Particle display: a new paradigm in high throughput discovery of ultra-high perfo

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DESCRIPTION (provided by applicant): Nucleic acid aptamers have shown great promise as the synthetic alternative to monoclonal antibodies in therapeutics, diagnostics, and R&D tools. Key advantages of aptamers comparing to antibodies include applicability to non-immunogenic targets, chemical and thermal stability, low production cost, and no batch-to-batch variation. Nevertheless, the potential of aptamers has not been fully realized due to the bottleneck in the discovery process: to date, the methods used to discover aptamers have been exclusively selection-based (i.e. SELEX). Unfortunately, these methods often fail to discover the highest performance aptamer in the starting library, due to a multitude of interfering factors such as library synthesis bias, PCR bias and non-specific binding. Furthermore, previous investigations suggest that these methods may discover DNA aptamers for only ~30% of the human proteome, greatly limiting aptamers' application scope. Previous innovations in the discovery process are all variants of SELEX and mainly focus on improving selection efficiency; in consequence, the fundamental aptamer performance issue has not yet been solved. The purpose of this SBIR project is to develop a screening-based method (referred as "Particle Display" or "PD" in this proposal) that overcomes the aptamer discovery barrier. We display each aptamer in the library on an aptamer particle (AP) at 105 copies, which allows us to use FACS to quantitatively measure the binding property of the aptamer on each AP in an ultra-high-throughput fashion. PD thus enables precise isolation of aptamers that pass a defined performance threshold. Moreover, we can use multi-color FACS to simultaneously measure multiple fluorescence wavelengths of the APs (each wavelength representing one binding property), and thus uniquely enable screening of multiple favorable binding properties such as affinity, specificity, and binding kinetics. The hypothesis of this project is that PD can overcome the limitations of conventional selection-based methods, and enable efficient discovery of the highest performance aptamers. In Phase I, we propose to first develop the PD platform for screen for high target affinity. We will then work to develop multi-color PD to simultaneously screen for multiple binding properties. In Phase II, we will use multi-color PD to screen for aptamer pairs to enable sandwich assays, to screen for application-ready aptamers in biological samples, and validate universal applicability of PD in different target types. At the end of phase II, we expect to have established the capability of Particle Display in developing high performance aptamers in a high throughput manner, which can serve various unmet needs in therapeutics, diagnostics, and life science R&D.