A Comparison of Hybridization Efficiency between Flat Glassand Channel Glass Solid Supports

Two different solid supports, channel glass andflat glass, were compared for their affect on the sensitivityand efficiency of DNA hybridization reactions. Both solidsupports were tested using a set of arrayed, synthetic oligonucleotidesthat are designed to detect short insertion/deletion polymorphisms (SIDPs). A total of 13 differenthuman SIDPs were chosen for analysis. Capture probes,designed for this test set, were covalently immobilized onsubstrates. Hybridization efficiency was assessed usingfluorescently labeled stacking probes which were preannealedto the target and then hybridized to the supportboundoligonucleotide array; the hybridization pattern wasdetected by fluorescence imaging. It was found thatstructural features of nucleic acid capture probes tetheredto a solid support and the molecular basis of their interactionwith targets in solution have direct implications onthe hybridization process. Our results demonstrate thatchannel glass has a number of practical advantages overflat glass including higher sensitivity and a faster hybridizationrate.