Isolation and characterization of RNA aptamers specific for the HCV minus-IRES domain I.
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.
Konno
Keisuke
K
Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan.
Fujita
Syusuke
S
Iizuka
Mana
M
Nishikawa
Satoshi
S
Hasegawa
Tsunemi
T
Fukuda
Kotaro
K
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
C541631:AP30 aptamer; D052157:Aptamers, Nucleotide; D012367:RNA, Viral; D012313:RNA