Tanaka Y, Kojima C, Yamazaki T, Kyogoku Y, Miyashita S, Ono A, Kainosho M
Institute for Protein Research, Osaka University, Japan.
Nucleic Acids Symp Ser. 1997(37):271-2.
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.
C-U错配碱基对的结构仅在晶体中被报道过，在溶液中尚未有相关报道。在此，我们研究了溶液中双链RNA中C-U错配碱基对的结构和物理化学性质。RNA寡聚物r(CGACUCAGG)和r(CCUGCGUCG)形成了含有C-U碱基对的双链结构。基于核Overhauser效应（nOe）构建模型得出的C-U碱基对排列方式与晶体中的结构特征相似。模型显示，胞嘧啶的氨基质子和尿嘧啶的酮基氧处于氢键作用距离内，而尿嘧啶的亚氨基质子暴露于大量水中。通过监测非交换质子化学位移的熔解实验发现，包括C-U碱基对在内的所有碱基对同时发生熔解。这表明C-U错配碱基对有可能在双螺旋中与相邻碱基对堆积在一起，直到双链解链为单链。
