Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications,ACS Environmental Au

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Influence of 5-Halogenation on the Base-Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of Synthetic i-Motif Structures for DNA Nanotechnology Applications
ACS Environmental Au ( IF 6.7 ) Pub Date : 2022-08-03 , DOI: 10.1021/jasms.2c00137
M. T. Rodgers ₁ , Yakubu S. Seidu ₁ , E. Israel ₁

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DNA nanotechnology has been employed to develop devices based on i-motif structures. The protonated cytosine-cytosine base pairs that stabilize i-motif conformations are favored under slightly acidic conditions. This unique property has enabled development of the first DNA molecular motor driven by pH changes. The ability to alter the stability and pH transition range of such DNA molecular motors is desirable. Understanding how i-motif structures are influenced by modifications, and which modifications enhance stability and/or affect the pH characteristics, are therefore of great interest. Here, the influence of 5-halogenation of the cytosine nucleobases on the base pairing of protonated cytidine nucleoside analogue base pairs is examined using complementary threshold collision-induced dissociation techniques and computational methods. The nucleoside analogues examined here include the 5-halogenated forms of the canonical DNA and RNA cytidine nucleosides. Comparisons among these systems and to the analogous canonical base pairs previously examined enable the influence of 5-halogenation and the 2′-hydroxy substituent on the base pairing to be elucidated. 5-Halogenation of the cytosine nucleobases is found to enhance the strength of base pairing of DNA base pairs and generally weakens the base pairing for RNA base pairs. Trends in the strength of base pairing indicate that both inductive and polarizability effects influence the strength of base pairing. Overall, the present results suggest that 5-halogenation, and in particular, 5-fluorination and 5-iodination, provide effective means of stabilizing DNA i-motif conformations for applications in nanotechnology, whereas only 5-iodination is effective for stabilizing RNA i-motif conformations but the enhancement in stability is less significant.

中文翻译：

5-卤化对质子化胞苷核苷类似物碱基对碱基配对能量的影响：对 DNA 纳米技术应用中合成 i-基序结构稳定性的影响

DNA 纳米技术已被用于开发基于i- motif 结构的设备。稳定i-基序构象的质子化胞嘧啶-胞嘧啶碱基对在微酸性条件下是有利的。这种独特的特性使得开发出第一个由 pH 变化驱动的 DNA 分子马达成为可能。需要能够改变这种 DNA 分子马达的稳定性和 pH 过渡范围。了解我如何-基序结构受修饰的影响，因此哪些修饰增强了稳定性和/或影响pH特性，因此引起了人们的极大兴趣。在这里，使用互补阈值碰撞诱导解离技术和计算方法检查了胞嘧啶核碱基的 5-卤化对质子化胞苷类似物碱基对碱基配对的影响。此处检查的核苷类似物包括典型 DNA 和 RNA 胞苷核苷的 5 卤代形式。这些系统之间的比较以及与先前检查的类似规范碱基对的比较能够阐明 5-卤化和 2'-羟基取代基对碱基配对的影响。发现胞嘧啶核碱基的 5-卤化增强了 DNA 碱基对的碱基配对强度，并且通常削弱了 RNA 碱基对的碱基配对。碱基配对强度的趋势表明，感应效应和极化效应都会影响碱基配对强度。总的来说，目前的结果表明 5-卤化，特别是 5-氟化和 5-碘化，提供了稳定 DNA 的有效方法i -motif 构象在纳米技术中的应用，而只有 5-碘化对稳定 RNA i -motif 构象有效，但稳定性的增强不太显着。

更新日期：2022-08-03

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