I-Corps: Gel-Tethered Molecular Beacons

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Molecular Beacons are self-reporting DNA hairpin probes that have been used in a variety of real-time detection applications. When they hybridize to an oligonucleotide target they fluoresce, thus removing the additional requirement of fluorescently labeling the target itself. Consequently, molecular beacons have found substantial scientific success over the past two decades. Molecular beacons have rarely been used in microarray-based applications. When tethered to solid substrates a large background emerges due to beacon-substrate interactions. This large background is absent when beacons are used un-tethered in an aqueous solution. Researchers have discovered that the signal-to-background ratio of molecular beacons can remain relatively high if they are tethered to a solid substrate by means of a hydrogel. This high performance has been attributed to the fact that the crosslink density of surface-patterned microgels gradually approaches infinity at the microgel-water interface, and the beacons conjugated to the microgel surface find themselves in as water-like an environment as possible. This project is designed to demonstrate the effective use of surface-tethered molecular beacons in clinically relevant DNA assays. Since their invention in the mid-1990's, molecular beacons and beacon-based assay platforms have served multiple scientific and commercial roles. However, one large applications area where beacons have rarely been used is in microarray technology where the oligonucleotide probes must be tethered to a solid surface. Site-specific surface tethering is important, because the nature of a specific probe and its target can be identified by position rather than by fluorophore color. Thousands of discrete surface positions can be interrogated simultaneously whereas the practical number of different fluorophores is less than ten. Applications involving the rapid identification of bacterial strains responsible for a broad range of different infections, the ability to simultaneously probe for tens or hundreds of genes can have substantial impact in health-care settings has the potential to be enhanced through the results of this project.