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 comparison with recent and planned structural and biological/biochemical 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 application have been chosen to maximize overlap with existing data or collaborations in the other projects within the program that will yield data of specific relevance to our goal of producing a workable device for analysis.
