In situ synthesis of DNA microarray on functionalized cyclic olefin copolymer substrate.

Thermoplastic materials such as cyclic-olefin copolymers (COC) provide a versatile and cost-effective alternative to the traditional glass or silicon substrate for rapid prototyping and industrial scale fabrication of microdevices. To extend the utility of COC as an effective microarray substrate, we developed a new method that enabled for the first time in situ synthesis of DNA oligonucleotide microarrays on the COC substrate. To achieve high-quality DNA synthesis, a SiO(2) thin film array was prepatterned on the inert and hydrophobic COC surface using RF sputtering technique. The subsequent in situ DNA synthesis was confined to the surface of the prepatterned hydrophilic SiO(2) thin film features by precision delivery of the phosphoramidite chemistry using an inkjet DNA synthesizer. The in situ SiO(2)-COC DNA microarray demonstrated superior quality and stability in hybridization assays and thermal cycling reactions. Furthermore, we demonstrate that pools of high-quality mixed-oligos could be cleaved off the SiO(2)-COC microarrays and used directly for construction of DNA origami nanostructures. It is believed that this method will not only enable synthesis of high-quality and low-cost COC DNA microarrays but also provide a basis for further development of integrated microfluidics microarrays for a broad range of bioanalytical and biofabrication applications.

Plasmonic Nanoparticles and Nanowires: Design, Fabrication and Application in Sensing.

This study involves two aspects of our investigations of plasmonics-active systems: (i) theoretical and simulation studies and (ii) experimental fabrication of plasmonics-active nanostructures. Two types of nanostructures are selected as the model systems for their unique plasmonics properties: (1) nanoparticles and (2) nanowires on substrate. Special focus is devoted to regions where the electromagnetic field is strongly concentrated by the metallic nanostructures or between nanostructures. The theoretical investigations deal with dimers of nanoparticles and nanoshells using a semi-analytical method based on a multipole expansion (ME) and the finite-element method (FEM) in order to determine the electromagnetic enhancement, especially at the interface areas of two adjacent nanoparticles. The experimental study involves the design of plasmonics-active nanowire arrays on substrates that can provide efficient electromagnetic enhancement in regions around and between the nanostructures. Fabrication of these nanowire structures over large chip-scale areas (from a few millimeters to a few centimeters) as well as FDTD simulations to estimate the EM fields between the nanowires are described. The application of these nanowire chips using surface-enhanced Raman scattering (SERS) for detection of chemicals and labeled DNA molecules is described to illustrate the potential of the plasmonics chips for sensing.