Horowitz Eric D, Hud Nicholas V
School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
J Am Chem Soc. 2006 Dec 6;128(48):15380-1. doi: 10.1021/ja065339l.
Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of RNA and DNA intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pi-pi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2',5'-linked RNA. Proflavine was found to bind 2',5' RNA with an association constant 25-fold greater than that measured for standard, 3',5'-linked RNA. In contrast, ethidium binds 2',5' RNA less favorably than standard RNA.
尽管进行了40多年的物理研究，但关于RNA和DNA嵌入的能量学仍存在一些基本问题。核酸双链在嵌入时的剧烈解旋立即表明，核酸主链在决定嵌入自由能方面应发挥重要作用。然而，鉴于与嵌入相关的相互交织的能量学（例如，π-π堆积和溶剂效应），主链对嵌入自由能的贡献难以评估。荧光滴定法用于测定两种已知嵌入剂（原黄素和溴化乙锭）与双链2',5'-连接的RNA的缔合常数。发现原黄素与2',5'-连接的RNA结合的缔合常数比标准的3',5'-连接的RNA测得的缔合常数大25倍。相比之下，溴化乙锭与2',5'-连接的RNA的结合不如标准RNA有利。
