title: Selection of RNA aptamers that bind specifically to the NS3 protease of hepatitis C virus.
abstract: The RNA genome of human hepatitis C virus (HCV) is translated into a large precursor polyprotein. The NS3 protease of HCV has a crucial role in the processing of the polyprotein into functional viral proteins. We have used an in vitro genetic-selection strategy to isolate high-affinity RNA aptamers that bind to the NS3 protein, especially to its protease domain. Starting from a RNA pool that had a random sequence core of 12-18 nucleotides, aptamers that bind specifically to the NS3 protein were selected after 10 rounds of selection and amplification. A single aptamer, 10G-1, was found predominantly (71%) in the selected pool. This aptamer could bind to the NS3 protein with a binding constant of 650 nM and inhibit the proteolytic activity in vitro. By phosphate-modification-interference analysis we showed that the phosphate residues that are critical for the binding of 10G-1 to NS3 lie within the selected regions of the aptamer and that binding involves electrostatic contacts with the phosphates of regions G28-U34 and A47-A55. The NS3-binding region in 10G-1 can serve as a basis for designing more potential inhibitors of the NS3 protein.
authors.affiliation: National Institute of Bioscience and Human Technology, AIST, Tsukuba Science City, Ibaraki, Japan.
authors.forename: P T
authors.initials: PT
authors.lastname: Urvil
authors.forename: N
authors.initials: N
authors.lastname: Kakiuchi
authors.forename: D M
authors.initials: DM
authors.lastname: Zhou
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 / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D017931:DNA Primers / Q000235:genetics; D015195:Drug Design; D016174:Hepacivirus / Q000187:drug effects / Q000201:enzymology* / Q000235:genetics*; D006801:Humans; D008024:Ligands; D058619:Maltose-Binding Proteins; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D012689:Sequence Homology, Nucleic Acid; D012697:Serine Endopeptidases / Q000235:genetics / Q000378:metabolism*; D015842:Serine Proteinase Inhibitors / Q000494:pharmacology; D055672:Static Electricity; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D002352:Carrier Proteins; D017931:DNA Primers; D008024:Ligands; D058619:Maltose-Binding Proteins; D010710:Phosphates; D012367:RNA, Viral; D011993:Recombinant Fusion Proteins; D012697:Serine Endopeptidases; D015842:Serine Proteinase Inhibitors; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases