Solution Structure of an RNA Duplex Including a C−U Base Pair

• Published in: Biochemistry (Easton) 2000-06, Vol.39 (24), p.7074-7080
• Main Authors: Tanaka, Yoshiyuki, Kojima, Chojiro, Yamazaki, Toshio, Kodama, Takashi S, Yasuno, Kazuhiro, Miyashita, Shin, Ono, Akira (Mei), Ono, Akira (Sho), Kainosho, Masatsune, Kyogoku, Yoshimasa
• Format: Article
• Language: English
• Subjects: Base Pairing - genetics; Hydrogen Bonding; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular Sequence Data; Nitrogen Isotopes; Nucleic Acid Conformation; Nucleic Acid Denaturation; Oligoribonucleotides - chemical synthesis; Oligoribonucleotides - chemistry; RNA, Double-Stranded - chemistry; Temperature
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi000018m

The formation of the C−U base pair in a duplex was observed in solution by means of the temperature profile of 15N 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 15N chemical shift showed a sigmoidal transition curve, indicating the presence of a hydrogen bond in the C−U pair in the duplex.