Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi Chuo-ku, 650-0047, Kobe, Japan.
Chembiochem. 2024 Jul 2;25(13):e202400276. doi: 10.1002/cbic.202400276. Epub 2024 Jun 16.
Living cells contain various types of organic cations that may interact with nucleic acids. In order to understand the nucleic acid-binding properties of organic cations of different sizes, we investigated the ability of simple organic cations to inhibit the RNA phosphodiester bond cleavage promoted by Mg, Pb, and RNA-cleaving serum proteins. Kinetic analysis using chimeric DNA-RNA oligonucleotides showed that the cleavage at ribonucleotide sites was inhibited in the presence of monovalent cations comprising alkyl chains or benzene rings. The comparison of the cleavage rates in the presence of quaternary ammonium and phosphonium ions indicated that the steric hindrance effect of organic cations on their binding to the RNA backbone is significant when the cation size is larger than the phosphate-phosphate distance of a single-stranded nucleic acid. The cleavage inhibition was also observed for ribonucleotides located in long loops but not in short loops of oligonucleotide structures, indicating less efficient binding of bulky cations to structurally constrained regions. These results reveal the unique nucleic acid-binding properties of bulky cations distinct from those of metal ions.
活细胞中含有各种类型的有机阳离子，这些阳离子可能与核酸相互作用。为了了解不同大小的有机阳离子与核酸结合的性质，我们研究了简单的有机阳离子抑制 Mg、Pb 和血清 RNA 切割蛋白促进的 RNA 磷酸二酯键断裂的能力。使用嵌合 DNA-RNA 寡核苷酸的动力学分析表明，在包含烷基链或苯环的单价阳离子存在下，核糖核苷酸位点的断裂受到抑制。季铵和鏻离子存在下的断裂速率比较表明，当阳离子尺寸大于单链核酸的磷酸-磷酸距离时，有机阳离子对其与 RNA 主链结合的空间位阻效应是显著的。这种断裂抑制也发生在寡核苷酸结构中的长环而不是短环中的核糖核苷酸上，表明较大的阳离子与结构受限区域的结合效率较低。这些结果揭示了大体积阳离子与金属离子不同的独特核酸结合性质。
