title: Analysis of interaction between RNA aptamer and protein using nucleotide analogs.
abstract: Non-structural protein 3 (NS3) derived from Hepatitis C virus (HCV) is essential for viral proliferation and has two functional domains; trypsin-like serine protease and helicase. Recently we obtained three types of RNA aptamers (G9-I, -II and -III) bound to NS3 protease domain (delta NS3) by in vitro selection and confirmed their strong inhibition for protease activity. These aptamers have a common sequence, 5'-GA(A/U)UGGGAC-3', forming a loop structure by Mulfold secondary structure modeling. G9-I shows a three-way junction and G9-II and -III have four-way junction structures. To characterize the active structure of these aptamers, we applied modification interference analysis using nucleotide analogs and identified common important nucleotides in these three aptamers.
authors.affiliation: National Institute of Bioscience and Human Technology, AIST, MITI, Institute of Applied Biochemistry, University of Tsukuba.
authors.forename: S
authors.initials: S
authors.lastname: Sekiya
authors.forename: K
authors.initials: K
authors.lastname: Fukuda
authors.forename: J
authors.initials: J
authors.lastname: Hwang
authors.forename: N
authors.initials: N
authors.lastname: Kakiuchi
authors.forename: K
authors.initials: K
authors.lastname: Taira
authors.forename: I
authors.initials: I
authors.lastname: Kusakabe
authors.forename: S
authors.initials: S
authors.lastname: Nishikawa
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D016174:Hepacivirus / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012265:Ribonucleotides / Q000737:chemistry; D012697:Serine Endopeptidases / Q000737:chemistry / Q000378:metabolism; D017361:Viral Nonstructural Proteins / Q000737:chemistry* / Q000378:metabolism*; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D012367:RNA, Viral; D012265:Ribonucleotides; D012697:Serine Endopeptidases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases