DNA Near Surfaces in Saline Solution: Theory for Design

描述（由申请人提供）：本项目的目标是提供一个分子图像（理论）的DNA表面上的溶液，这是符合已知的热力学和结构数据。我们将用我们的新方法进行详细的计算，试图与最近和计划中的热力学，结构和生物物理实验进行最直接的比较。我们将考虑核苷酸的热力学溶解度，结合和允许构象与其溶液环境和盐浓度的关系。一个关键的问题是理解实验观察到的可能性增加的亲和力和增加的选择性附近的某些表面/溶液条件组合的表面。使用理论方法，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。这项工作的一个目标是开发和应用新的理论技术来解决溶剂化/构象相关的设计问题的寡核苷酸覆盖的表面。测试案例和应用程序的选择是为了最大限度地与现有数据或合作重叠，从而产生与表面DNA分析特定相关的数据。

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. We will make detailed calculations with our new methods in an attempt to make the most direct possible comparisons with recent and planned thermodynamic, structural and biophysical experiments. We will consider the relation of thermodynamic solubilities, binding and allowed conformations of nucleotides to their solution environment and salt concentration. A key question is understanding the experimentally observed possibility of both increased affinity and increased selectivity near surfaces for certain surface/solution condition combinations. Using theoretical methods, 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. A goal of this work is the development and application of new theoretical techniques to solve solvation/conformation related design problems of oligonucleotide covered surfaces. 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.