Solution structure of an RNA duplex including a C-U base pair

Yoshiyuki Tanaka, Chojiro Kojima, Toshio Yamazaki, Takashi S. Kodama, Kazuhiro Yasuno, Shin Miyashita, Akira Ono, Masatsune Kainosho, Yoshimasa Kyogoku

Research output: Contribution to journalArticlepeer-review

27 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)7074-7080
Number of pages7
JournalBiochemistry
Volume39
Issue number24
DOIs
Publication statusPublished - 2000 Jun 20

ASJC Scopus subject areas

  • Biochemistry

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