title: Formation of sheared G:A base pairs in an RNA duplex modelled after ribozymes, as revealed by NMR.
abstract: The thermal stability and structure of an RNA duplex, r(GGACGAGUCC)2, the base sequence of which was modelled after both a hammerhead ribozyme and a lead ribozyme, were studied by CD and NMR. We previously demonstrated that the corresponding DNA duplex, d(GGACGAGTCC)2, formed unique 'sheared' G:A base pairs, where an amino proton, instead of an imino proton, of G is involved in the hydrogen bonding, and G and A bases are arranged 'side by side' instead of 'head to head' (Nucleic Acids Res. (1993) 21, 5418-5424). CD melting profiles showed that the RNA duplex is thermally more stable than the corresponding DNA duplex. NMR studies revealed that sheared G:A base pairs are formed in the RNA duplex, too, although the overall structure of the RNA is the A form, which differs from the B form taken on by the corresponding DNA. A model building study confirmed that sheared G:A base pairs can be accommodated in the double helical structure of the A form. A difference between the RNA and DNA duplexes in the stacking interaction involving G:A mismatch bases is also suggested. The demonstration that sheared G:A base pairs can be formed not only in DNA but also in RNA suggests that this base pairing plays an important role regarding the RNA structure.
authors.affiliation: Department of Bioengineering, Faculty of Engineering, Yokohama National University, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Katahira
authors.forename: M
authors.initials: M
authors.lastname: Kanagawa
authors.forename: H
authors.initials: H
authors.lastname: Sato
authors.forename: S
authors.initials: S
authors.lastname: Uesugi
authors.forename: S
authors.initials: S
authors.lastname: Fujii
authors.forename: T
authors.initials: T
authors.lastname: Kohno
authors.forename: T
authors.initials: T
authors.lastname: Maeda
mesh_terms: D000225:Adenine; D001482:Base Composition; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004355:Drug Stability; D006147:Guanine; D006358:Hot Temperature; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009843:Oligoribonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D016337:RNA, Catalytic / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D016337:RNA, Catalytic; D006147:Guanine; D012313:RNA; D004247:DNA; D000225:Adenine