DNA Near Surfaces in Saline Solution: Theory for Design

描述（由申请人提供）： 该项目的目标是提供DNA在溶液中表面上的分子图像（理论），该图像与已知的热力学和结构数据一致，可用于考虑各种实验的设计优化问题。一个关键的问题是理解实验观察到的某些表面/溶液条件组合的表面附近的杂交亲和力和选择性的变化。 使用理论方法，包括分析理论和分子模拟，我们将量化一般的解决方案的影响（如筛选和溶剂化）和特定的影响之间的平衡，由于在确定DNA的热力学的解决方案中的表面和分子缔合。我们将用我们新的分析方法和模拟进行详细的计算，试图使最直接的 与最近和计划中的热力学、结构和生物物理实验进行可能的比较。将计算热力学特异性、检测灵敏度和核苷酸浓度与其溶液/表面环境（包括电场和盐浓度）的关系。测试用例 和应用程序已被选择，以最大限度地与现有的数据或合作，将产生数据的具体相关的DNA分析的表面上的重叠。

DESCRIPTION (provided by applicant): The goal of this project is to provide a molecular picture (theory) of DNA on surfaces in solution, which is consistent with known thermodynamic and structural data, which can be used to consider design optimization problems for a variety of experiments. A key question is understanding the experimentally observed changes in hybridization affinity and selectivity near surfaces for certain surface/solution condition combinations. Using theoretical methods, including analytic theory and molecular simulations, we will quantify the balance between general solution effects (such as screening and solvation) and specific effects due to the surface and molecular association in solutions in determining the thermodynamics of DNA. We will make detailed calculations with our new analytic methods and simulations in an attempt to make the most direct possible comparisons with recent and planned thermodynamic, structural and biophysical experiments. The relation of thermodynamic specificity, sensitivity of detection and the concentration of nucleotides to their solution/surface environment, including electric fields and salt concentration will be calculated. Test cases and applications have been chosen to maximize overlap with existing data or collaborations that will yield data of specific relevance to DNA analyses on surfaces.