a simple and convenient selection method using a hybridized tag for fixing domain II RNA on magnetic beads instead of synthesizing long RNA. In addition, we employed surface plasmon resonance (SPR) technology to measure the binding affinity of each generation and to obtain detailed kinetic constants. The selected aptamers have a consensus sequence, 5'-UAUGGCU-3', which is complementary to the apical loop of domain II. The loop-loop interaction between the consensus sequence and domain II was confirmed by mutagenesis and nuclease mapping analyses. Binding affinities were dependent on the local structure containing the conserved sequence. The aptamers could inhibit IRES-dependent translation.
authors.affiliation: Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), 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: Joonsung
authors.initials: J
authors.lastname: Hwang
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: D001483:Base Sequence; D001665:Binding Sites / Q000502:physiology; D016503:Drug Delivery Systems / Q000379:methods*; D016174:Hepacivirus / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary / Q000235:genetics; D012335:RNA, Ribosomal / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D012335:RNA, Ribosomal; D012367:RNA, Viral