Misra V K, Draper D E
Department of Chemistry, The Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.
J Mol Biol. 1999 Dec 17;294(5):1135-47. doi: 10.1006/jmbi.1999.3334.
Magnesium ions play a crucial role in the structural integrity and biological activity of nucleic acids. Experimental thermodynamic descriptions of Mg(2+) interactions with nucleic acids in solution have generally relied on the analyses of binding polynomials to estimate the energetic contributions of diffuse and site-bound ions. However, since ion binding is dominated by long-range electrostatic forces, such models provide only a phenomenological description of the experimental Mg(2+) binding data and provide little insight into the actual mechanism of the binding equilibria. Here, we present a rigorous theoretical framework based on the non-linear Poisson-Boltzmann (NLPB) equation for understanding diffuse ion interactions that can be used to interpret experimental Mg(2+) binding isotherms. As intuitively expected, in the NLPB model binding is simply the total accumulation of the ion around the nucleic acid. Comparing the experimental data to the calculated curves shows that the NLPB equation provides a remarkably accurate description of Mg(2+) binding to linear polynucleotides like DNA and poly(A x U) without any fitted parameters. In particular, the NLPB model explains two general features of magnesium binding; the strong dependence on univalent salt concentration, and its substantial anticooperativity. Each of these effects can be explained by changes in the Mg(2+) distribution around the polyion under different solution conditions. In order to more fully understand these different aspects of magnesium binding, the free energy of Mg(2+) binding, DeltaGMg, is calculated and partitioned into several salt-dependent contributions: the change in the electrostatic interaction free energy of the charges, DeltaDeltaGE.D (including Mg(2+)-phosphate, Mg(2+)-Mg(2+), Mg(2+)-Na(+), Na(+)-Na(+), Na(+)-phosphate interactions, and similar contributions for Cl(-)) and the cratic free energies of (re)organizing the MgCl2 and NaCl atmospheres, DeltaG(Mg)org and DeltaDeltaG(Na)org, respectively. For the systems studied here, DeltaGMg is strongly influenced by entropic free energy changes in the distributions of both NaCl and MgCl2, DeltaG(Mg)org and DeltaDeltaG(Na)org. From this analysis, we also raise the possibility that coions added with the magnesium salt might play an important role in the overall stability of nucleic acids under some conditions.
镁离子在核酸的结构完整性和生物活性中起着至关重要的作用。对溶液中镁离子与核酸相互作用的实验热力学描述通常依赖于对结合多项式的分析，以估计扩散离子和位点结合离子的能量贡献。然而，由于离子结合主要由长程静电力主导，此类模型仅对实验镁离子结合数据提供了唯象描述，几乎没有深入了解结合平衡的实际机制。在此，我们提出一个基于非线性泊松 - 玻尔兹曼（NLPB）方程的严格理论框架，用于理解扩散离子相互作用，该框架可用于解释实验镁离子结合等温线。正如直观预期的那样，在NLPB模型中，结合仅仅是离子在核酸周围的总积累。将实验数据与计算曲线进行比较表明，NLPB方程对镁离子与线性多核苷酸（如DNA和聚（A x U））的结合提供了非常准确的描述，且无需任何拟合参数。特别地，NLPB模型解释了镁离子结合的两个一般特征：对单价盐浓度的强烈依赖性及其显著的反协同性。这些效应中的每一个都可以通过不同溶液条件下聚离子周围镁离子分布的变化来解释。为了更全面地理解镁离子结合的这些不同方面，计算了镁离子结合的自由能ΔGMg，并将其划分为几个依赖于盐的贡献：电荷静电相互作用自由能的变化ΔΔGE.D（包括镁离子 - 磷酸根、镁离子 - 镁离子、镁离子 - 钠离子、钠离子 - 钠离子、钠离子 - 磷酸根相互作用，以及氯离子的类似贡献）以及重组氯化镁和氯化钠气氛的克拉提自由能，分别为ΔG(Mg)org和ΔΔG(Na)org。对于此处研究的系统，ΔGMg受到氯化钠和氯化镁分布中的熵自由能变化ΔG(Mg)org和ΔΔG(Na)org的强烈影响。通过此分析，我们还提出了在某些条件下与镁盐一起添加的共离子可能在核酸的整体稳定性中起重要作用的可能性。
