Solution structure of an RNA duplex including a C-U base pair.
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.
Tanaka
Y
Y
Institute for Protein Research, Osaka University, Japan.
Kojima
C
C
Yamazaki
T
T
Kodama
T S
TS
Yasuno
K
K
Miyashita
S
S
Ono
A
A
Ono
A
A
Kainosho
M
M
Kyogoku
Y
Y
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
D009587:Nitrogen Isotopes; D009843:Oligoribonucleotides; D012330:RNA, Double-Stranded