Model of the SARS-CoV-2 Virus for Development of a DNA-Modified, Surface-Enhanced Raman Spectroscopy Sensor with a Novel Hybrid Plasmonic Platform in Sandwich Mode

Abstract

The recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has posed a great challenge for the development of ultra-fast methods for virus identification based on sensor principles. We created a structure modeling surface and size of the SARS-CoV-2 virus and used it in comparison with the standard antigen SARS-CoV-2—the receptor-binding domain (RBD) of the S-protein of the envelope of the SARS-CoV-2 virus from the Wuhan strain—for the development of detection of coronaviruses using a DNA-modified, surface-enhanced Raman scattering (SERS)-based aptasensor in sandwich mode: a primary aptamer attached to the plasmonic surface—RBD-covered Ag nanoparticle—the Cy3-labeled secondary aptamer. Fabricated novel hybrid plasmonic structures based on “Ag mirror-SiO2-nanostructured Ag” demonstrate sensitivity for the detection of investigated analytes due to the combination of localized surface plasmons in nanostructured silver surface and the gap surface plasmons in a thin dielectric layer of SiO2 between silver layers. A specific SERS signal has been obtained from SERS-active compounds with RBD-specific DNA aptamers that selectively bind to the S protein of synthetic virion (dissociation constants of DNA-aptamer complexes with protein in the range of 10 nM). The purpose of the study is to systematically analyze the combination of components in an aptamer-based sandwich system. A developed virus size simulating silver particles adsorbed on an aptamer-coated sensor provided a signal different from free RBD. The data obtained are consistent with the theory of signal amplification depending on the distance of the active compound from the amplifying surface and the nature of such a compound. The ability to detect the target virus due to specific interaction with such DNA is quantitatively controlled by the degree of the quenching SERS signal from the labeled compound. Developed indicator sandwich-type systems demonstrate high stability. Such a platform does not require special permissions to work with viruses. Therefore, our approach creates the promising basis for fostering the practical application of ultra-fast, amplification-free methods for detecting coronaviruses based on SARS-CoV-2.

Tailoring of the Distribution of SERS-Active Silver Nanoparticles by Post-Deposition Low-Energy Ion Beam Irradiation

“…Low-energy techniques are favorable for the formation of the structures on various substrates, owing to the reduction of the substrate heating during the synthesis, allowing the modification of the structures deposited on the substrates vulnerable to heat, such as polymers and fabrics. The modification of the plasmonic structures via low-energy ion irradiation is of recent interest [ 29 , 30 , 31 ], as this technique allows altering the structure without the amorphization or ion-beam mixing [ 28 ].…”

New and Improved Nanomaterials and Approaches for Optical Bio- and Immunosensors

“…Mariia V. Samodelova et al developed a SERS-based sensor for detecting the SARS-CoV-2 virus using aptamers as recognizing molecules [ 9 ]. The formed sandwich complexes of the primary aptamer at the plasmonic surface, antigen-coated silver nanoparticles, and fluorophore-labeled secondary aptamer allowed an investigation of the impact of the distance between the SERS-active compound and the quencher and proposal of a protocol for high-sensitive detection.…”