DREAM Sentinels: Selection of aptamers that target viral variants with high specificity

To combat infectious diseases, this project will develop a versatile platform that has a much shorter turn-around time in generating a new capture molecule that specifically binds a new viral variant with high affinity. The investigators will further convert the captured molecule into a sensor for virus detection, and also turn it into a blocking molecule to neutralize the virus. The current selection process is time-consuming and labor intensive. The goal of this project is to develop a streamlined process that can rapidly target emerging viral variants with high affinity and specificity. The proposed work will advance our knowledge in virus sensing and therapeutics, establishing a quick-responsive biosensing/actuating All-In-One platform that can be easily adapted to address future infectious diseases. To increase impact, the investigators will work with local K-12 students in several outreach programs, with the goal of training the students to develop novel tools and encouraging them into a career path in science, technology, engineering and mathematics. Development of aptamer sensors and therapeutics is hampered by the bottleneck in the workflow of current gold standard SELEX (systematic evolution of ligands by exponential enrichment), especially the counterselection process, which aims to eliminate the candidates that bind structurally similar relatives of the target. While the counterselection is key to selecting highly specific aptamers against a specific target, it is a time-consuming, labor-intensive process that often fails. To address this issue, this project will combine SELEX workflow with a complementary high-throughput chip selection approach that can fully characterize the binding affinity, kinetics and specificity of each aptamer variant in the library against a number of structurally similar viral targets. This total-analysis approach not only bypasses the need to perform counterselections but also allows selection of aptamers that can differentiate structurally similar viral targets. The virus-binding aptamers will then be integrated with novel fluorogenic aptamer design to create new sensors that light up upon binding the target viruses and can be turned into virus inhibitors that bind and block the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from interacting with the angiotensin-converting enzyme 2 (ACE2) receptors on human host cells. The proposed research thus has both biosensing and bioactuation components that address new biological threats. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.