Multiplexed DNA Detection Using Spectrally Encoded Porous SiO2 Photonic Crystal Particles

Abstract

A particle-based multiplexed DNA assay based on encoded porous SiO₂ photonic crystal disks is demonstrated. A “spectral barcode” is generated by electrochemical etch of a single-crystal silicon wafer using a programmed current−time waveform. A lithographic procedure is used to isolate cylindrical microparticles 25 μm in diameter and 10 μm thick, which are then oxidized, modified with a silane linker, and conjugated to various amino-functionalized oligonucleotide probes via cyanuric chloride. It is shown that the particles can be decoded based on their reflectivity spectra and that a multiple analyte assay can be performed in a single sample with a modified fluorescence microscope. The homogeneity of the reflectivity and fluorescence spectra, both within and across the microparticles, is also reported.