Improved Sensitivity of DNA Microarrays Using Photonic Crystal Enhanced Fluorescence

摘要

DNA microarrays are used to profile changes in genenexpression between samples in a high-throughput manner,nbut measurements of genes with low expressionnlevels can be problematic with standard microarray substrates.nIn this work, we expand the detection capabilitiesnof a standard microarray experiment using a photonicncrystal (PC) surface that enhances fluorescence observednfrom microarray spots. This PC is inexpensively andnuniformly fabricated using a nanoreplica molding technique,nwith very little variation in its optical propertiesnwithin- and between-devices. By using standard protocolsnto process glass microarray substrates in parallel withnPCs, we evaluated the impact of this substrate on a onecolornmicroarray experiment comparing gene expressionnin two developmental stages of Glycine max. The PCsnenhanced the signal-to-noise ratio observed from microarraynspots by 1 order of magnitude, significantly increasingnthe number of genes detected above substrate fluorescencennoise. PC substrates more than double the numbernof genes classified as differentially expressed, detectingnchanges in expression even for low expression genes. Thisnapproach increases the dynamic range of a surface-boundnfluorescence-based assay to reliably quantify small quantitiesnof DNA that would be impossible with standardnsubstrates.