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. ? ?
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