Isolation 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 that is specific for the (-)IRES domain I. After confirming the binding convergence in the ninth RNA pool, 42 RNA clones were sequenced and analyzed. Of these, 25 clones (Family-I) had the consensus sequence, 5'-UGGAUC-3', which is complementary to the apical loop of SL-E1, an important region for NS5B recognition. Another 13 clones (Family-II) had the consensus sequence, 5'-GAGUAC-3', which is complementary to the apical loop of SL-D1. Biochemical analyses are in progress to evaluate whether these RNA aptamers have the ability to inhibit HCV replication.
Konno
Keisuke
K
Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan.
Nishikawa
Satoshi
S
Hasegawa
Tsunemi
T
Fukuda
Kotaro
K
D020121:5' Untranslated Regions / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000302:isolation & purification; D001483:Base Sequence; D016384:Consensus Sequence; D016174:Hepacivirus / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*
D020121:5' Untranslated Regions; D052157:Aptamers, Nucleotide; D012367:RNA, Viral