STTR Phase I: Cooperative Selection of Aptamer Pairs by Unlocking Parallel Enrichment Paths

The broader impact/commercial potential of this Small Business Technology Transfer (STTR) Phase I project will be to develop reliable technology for the production of aptamer pairs. Aptamers are core reagents in emerging markets, regarded as alternatives to monoclonal antibodies in therapeutics, diagnostics, and imaging. They possess several appealing qualities: Ease of in vitro synthesis, flexible modification, broad target ranges, reusability, and high thermal/chemical stability. The market value is expected to reach $5.4 billion by 2019 with a compound annual growth rate of 73.5%. One prominent negative aspect of aptamers in practical use is the lack of aptamer pairs. Pairing of monoclonal antibodies is fairly easily accomplished due to their tailor-made target binding sites. In contrast, aptamers are enriched from a random pool without such knowledge, so that it is impossible to assign the binding site of individual aptamers in pools with currently available methodologies. The proposed innovation in developing aptamers permits screening of pairs of aptamers directly from random pools. This type of direct selection from uncharacterized pools with the proposed simple workflow is a market driver to generate high revenue potential in the aptamers industry. This STTR Phase I project proposes to further develop and validate methodology for screening aptamer pairs from uncharacterized aptamer pools. Currently, available tools involve massive screening with multiple post-selection steps that heavily depend on instrumentation such as next generation sequencing, automated cloning tools, and bead-based multiplex binding assays. These "brute-force" strategies may eventually produce aptamer pairs, but they are time-consuming, expensive, and inefficient, perhaps explaining why few aptamer pairs exist today. The proposed aptamer pair selection methodology addresses this unmet need in the industry by allowing only pairs to survive during the selection process against free-solution targets. The homogeneous nature of the proposed selection platform enables this tool to be scalable and multiplexable. This technology has been reduced to practice in preliminary proof-of-principle experiments. During this NSF STTR Phase I project, the objective is to test the generalizability of the innovation by applying/improving the tool to find more DNA/RNA aptamer pairs against variety of protein targets.