IONIC DISTRIBUTIONS IN POLYNUCLEOTIDE SOLUTIONS

生物聚合物与其分子间的强相互作用 解决方案环境对 这种大分子的结构和功能。这是 尤其是高电荷态的多核苷酸。然而， 无法完全解释溶剂化、静电作用 相互作用，以及盐分环境的贡献 生物聚电解质的建模是其中最引人注目的一个 该领域的缺点。这种环境的两个主要方面 建模将在拟议的研究中讨论。第一, 将进行的研究将提供一个严格的 了解替代方案的能力和局限性 描述溶剂的近似理论方法-- 介导的离子相互作用。第二，必要的信息，以 以核磁共振为对照，严格测试这些方法的预测 将开发实验数据，并进行测试 被处死。为了更好地做到这一点，基准模拟 模型原子与分子间溶剂相互作用的研究 水中的分子离子体系将首先按顺序进行 要解决对溶剂模型和模拟的依赖 程序，例如可能的截断。结果将提供 对目前在全原子中常用的技术进行必要的测试 复杂生物聚合物体系的建模和对生物聚合物的预测 这类问题的计算方便的近似理论 互动。同样的数据将为评估提供基础 来自模型的核磁共振自旋弛豫数据，从而使 可以对实际系统的模型进行评估，两者都是相对的 简单的盐溶液和DNA溶液。为了进一步澄清 DNA溶液中小离子行为的随机模拟 将继续进行DNA溶液动力学的研究，特别强调 关于DNA构象和灵活性在决定 在最近的核磁共振实验中观察到的。这一努力将既 阐明实验数据的信息内容和 就模型的相关性提供进一步的证据。 最后，我们将重点介绍计算的发展和理论 环境对生物多聚电解质的作用力。 所描述的研究的性能将提供明确的定义 现有模型的精确度和相关性的界限 理论方法和勾勒出可行的路线 多核苷酸溶液环境的处理 特别是生物聚合物，一般如此。

The strong mutual interaction between biopolymers and their solution environment exerts a widely appreciated influence on the structures and function of such macromolecules. This is particularly true of the highly charged polynucleotides. However, the inability to fully account for solvation, electrostatic interactions, and the contribution of a salt environment in the modelling of biopolyelectrolytes is one of the most conspicuous shortcomings in the area. Two major aspects of such environmental modelling will be addressed in the proposed studies. First, studies will be carried out that will provide a rigorous understanding of the abilities and limitations of alternative approximate theoretical approaches for the description of solvent- mediated ionic interactions. Second, the necessary information to rigorously test the predictions of such methods against NMR experimental data will be developed, and the tests will be executed. In order to do this incisively, benchmark simulation studies of solvent-mediated interactions for model atomic and molecular ionic systems in water will first be carried out in order to address the dependence on solvent model and on simulation procedures, such as potential truncation. The results will provide needed tests of the techniques now commonly employed in all-atom modelling of complex biopolymer systems and of the predictions of computationally convenient approximate theories for such interactions. The same data will provide a basis for evaluating NMR spin relaxation data from the models, so that the relevance of the models to real systems can be evaluated, both in relatively simple salt solutions and in DNA solutions. To further elucidate the small ion behavior in DNA solutions, the stochastic simulation of DNA solution dynamics will be pursued, with particular emphasis on the role of DNA conformation and flexibility in determining the observations in recent NMR experiments. This effort will both elucidate the informational content of the experimental data and provide further evidence regarding the relevance of models. Finally, we will focus on the computational development and theory for the environmentally induced forces on biopolyelectrolytes. The performance of the research described will provide well defined bounds on both the precision and relevance of available models and theoretical methods and delineate the viable routes for the treatment of the solution environment of polynucleotides, in particular, and biopolymers, in general.