RAPID: Aptamer-Linked Nano-Plasmon Sensor for Rapid Detection of SARS-CoV-2

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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been wreaking havoc around the globe, infecting more than 2 million people with COVID-19 and taking hundreds of thousands of lives to date. One of the major challenges in stopping the pandemic is the development of diagnostic tools for the rapid detection of the coronavirus at point-of-care in real time. Existing tests for active infections rely on the detection of virus genetic materials with amplification methods that often require long turn-around times in a centralized laboratory setup. The limited and delayed detection of SARS-CoV-2 infections so far has become the bottleneck for stopping the continued community transmission of the virus. In this RAPID application, the investigators will break this bottleneck by developing a novel nanomaterial-based sensor with the capability to detect virus proteins in real time. Validation of the method for detecting actual virus will allow fast screening and isolation of COVID-19 patients, critical for breaking the chain of transmission during current and future pandemics, including potential new waves of the SARS-CoV-2 after the end of the current quarantine. This research project will also provide training opportunities for both graduate and undergraduate students at the interface of physics, biology, and nanotechnology. Existing test for active SARS-CoV-2 infections relies on the detection of virus RNAs by the reverse transcription polymerase chain reaction method, which usually requires long turn-around times in a centralized laboratory setup. In order to break this bottleneck and to stop the pandemic, alternative approaches for fast virus detection are required. The investigators plan to develop aptamer-linked nano-plasmon sensors for real-time detection of virus proteins that are highly abundant in virus-infected cells, including the receptor-binding domain of the spike glycoprotein and the nucleocapsid protein. This novel approach combines several lines of technological advancements in nano- and bio-engineering: 1) the localized surface plasmon resonance coupling between two linked gold nanoparticles that is sensitive to their inter-particle distance; 2) single-stranded DNA or RNA aptamers with well-defined secondary and tertiary structures that can recognize specific proteins with strong binding affinities comparable to antibodies; and 3) naturally-occurring riboswitches comprised of an aptamer and a regulatory domains in gene regulation that can change conformations upon binding the target molecule by the aptamer domain. The principal investigator will utilize high-affinity aptamer sequences that have been reported in the literature to specifically recognize the targeted virus proteins and design conformationally “switchable” sequences by mimicking riboswitches and introducing regulatory sequences. Using the computationally designed sequences, the co-principal investigator will synthesize the nano-plasmon sensors and experimentally validate the functionality in recognizing the targeted virus proteins. Compared to antibodies used for sensor design, nucleotides are much easier and cheaper to synthesize, which is critical for producing testing kits in large quantities. Upon successful completion of the proposed research project, the developed sensors will offer an alternative approach for rapid detection of SARS-CoV-2 at the point-of-care in real time and can also be used as a scientific tool to study the virus infection mechanism. Moreover, funding of this application will foster student training at the interface of physics, biology, and nanotechnology.This project is jointly funded by the Chemical, Bioengineering, Environmental and Transport Systems (CBET) Division and the Established Program to Stimulate Competitive Research (EPSCoR).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.