title: Design and NMR analysis of HDV ribozymes for structural investigation.
abstract: Three variants of minimized hepatitis delta virus (HDV) RNA ribozyme systems (Rz-1 to approximately Rz-3) (Fig. 1) were designed on the basis of the "pseudoknot" structure model and synthesized. Rz-1 is a cis-acting ribozyme system (a cleaved form, 56-mer) in which stem IV is deleted from the active domain of genomic HDV RNA. Rz-1 was uniformly labeled with stable isotopes, 13C and 15N. The 2D-NOESY and 2D-HSQC data for Rz-1 suggest that Rz-1 forms the pseudoknot structure and G38 which is opposite to the cleavage site makes a base-pair. Rz-2 is a trans-acting ribozyme system which consists of three RNA oligomer strands (substrate: 8-mer, the cytidine residue at the cleavage site is replaced by 2'-O-methylcytidine; enzyme: 16-mer plus 35-mer). Rz-3 is a ribozyme in which the three RNA strands of Rz-2 are connected. It turns out that Rz-3 forms an inactive structure with low cleavage activity (k(obs) = 0.009) and final cleavage yield (6%). Rz-3 has the highest cleavage activity at pH 5.5. The optimal activity at acidic pH is similar to that of the wild type ribozyme. We also synthesized and examined the activity and structure of Rz-4 (designed by Perrotta and Been) which consists of two RNA strands (1).
authors.affiliation: Faculty of Engineering, Yokohama National University, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Tanaka
authors.forename: T
authors.initials: T
authors.lastname: Hori
authors.forename: M
authors.initials: M
authors.lastname: Katahira
authors.forename: F
authors.initials: F
authors.lastname: Nishikawa
authors.forename: T
authors.initials: T
authors.lastname: Sakamoto
authors.forename: Y
authors.initials: Y
authors.lastname: Fukunaga
authors.forename: Y
authors.initials: Y
authors.lastname: Kurihara
authors.forename: S
authors.initials: S
authors.lastname: Nishikawa
authors.forename: S
authors.initials: S
authors.lastname: Uesugi
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D015195:Drug Design; D003698:Hepatitis Delta Virus / Q000235:genetics*; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis; D016337:RNA, Catalytic / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D009843:Oligoribonucleotides; D016337:RNA, Catalytic