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 N-15 chemical shifts, and the precise g eometry of the C-U base pair was also determined by NOE-based structure cal culation. From the solution structure of the RNA oligomer, r[CCTACUCAGG] .r [CCUGCGUCG], it was found that a single C-U mismatch preferred being stacke d in the duplex rather than being flipped-out even in solution. Moreover, i t adopts an irregular geometry, where the amino nitrogen (N4) of the cytidi ne 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 n itrogen of the cytidine in the C-U pair. The temperature profile of its N-1 5 chemical shift showed a sigmoidal transition curve, indicating the presen ce of a hydrogen bond in the C-U pair in the duplex.