(638f) Modeling DNA Hybridization On Surfaces for Improved Microarray Design

DNA microarrays are high throughput, parallel assays for determining which genes are present in a sample and the level of expression of those genes. They have been identified as a key technology in genomic sciences and emergent medical techniques. Despite their abundant use in research laboratories, microarrays have not been used in the clinical setting to the fullest potential due to the difficulty of obtaining reproducible results. Improved understanding of DNA hybridization at the molecular level is key to refining these devices. To this end, we have used a mesoscale model for DNA, which captures both the thermal and mechanical properties of the molecule, to investigate the factors affecting hybridization on surfaces to an extent not previously possible. After briefly describing the model, we will demonstrate how the thermodynamics of hybridization changes in the bulk compared to on a surface, how the crowding of probes on the surface affects hybridization efficiencies, and how targets in solution compete to bind with probes on the surface. We will also demonstrate possible strategies that can be used to enhance hybridization on the surface, including the effect of stretching probe molecules.