Simple DNA/RNA Probes for Protein Targets

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DESCRIPTION (provided by applicant): We describe an integrated approach for rapid discovery of small, structurally defined nucleic acid "probe" sequences that bind with high affinity and selectivity to a target of interest. Such targets are proteins, bio-terror agents, pathogenic organisms and viruses. The probes will be engineered into proprietary AlloSwitchTM indicators that respond rapidly to the presence of the target, giving rise to a fluorescent or luminescent signal. In this phase I project we propose to rapidly screen and isolate high-affinity combining probes (c-probes). We will use high throughput methods to isolate at least the known probe sequences specific for alpha-thrombin and platelet derived growth factor (PDGF) from a defined library containing billions of DNA sequences. Alternative c-probes for thrombin and PDGF will be sought in libraries that have a predefined secondary structure. In phase II, the approach will be expanded to include a wider variety of structural motifs and new targets. The targets for discovery of probes and creation of AlloSwitches will include proteins involved in clotting and thrombosis, and growth factors involved in wound healing, angiogenesis, and proliferative diseases. AlloSwitch based assays will assist in the discovery of small molecules that can be used for therapies to regulate the interactions of these proteins in blood. This stands in contrast to therapies based on aptamers or antibodies, which are difficult to protect from hydrolysis by enzymes in plasma. Establishing a highly efficient and rapid screening approach for short DNA/RNA probe discovery will accelerate the commercialization of our biosensor technology in other fields.