title: Specific RNA aptamers to NS3 protease domain of hepatitis C virus.
abstract: In order to isolate RNA aptamers that bind specifically to NS3 protease domain (delta NS3) of hepatitis C virus, we carried out in vitro selection procedure using RNA pool that had 30 N random core region. After repeating nine cycles of selections and amplifications, a pool of RNAs that bind specifically to the delta NS3 were selected. A comparative analysis of 45 clones that were isolated from 9th cycle revealed three main classes that contain the conserved loop sequences GANUGGGAC. Moreover, the predominant class of aptamer (class I and III) appear to inhibit the protease activity efficiently.
authors.affiliation: Natioal Institute of Bioscience and Human Technology, Tsukuba Science City, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Fukuda
authors.forename: D
authors.initials: D
authors.lastname: Vishinuvardhan
authors.forename: S
authors.initials: S
authors.lastname: Sekiya
authors.forename: N
authors.initials: N
authors.lastname: Kakiuchi
authors.forename: K
authors.initials: K
authors.lastname: Shimotohno
authors.forename: P K
authors.initials: PK
authors.lastname: Kumar
authors.forename: S
authors.initials: S
authors.lastname: Nishikawa
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D016174:Hepacivirus / Q000201:enzymology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D011480:Protease Inhibitors / Q000737:chemistry / Q000494:pharmacology*; D020365:RNA Helicases; D012316:RNA Nucleotidyltransferases / Q000378:metabolism; D012697:Serine Endopeptidases; D013379:Substrate Specificity; D017361:Viral Nonstructural Proteins / Q000378:metabolism*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D009843:Oligoribonucleotides; D011480:Protease Inhibitors; D020365:RNA Helicases; D012316:RNA Nucleotidyltransferases; D012697:Serine Endopeptidases; D017361:Viral Nonstructural Proteins; C060028:NS3 protein, flavivirus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases