title: Solution structure of an RNA duplex including a C-U base pair.
abstract: The formation of the C-U base pair in a duplex was observed in solution by means of the temperature profile of (15)N chemical shifts, and the precise geometry of the C-U base pair was also determined by NOE-based structure calculation. From the solution structure of the RNA oligomer, r[CGACUCAGG].r[CCUGCGUCG], it was found that a single C-U mismatch preferred being stacked in the duplex rather than being flipped-out even in solution. Moreover, it adopts an irregular geometry, where the amino nitrogen (N4) of the cytidine and keto-oxygen (O4) of the uridine are within hydrogen-bonding distance, as seen in crystals. To further prove the presence of a hydrogen bond in the C-U pair, we employed a point-labeled cytidine at the exocyclic amino nitrogen of the cytidine in the C-U pair. The temperature profile of its (15)N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C-U pair in the duplex.
authors.affiliation: Institute for Protein Research, Osaka University, Japan.
authors.forename: Y
authors.initials: Y
authors.lastname: Tanaka
authors.forename: C
authors.initials: C
authors.lastname: Kojima
authors.forename: T
authors.initials: T
authors.lastname: Yamazaki
authors.forename: T S
authors.initials: TS
authors.lastname: Kodama
authors.forename: K
authors.initials: K
authors.lastname: Yasuno
authors.forename: S
authors.initials: S
authors.lastname: Miyashita
authors.forename: A
authors.initials: A
authors.lastname: Ono
authors.forename: A
authors.initials: A
authors.lastname: Ono
authors.forename: M
authors.initials: M
authors.lastname: Kainosho
authors.forename: Y
authors.initials: Y
authors.lastname: Kyogoku
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009587:Nitrogen Isotopes; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013696:Temperature
chemical_list: D009587:Nitrogen Isotopes; D009843:Oligoribonucleotides; D012330:RNA, Double-Stranded