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 microns in diameter and 10 microns 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.

Microfluidic Synthesis of Barcode Particles for Multiplex Assays

“…[ 38,39 ] These optically encoded particles could have also been achieved by incorporating quantum dots (QDs) and other spectrum tags into the particles (Figure 2 f) [40][41][42][43][44][45] or by constructing the particles with photonic crystal (PhC) structures (Figure 2 g,h). [46][47][48] A huge number of barcode particles with ID codes could be generated in theory based on these encoding strategies. This would render the barcode particles with a very high throughput capability for multiplex assays.…”

Sensitive fluorescent sensing for DNA assay

“…Silica NPs have been investigated intensively and have proved to be an ideal substrate, since they are very stable, chemically and thermally [86][87][88], and possess several advantages. Silica NPs are easy to separate via centrifugation during particle preparation, surface modification, and other solution-treatment processes.…”

Origin of the Optical Response of a Dye-doped Plasticized Poly(vinyl chloride)-based Photonic Crystal Ion Sensor

“…2 These behaviors depend on the relative refractive index between the base material of the PhC and the surrounding medium; thus, these materials can be used to create highly sensitive label-free optical sensors. These sensors detect surface refractive index changes 3 based on DNA-DNA hybridization, 4,5 and immuno-reaction at the PhC surface. 6 However, detecting small molecules, such as ions and enzyme reaction products, is generally difficult because high concentrations of such molecules are required to induce a refractive index change in the surrounding medium.…”