Spectroscopic investigation on the affinity of SARS-CoV-2 spike protein to gold nano-particles

Nano-size dependent protein corona formation by SARS-CoV-2 Omicron spike protein over gold nano-colloid and reversible aggregation

The adsorption process of SARS-CoV-2 Omicron spike protein to the nano-gold colloid surfaces was examined by monitoring the surface plasmon resonance (SPR) band shift of gold-nano particles ranging between diameters of d = 10–100 nm. The externally changed pH between 3 and 11 at 24.5 ± 0.4 °C initiated a reversible formation of the gold colloid aggregates, where formation/deformation of the aggregates were monitored by red/blue shift of the peak of the SPR band. There was no sign of reversible aggregation for d = 10, 15, and 20 nm gold colloids. A clear undulation of the peak shift corresponding to pH hopping between pH ~3 and ~11 was confirmed for colloidal d > 30 nm. This degree of the reversibility was compared to previously reported SARS-CoV-2 Alpha spike protein coated gold colloids. It was concluded that Omicron spike protein possesses a similar low affinity for gold nano particle d < 20 nm and possesses the higher affinity to the gold nanoparticles of d > 30 nm. However, the Omicron spike protein conformation was presumed to be more denatured compared to the SARS-CoV-2 Alpha spike protein. Our finding suggested Omicron spike protein was more acid labile/flexible.

DFT calculations to investigate silver ions as a virucide from SARS-CoV-2

The world has face the COVID-19 pandemic which has already caused millions of death. Due to the urgency in fighting the virus, we study five residues of free amino acids present in the structure of the SARS-CoV-2 spike protein (S). We investigated the spontaneous interaction between amino acids and silver ions (Ag⁺), considering these ions as a virucide chemical agent for SARS-CoV-2. The amino acid-Ag⁺ systems were investigated in a gaseous medium and a simulated water environment was described with a continuum model (PCM) the calculations were performed within the framework of density functional theory (DFT). Calculations related to the occupied orbitals of higher energy showed that Ag⁺ has a tendency to interact with the nitrile groups (-NH). The negative values of the Gibbs free energies show that the interaction process between amino acids-Ag⁺ in both media occurs spontaneously. There is a decrease in Gibbs free energy from the amino acid-Ag⁺ interactions immersed in a water solvation simulator.

Nano-size dependence in the adsorption by the SARS-CoV-2 spike protein over gold colloid

Gold nano-particles were coated with the spike protein (S protein) of SARS-CoV-2 and exposed to increasingly acidic conditions. Their responses were investigated by monitoring the surface plasmon resonance (SPR) band shift. As the external pH was gradually changed from neutral pH to pH ∼2 the peak of the SPR band showed a significant red-shift, with a sigmoidal feature implying the formation of the gold-protein aggregates. The coating of S protein changed the surface property of the gold enough to extract the coverage fraction of protein over nano particles, Θ, which did not exhibit clear nano-size dependence. The geometrical simulation to explain Θ showed the average axial length to be a = 7. 25 nm and b =8.00 nm when the S-protein was hypothesized as a prolate shape with spiking-out orientation. As the pH value externally hopped between pH∼3 and pH∼10, a behavior of reversible protein folding was observed for particles with diameters >30 nm. It was concluded that S protein adsorption conformation was impacted by the size (diameter, d) of a core nano-gold, where head-to-head dimerized S protein was estimated for d ≤ 80 nm and a parallel in opposite directions formation for d = 100 nm.

Biosensing Amplification by Hybridization Chain Reaction on Phase-Sensitive Surface Plasmon Resonance

Surface Plasmon Resonance (SPR) is widely used in biological and chemical sensing with fascinating properties. However, the application of SPR to detect trace targets is hampered by non-specific binding and poor signal. A variety of approaches for amplification have been explored to overcome this deficiency including DNA aptamers as versatile target detection tools. Hybridization chain reaction (HCR) is a high-efficiency enzyme-free DNA amplification method operated at room temperature, in which two stable species of DNA hairpins coexist in solution until the introduction of the initiator strand triggers a cascade of hybridization events. At an optimal salt condition, as the concentrations of H1 and H2 increased, the HCR signals were enhanced, leading to signal amplification reaching up to 6.5-fold of the detection measure at 30 min. This feature enables DNA to act as an amplifying transducer for biosensing applications to provide an enzyme-free alternative that can easily detect complex DNA sequences. Improvement of more diverse recognition events can be achieved by integrating HCR with a phase-sensitive SPR (pSPR)-tested aptamer stimulus. This work seeks to establish pSPR aptamer system for highly informative sensing by means of an amplification HCR. Thus, combining pSPR and HCR technologies provide an expandable platform for sensitive biosensing.