Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH(+)·C Wobble Formation in Double-Stranded DNA.
Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH(+)·C Wobble Formation in Double-Stranded DNA.
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DOI：
10.1021/jacs.7b01830
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发表时间：
2017-06-07
影响因子：
15
通讯作者：
Herschlag D
中科院分区：
文献类型：
--
作者：
Allred BE;Gebala M;Herschlag D
核酸的高电荷密度和由此产生的离子气氛深刻地影响了RNA和DNA的构象景观及其与小分子和蛋白质的关联。静电理论已被应用于定量模拟周围的核酸和周围的离子气氛的影响的静电势，但这些模型的电位和测试的实验措施往往复杂的构象变化和多位点结合平衡，除其他因素外。我们寻求一个简单的系统来进一步测试静电理论的基本预测，并测量核酸静电场的能量后果。我们转向由贝维拉夸及其同事开发的DNA系统，该系统涉及质子作为配体，其结合伴随着内部AH+·C摆动对的形成[齐格弗里德，N.一、等人Biochemistry，2010，49，3225]。我们观察到质子亲和力与盐浓度的对数依赖性，分别为−0.96 ± 0.03和−0.52 ± 0.01，与一价和二价阳离子的预测一致，这些结果有助于澄清先前的结果，这些结果似乎与这些基本模型相冲突。引人注目的是，离子气氛含量的定量表明，二价阳离子优先失去一价阳离子后A·C质子化，提供了实验指示的优先本地化的更高电荷的阳离子的离子气氛的内壳。内部AH+·C摆动系统进一步使我们能够解析能量贡献，并提取质子化位置的静电势估计。结果显示，在20 mM Mg 2+时，DNA表面附近的电位远低于20 mM K+（−120 mV vs −210 mV）。这些值和差异与理论预测相似，并且在较高盐下电位大幅降低，也如预测的那样;然而，即使在1 M K+下，电位仍然很大，与常见假设相反。A·C质子化模块允许提取离子气氛的新特性，并提供静电计，允许测量核酸及其与蛋白质的复合物内的局部静电势和能量。
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.