Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

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• 作者：Yu Bai ; Max Greenfeld ; Kevin J. Travers ; Vincent B. Chu ; Jan Lipfert ; Sebastian Doniach ; Daniel Herschlag
• 刊名：Journal of the American Chemical Society
• 出版年：2007
• 出版时间：December 5, 2007
• 年：2007
• 卷：129
• 期：48
• 页码：14981 - 14988
• 全文大小：176K
• 年卷期：v.129,no.48(December 5, 2007)
• ISSN：1520-5126

文摘

The ion atmosphere around nucleic acids critically affects biological and physical processessuch as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature ofthe ion atmosphere renders it difficult to characterize. The basic thermodynamic description of thisatmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here weprovide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emissionspectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We haveexamined 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 cationsassociate preferentially over monovalent cations; e.g., with Na⁺ in 4-fold excess of Mg²⁺ (20 vs 5 mM), theion 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 itslower charge density. These and other BE-AES results can be used to evaluate and guide the improvementof electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widelyused 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 bindingand folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from theoverall thermodynamics of important biological processes.