Paper BM+BI+BO+NC-TuA5
Nanoscale Determination of Conformation of a Polymeric Coating on Layered Surfaces

Tuesday, October 21, 2008, 3:00 pm, Room 309

With microarrays becoming a main tool in genetics and proteomics research, advancement of microarray technology through optimization of surface chemistries and probe-target interactions has become a major research area. Ideally, surface chemistries should provide functional groups for probe attachment, minimal nonspecific adsorption, stability to environmental changes, and probe activity after immobilization for efficient target capture. Among existing surface chemistries, three-dimensional coatings are the most promising in meeting these criteria. One such 3-D polymeric coating, copoly(DMA-NAS-MAPS), has been introduced previously for use in DNA and protein microarrays. The polymer self adsorbs to the surface and forms a hydrophilic coating, where each monomer has a specific function: Dimethylacrylamide(DMA) provides self-adsorption, 3-(trimethoxysilyl)propyl methacrylate(MAPS) increases the strength of the binding through covalent attachment to the surface with silane functionalities, and acryloyloxysuccinimide(NAS) provides functional groups to covalently bind the probes. Earlier studies with copoly(DMA-NAS-MAPS) have shown an improved performance in DNA hybridization efficiency when compared to existing organosilanization-based surface chemistries. With the aim of understanding the effect of the conformation of the polymer on the obtained results, we use an interferometric technique, Spectral Self-Interference Fluorescence Microscopy (SSFM) for characterization of the conformation, specifically swelling, of the polymer on oxide surfaces. SSFM is used in combination with a standard white light reflection spectroscopy technique, which allows for measuring the average optical thickness of a biolayer on the oxide surface, as well as the axial position of fluorescent markers with sub-nanometer accuracy. In this study, we covalently attach short strands of fluorescently labeled DNA (23mers) to the functional groups of the polymer and use them to probe conformational changes. Fluorophore heights obtained at single-stranded DNA spots indicate an axial increase of 8nm upon hydration. No increase, indicating no swelling, is measured on the epoxysilanized control surface. Furthermore, we measure the swelling using different probe molecules, and report interesting results that reveal information about the size dependent probe penetration in the polymer and the dependence of hybridization efficiency to the axial position of the probes with respect to the surface.