Improved Sensitivity of DNA Microarrays Using Photonic Crystal Enhanced Fluorescence

Abstract

DNA microarrays are used to profile changes in gene expression between samples in a high-throughput manner, but measurements of genes with low expression levels can be problematic with standard microarray substrates. In this work, we expand the detection capabilities of a standard microarray experiment using a photonic crystal (PC) surface that enhances fluorescence observed from microarray spots. This PC is inexpensively and uniformly fabricated using a nanoreplica molding technique, with very little variation in its optical properties within- and between-devices. By using standard protocols to process glass microarray substrates in parallel with PCs, we evaluated the impact of this substrate on a one-color microarray experiment comparing gene expression in two developmental stages of Glycine max. The PCs enhanced the signal-to-noise ratio observed from microarray spots by 1 order of magnitude, significantly increasing the number of genes detected above substrate fluorescence noise. PC substrates more than double the number of genes classified as differentially expressed, detecting changes in expression even for low expression genes. This approach increases the dynamic range of a surface-bound fluorescence-based assay to reliably quantify small quantities of DNA that would be impossible with standard substrates.

Photonic crystal-enhanced fluorescence through the extraction of dually polarized modes

“…These two mechanisms function independently, and can be multiplied to substantially enhance fluorescence [16]. Previous research has focused on enhancing extraction by designing a PC such that a specific polarized resonant mode overlaps with fluorophore emission [13][14][15]. In this Letter, we demonstrate that fluorescence can be further enhanced by coupling fluorophore emission with both polarized resonant modes simultaneously.…”

“…The leaky modes are highly localized within and in direct proximity to the PC surface during their finite lifetimes, which are associated with a high-energy density that can be observed at these locations in the form of enhanced electrical field intensity. Using a PC surface yields substantial enhancements because of the narrow bandwidth optical resonance that is designed to occur at specific combinations of illumination angles and excitation wavelengths [13,14]. The fluorescence enhancement achieved using a PC surface is attributed to two distinct mechanisms: enhanced excitation and enhanced extraction [7,8,15].…”

Enhanced sandwich immunoassay using antibody-functionalized magnetic iron-oxide nanoparticles for extraction and detection of soluble transferrin receptor on a photonic crystal biosensor

“…PC biosensor detection systems have various diagnostic and screening applications in DNA microarrays (Mathias et al, 2010), cancer cell analysis (Chen et al, 2013), virus detection (Shafiee et al, 2014) protein detection (Peterson et al, 2014a) and high throughput drug screening (Heeres and Hergenrother, 2011). Although current PC biosensor methodologies require a laboratory setting, a portable optical interface capable of converting a smartphone into a detection instrument was recently designed for the PC biosensor (Gallegos et al, 2013).…”

Photonic crystals: a versatile platform for optics-based biological detection

“…Photonic crystal surfaces can be inexpensively produced over large surface areas in many material systems, including flexible plastic [5], and have been used to produce high sensitivity label-free biosensors [6], substrates for fluorescence enhancement [7,8], and discrete frequency chemical imaging systems. This talk will summarize recent technical advancements and life science applications for photonic crystal surfaces and related detection instrumentation.…”