Structure model and physicochemical properties of the C-U mismatch pair in the double stranded RNA in solution

Structure of the C-U mismatch pair was reported only in crystal but none in solution. Here we have studied the structure and physicochemical properties of the C-U mismatch pair in a double stranded RNA in solution. RNA oligomers r(CGACUCAGG) and r(CCUGCGUCG) form a double stranded structure with the C-U pair. The arrangement of the C-U pair derived from the model building based on nOe gives a similar structural feature to that in crystal. The modeling reveals that the amino-proton of cytidine and the keto-oxygen of uridine are located within hydrogen bonding distance, and the imino proton of uridine is exposed to bulk water. From the melting experiment which monitors chemical shifts of non-exchangeable protons, the melting of all the base-pairs including the C-U pair occurs simultaneously. This suggests the possibility where the C-U mismatch pair is stacked on the neighboring base-pairs in the double helix until the duplex is denatured to single strands.