Dimerization of Nucleic Acid Hairpins in the Conditions Caused by Neutral Cosolutes
Dimerization of Nucleic Acid Hairpins in the Conditions Caused by Neutral Cosolutes
复制标题
DOI：
10.1021/jp302170f
复制
发表时间：
2012-06-28
影响因子：
3.3
通讯作者：
Sugimoto, Naoki
中科院分区：
文献类型：
--
作者：
Nakano, Shu-ichi;Hirayama, Hidenobu;Sugimoto, Naoki
表征金属离子与RNA和DNA碱基对的结合对于理解它们对核酸结构的折叠和构象变化的能量贡献是重要的。在这项研究中，我们研究的平衡转变从发夹向二聚体的形成，诱导非特异性结合的金属离子。在高背景浓度的聚乙二醇（PEG）和几种有机小分子的存在下，发夹二聚化显着增强。简单的体积排阻效应和碱基对稳定性不能完全解释这种增加。我们发现，介电常数以及相关的二聚效率的条件下所造成的小分子醇和酰胺化合物以及PEG。发夹二聚化实验揭示了PEG通过降低溶液介电常数而不降低核酸结构的热力学稳定性来增强核酸与金属离子之间的结合亲和力的潜力。本文的结果有助于理解核酸折叠及其在有限阳离子可用性和细胞生理条件下在替代构象之间切换的能力。
Characterization of metal ion binding to RNA and DNA base pairs is important for understanding their energy contribution to the folding and conformational changes of nucleic acid structures. In this study, we examine the equilibrium shift from the hairpin toward the dimer formation, induced by nonspecifically bound metal ions. The hairpin dimerization is markedly enhanced in the presence of high background concentrations of poly(ethylene glycol) (PEG) and several small organic molecules. The simple volume exclusion effect and the base pair stability cannot entirely account for this increase. We find that the dielectric constant correlates well with the dimerization efficiency in the conditions caused by small alcohol molecules and amide compounds as well as PEG. The hairpin dimerization experiments reveal the potential of PEG for enhancing the binding affinity between nucleic acids and metal ions, by reducing the solution dielectric constant without decreasing the thermodynamic stability of nucleic acid structures. The results presented here contribute to the understanding of nucleic acid folding and its ability to switch between alternative conformations under the condition of limited cation availability and cellular physiology.