Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA,Journal of the American Chemical Society

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Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA
Journal of the American Chemical Society ( IF 14.4 ) Pub Date : 2017-05-10 00:00:00 , DOI: 10.1021/jacs.7b01830
Benjamin E. Allred ₁ , Magdalena Gebala ₁ , Daniel Herschlag _{1,

2,

3}

Affiliation

The high charge density of nucleic acids and resulting ion atmosphere profoundly influence the conformational landscape of RNA and DNA and their association with small molecules and proteins. Electrostatic theories have been applied to quantitatively model the electrostatic potential surrounding nucleic acids and the effects of the surrounding ion atmosphere, but experimental measures of the potential and tests of these models have often been complicated by conformational changes and multisite binding equilibria, among other factors. We sought a simple system to further test the basic predictions from electrostatics theory and to measure the energetic consequences of the nucleic acid electrostatic field. We turned to a DNA system developed by Bevilacqua and co-workers that involves a proton as a ligand whose binding is accompanied by formation of an internal AH⁺·C wobble pair [Siegfried, N. A., et al. Biochemistry, 2010, 49, 3225]. Consistent with predictions from polyelectrolyte models, we observed logarithmic dependences of proton affinity versus salt concentration of −0.96 ± 0.03 and −0.52 ± 0.01 with monovalent and divalent cations, respectively, and these results help clarify prior results that appeared to conflict with these fundamental models. Strikingly, quantitation of the ion atmosphere content indicates that divalent cations are preferentially lost over monovalent cations upon A·C protonation, providing experimental indication of the preferential localization of more highly charged cations to the inner shell of the ion atmosphere. The internal AH⁺·C wobble system further allowed us to parse energetic contributions and extract estimates for the electrostatic potential at the position of protonation. The results give a potential near the DNA surface at 20 mM Mg²⁺ that is much less substantial than at 20 mM K⁺ (−120 mV vs −210 mV). These values and difference are similar to predictions from theory, and the potential is substantially reduced at higher salt, also as predicted; however, even at 1 M K⁺ the potential remains substantial, counter to common assumptions. The A·C protonation module allows extraction of new properties of the ion atmosphere and provides an electrostatic meter that will allow local electrostatic potential and energetics to be measured within nucleic acids and their complexes with proteins.

中文翻译：

用双链DNA中的AH ⁺ ·C摆动形成确定离子气氛对核酸静电势和配体缔合的影响

核酸的高电荷密度和所产生的离子气氛深刻影响RNA和DNA的构象结构以及它们与小分子和蛋白质的结合。静电学理论已被用于对核酸周围的静电势和周围离子气氛的影响进行定量建模，但是除其他因素外，构象变化和多位点结合平衡常常使电势的实验测量和这些模型的测试变得复杂。我们寻求一个简单的系统，以进一步测试来自静电学理论的基本预测，并测量核酸静电场的能量结果。⁺ ·C摆动对[Siegfried，NA，等。生物化学，2010，49，3225]。与聚电解质模型的预测一致，我们观察到质子亲和性与单价和二价阳离子的盐浓度分别为-0.96±0.03和-0.52±0.01的对数依赖性，这些结果有助于弄清似乎与这些基本模型冲突的先前结果。令人惊讶的是，对离子气氛含量的定量表明，在A·C质子化后，二价阳离子比单价阳离子优先丢失，这为更高电荷的阳离子优先定位到离子气氛的内壳提供了实验指示。内部AH ⁺·C摆动系统进一步使我们能够解析能量的贡献，并提取质子化位置上的静电势的估计值。结果显示，在20 mM Mg ^2+处，DNA表面附近的电势远不如20 mM K ^+时（-120 mV对-210 mV）大。这些值和差异与理论上的预测相似，并且在较高盐含量下，电位也大大降低了，这也是如所预测的。但是，即使是1 MK ⁺与通常的假设相反，潜力仍然很大。A·C质子化模块可提取离子气氛的新特性，并提供静电计，可测量核酸及其与蛋白质的复合物中的局部静电势和能量。

更新日期：2017-05-27

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