Bai Yu, Greenfeld Max, Travers Kevin J, Chu Vincent B, Lipfert Jan, Doniach Sebastian, Herschlag Daniel
Biophysics Program, Stanford University, Stanford, California 94305, USA.
J Am Chem Soc. 2007 Dec 5;129(48):14981-8. doi: 10.1021/ja075020g. Epub 2007 Nov 9.
The ion atmosphere around nucleic acids critically affects biological and physical processes such as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature of the ion atmosphere renders it difficult to characterize. The basic thermodynamic description of this atmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here we provide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emission spectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We have examined the influence of ion size and charge on ion occupancy around simple, well-defined DNA molecules. The relative affinity of monovalent and divalent cations correlates inversely with their size. Divalent cations associate preferentially over monovalent cations; e.g., with Na+ in 4-fold excess of Mg2+ (20 vs 5 mM), the ion atmosphere nevertheless has 3-fold more Mg2+ than Na+. Further, the dicationic polyamine putrescine2+ does not compete effectively for association relative to divalent metal ions, presumably because of its lower charge density. These and other BE-AES results can be used to evaluate and guide the improvement of electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widely used nonlinear Poisson Boltzmann (NLPB) theory and assess the applicability and precision of this theory. In the future, BE-AES in conjunction with improved theoretical models, can be applied to complex binding and folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from the overall thermodynamics of important biological processes.
核酸周围的离子氛围对诸如染色体包装、RNA折叠和分子识别等生物学和物理过程有着至关重要的影响。然而，离子氛围的动态特性使其难以被表征。对这种氛围的基本热力学描述，即对相关离子的类型和数量进行全面统计，一直难以实现。在此，我们首次对离子氛围进行了全面统计，利用缓冲液平衡和原子发射光谱法（BE-AES）准确地定量了阳离子的结合和阴离子的消耗。我们研究了离子大小和电荷对简单、明确的DNA分子周围离子占据情况的影响。单价和二价阳离子的相对亲和力与其大小呈反比。二价阳离子比单价阳离子更优先结合；例如，当Na+的浓度比Mg2+高4倍（20 mM对5 mM）时，离子氛围中的Mg2+数量仍比Na+多3倍。此外，二价多胺腐胺2+相对于二价金属离子而言，在结合竞争中效果不佳，大概是因为其电荷密度较低。这些以及其他BE-AES结果可用于评估和指导静电处理方法的改进。作为第一步，我们将BE-AES结果与广泛使用的非线性泊松玻尔兹曼（NLPB）理论的预测结果进行比较，并评估该理论的适用性和精度。未来，BE-AES结合改进的理论模型，可应用于核酸及其复合物的复杂结合和折叠平衡，以从重要生物学过程的整体热力学中解析出静电贡献。
