Net-Shaped DNA Nanostructures Designed for Rapid/Sensitive Detection and Potential Inhibition of the SARS-CoV-2 Virus

Neha Chauhan, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Yanyu Xiong, Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Shaokang Ren, Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Abhisek Dwivedy, Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Nicholas Magazine, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803, United States.
Lifeng Zhou, Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Xiaohe Jin, Atom Bioworks Inc., Cary, North Carolina 27513, United States.
Tianyi Zhang, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803, United States.
Brian T. Cunningham, Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.
Sherwood Yao, Atom Bioworks Inc., Cary, North Carolina 27513, United States.
Weishan Huang, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, Louisiana 70803, United States.
Xing Wang, Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

Document Type

Article

Publication Date

7-26-2022

Abstract

We present a net-shaped DNA nanostructure (called "DNA Net" herein) design strategy for selective recognition and high-affinity capture of intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild-type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers release fluorescence signals upon virus binding that are easily read with a handheld fluorimeter for a rapid (in 10 min), simple (mix-and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼$1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1 × 10-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

Publication Source (Journal or Book title)

Journal of the American Chemical Society

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