DNA hybridization on silica microbeads that are physically adsorbed as arrays on glass surfaces

Detection of DNA hybridization was done on silica microbeads that were physically adsorbed onto glass surfaces. DNA oligonucleotide probes of approximately 20 mer size were immobilized on beads of 5 μm diameter after the microbeads were first silanized with 3-glycidoxypropyltrimethoxysilane. The suspension of silica microbeads in aqueous solution was spotted on the glass slides. After drying, the glass surface was washed with water and 1 × SSC buffer. Significant numbers of microbeads remained physically adsorbed onto the glass surfaces even after vigorous washing with buffer solution. After hybridization using approximately 200 mer PCR targets strands, the glass slides were scanned using a standard laser confocal fluorescence microscope microarray reader. The total time for completion of hybridization assays was less than 20 min for 100 nM samples of target oligonucleotide. The clinical utility of the method was demonstrated by detection of single base pair mutations in the survival motor neuron gene that is associated with the childhood disease Spinal Muscular Atrophy. The method proved to provide a readily adaptable strategy for immobilization of different probes in an array format, and provided for SNP detection on a disposable slide without cross contamination.