Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan.
Frontier Institute for Biomolecular Engineering Research (FIBER) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan.
J Phys Chem B. 2019 Sep 12;123(36):7687-7694. doi: 10.1021/acs.jpcb.9b06074. Epub 2019 Aug 29.
The DNA-binding properties of large cations differ from those of metal ions due to steric exclusion from base-paired regions. In this study, the thermal stability of DNA secondary structures, including duplexes, internal loops, bulge loops, hairpin loops, dangling ends, and G-quadruplexes, was investigated in the presence of cations of different sizes. Large cations, such as tetrabutylammonium and tetrapentylammonium ions, reduced the stability of fully matched duplexes but increased the stability of duplexes with a long loop. The cations also increased the stability of G-quadruplexes with a long loop, and the degree of stabilization was greater for low-stability G-quadruplexes. Analysis of the salt concentration dependence indicates that large cations bind to the loop nucleotides, leading to counteracting the destabilization effect on base pairing. It is likely that binding occurs when loop nucleotides are sufficiently flexible to allow for greater accessibility for large cations. These results provide insight into nucleic acid interactions with large cationic molecules and suggest a potential method for stabilizing noncanonical DNA structures under intracellular conditions.
大离子的 DNA 结合性质与金属离子不同，因为它们会受到碱基配对区域的空间排斥。在这项研究中，研究了不同大小的阳离子存在时 DNA 二级结构（包括双链体、内环、凸起环、发夹环、悬垂末端和 G-四链体）的热稳定性。大离子，如四丁基铵和四戊基铵离子，降低了完全匹配双链体的稳定性，但增加了长环双链体的稳定性。这些阳离子还增加了长环 G-四链体的稳定性，并且对于低稳定性的 G-四链体，稳定化程度更大。对盐浓度依赖性的分析表明，大离子结合到环核苷酸上，从而抵消了碱基配对的去稳定化效应。当环核苷酸具有足够的灵活性以允许大离子更大的可及性时，可能会发生结合。这些结果深入了解了核酸与大阳离子分子的相互作用，并提出了一种在细胞内条件下稳定非规范 DNA 结构的潜在方法。
