Enhancing dna microarray detection limits using optical resonances from photonic crystal surfaces

Abstract

DNA microarrays are typically composed of micron-scale spots of specific genetic sequences attached to a glass microscope slide for the purpose of gene expression analysis. By replacing the glass microarray substrate with a photonic crystal surface, fluorescence enhancement effects can be utilized to improve the performance of the microarray. This work describes the design of photonic crystal surfaces by Rigorous Coupled-Wave Analysis to align guided-mode resonances with Cyanine-5 excitation and emission wavelengths at approximately 633 nm and 680 nm, respectively. The resonances from photonic crystals fabricated by nanoreplica molding are characterized by optical transmission measurements, and 20x enhancement from the fluorophore Cyanine-5 is demonstrated relative to a glass slide. Finally, a DNA microarray experiment probing the expression of genes in Glycine max (soybean) is performed, demonstrating the photonic crystal microarray detects 20% more genes from the sample than are detected by the glass microarray.