Evanescent field enhanced fluorescence on a photonic crystal surface

Photonic crystal (PC) surfaces have been demonstrated to be a compelling platform for improving the sensitivity of surface-based fluorescent assays used in disease diagnostics and life science research. PCs can be engineered to support optical resonances at specific wavelengths at which strong electromagnetic fields are utilized to enhance the intensity of surface-bound fluorophore excitation. Meanwhile, the leaky resonant modes of PCs can be used to direct emitted photons within a narrow range of angles for more efficient collection by a fluorescence detection system. The multiplicative effects of enhanced excitation and enhanced photon extraction combine to provide improved signal-to-noise ratios for detection of fluorescent emitters, which in turn can be used to reduce the limits of detection of low concentration analytes, such as disease biomarker proteins. Fabrication of PCs using inexpensive manufacturing methods and materials that include replica molding on plastic and nano-imprint lithography on quartz substrates result in devices that are practical for single-use disposable applications. In this dissertation I will address design, fabrication and characterization of PCs that employ the guided mode resonance effect to enhance fluorescence detection in the context of molecular diagnosis and gene expression analysis though the use of PC surfaces. A PC that can enhance the emission from multiple fluorescent species on its surface will be demonstrated. This capability is desirable in experiments using multiple fluorophores within a single imaged area like DNA microarrays. I will also demonstrate the design and fabrication of a PC on a low autofluorescence quartz substrate. This new quartz-based PC is shown to further lower the limits of detection of analytes and improve the signal-to-noise ratio. For the first time, a PC coupled to an optical cavity will be demonstrated. A metal layer added to the bottom of a PC forming an optical cavity will be shown to further improve the signal-to-noise ratio of fluorescence detection by a factor of 6x compared to detection on a PC without an underlying cavity. Finally a new photonic crystal enhanced fluorescence detection technique will be demonstrated, where fluorophores will be imaged on the surface of the PC while it acts as a feedback reflector of an external cavity laser. This new detection scheme will not only ensure optimal on-resonance coupling even in the presense of variable device parameters and variations in the density of surface-adsorbed capture molecules but also give ~10x increase in the electromagnetic enhancement factor compared to ordinary photonic crystal enhanced fluorescence.