Investigation of SARS-CoV-2 nucleocapsid protein interaction with a specific antibody by combined spectroscopic ellipsometry and quartz crystal microbalance with dissipation

Detailed evaluations of the antigen and antibody interaction rate and strength of the immune complex formed are very important for medical and bioanalytical applications. These data are crucial for the development of sensitive and fast immunosensors suitable for continuous measurements. Therefore, combined spectroscopic ellipsometry (SE) and quartz crystal microbalance with dissipation (QCM-D) technique (SE/QCM-D) was used for the evaluation: (i) of covalent immobilization of SARS-CoV-2 nucleocapsid protein (SCoV2-N) on QCM-D sensor disc modified by self-assembled monolayer based on 11-mercaptoundecanoic acid and (ii) interaction of immobilized SCoV2-N with specific polyclonal anti-SCoV2-N antibodies followed by immune complex formation process. The results show that the SCoV2-N monolayer is rigid due to the low energy dissipation registered during the QCM-D measurement. In contrast, the anti-SCoV2-N layer produced after interaction with the immobilized SCoV2-N formed a soft and viscous layer. It was determined, that the sparse distribution of SCoV2-N on the surface affected the spatial arrangement of the antibody during the formation of immune complexes. The hinge-mediated flexibility of the antibody Fab fragments allows them to reach the more distantly located SCoV2-N and establish a bivalent binding between proteins in the formed SCoV2-N/anti-SCoV2-N complex. It was noted that the SE/QCM-D method can provide more precise quantitative information about the flexibility and conformational changes of antibody during the formation of the immune complex on the surface over time.

Hybrid Tamm-surface plasmon polariton mode for highly sensitive detection of protein interactions

The total internal reflection ellipsometry (TIRE) method was used for the excitation and study of the sensitivity properties of the hybrid Tamm plasmon polariton - surface plasmon polariton (TPP-SPP) and single surface plasmon resonance (SPR) modes of the GCSF receptor immobilization. Additionally, the optimized sensitivity of the hybrid TPP-SPP mode was investigated and compared with the single SPR mode when the BSA proteins formed a layer on the gold surface. The dispersion relations for the hybrid TPP-SPP and single SPR modes were used to explain the enhanced sensitivity of the ellipsometric parameters for the hybrid TPP-SPP mode over the conventional SPR. The SPP component (δΔ_h-SPP/δλ=53.9°/nm) of the hybrid TPP-SPP mode was about 6.4 times more sensitive than single SPR (δΔ_SPR/δλ=8.4°/nm) for the BSA protein layer on the gold film. It was found that the sensitivity of the hybrid plasmonic mode can be made controllable by using the strong coupling effect between the TPP and SPP components. The strong coupling regime reduces absorption and scattering losses of the metal for the SPP component in the hybrid TPP-SPP mode and, as a result, narrows the plasmonic resonance.

Influence of the graphene layer on the strong coupling in the hybrid Tamm-plasmon polariton mode

The total internal refection ellipsometry (TIRE) method was used for the generation and study of the hybrid TPP-SPP mode on a photonic crystal structure with a thin layer of silver and graphene/PMMA. Raman spectroscopy showed a consistent monolayer graphene present on the Ag layer. Recent studies have also shown that TPP and SPP components in the hybrid plasmonic mode is sensitive to the variation of coupling strength due to presence of the graphene monolayer. The decrease of the TPP and SPP dip components in the TPP-SPP hybrid mode can be explained by the changes of the conductivity of the silver layer due to the presence of this additional graphene/PMMA structure, which results in the non-optimal resonance conditions for the hybrid plasmonic mode. The modified positions of the TPP and SPP components in the wavelength spectra when compared to their original, separate excitations, indicates a strong coupling regime. The design of these hybrid plasmonic/graphene-based nanostructures has attractive capabilities for the development of advanced optical sensors and integrated optical circuit technologies.

Evaluation of affinity sensor response kinetics towards dimeric ligands linked with spacers of different rigidity: Immobilized recombinant granulocyte colony-stimulating factor based synthetic receptor binding with genetically engineered dimeric analyte derivatives

The modelling of protein-protein binding kinetics is important for the development of affinity-sensors and the prediction of signaling protein based drug efficiency. Therefore, in this research we have evaluated the binding kinetics of several genetically designed protein models: (i) three different ligands based on granulocyte colony-stimulating factor GCSF homo-dimeric derivatives linked by differed by linkers of different length and flexibility; (ii) an antibody-like receptor (GCSF-R) based on two GCSF-receptor sites immobilized to Fc domains, which are common parts of protein structures forming antibodies. Genetically engineered GCSF-R is similar to an antibody because it, like the antibody, has two binding sites, which both selectively bind with GCSF ligands. To design the affinity sensor model studied here, GCSF-R was immobilized on a thin gold layer via self-assembled monolayer conjugated with Protein-G. Binding kinetics between immobilized GCSF-R and all three different recombinant GCSF-based homo-dimeric derivatives were evaluated by total internal reflection ellipsometry. Association constants were determined by fitting mathematical models to the experimental data. It was clearly observed that both (i) affinity and (ii) binding kinetics depend on the length and flexibility of the linker that connects both domains of a GCSF-based ligand. The fastest association between immobilized GCSF-R and GCSF-based ligands was observed for ligands whose GCSF domains were interconnected by the longest and the most flexible linker. Here we present ellipsometry-based measurements and models of the interaction kinetics that advance the understanding of bidentate-receptor-based immunosensor action and enables us to predict the optimal linker structure for the design of GCSF-based medications.

Hybrid Tamm-surface plasmon polaritons mode for detection of mercury adsorption on 1D photonic crystal/gold nanostructures by total internal reflection ellipsometry

Spectroscopic ellipsometry was used for the generation and study of the hybrid TPP-SPP mode as a sensor probe for the real-time formation of amalgam structures on the surface of a plasmon active gold layer. The Au/Hg amalgam formation features and the mercury atoms' penetration into the gold layer were determined by means of the experimental TIRE data and a regression analysis of a multi-layer model containing the index-profile amalgam layer. The hybrid TPP-SPP mode behavior of the coupled excitations provided more information about the mercury atoms' penetration into the gold layer than the single TPP and SPP resonances did. The present study demonstrated the possibility of using the hybrid TPP-SPP mode to design advanced optical gas sensor technologies.

Compact high-sensitivity potentiometer for detection of low ion concentrations in liquids

The compact potentiometer, based on an electronic circuit protected from electrostatic and electromagnetic interference, was developed for the measurement of low ion concentrations in liquids. The electronic circuit of the potentiometer, consisting of analogous and digital parts, enables the measurement of fA currents. This makes it possible to perform reliable measurements of ion concentrations in liquids that are as small as 10^-8-10^-7M. The instrument was tested using electrodes that were selective for tetraphenylphosphonium (TPP⁺) ions. It was demonstrated that the characteristic response time of the potentiometer electronic circuit to changes in the concentration of these ions in a liquid was in the order of 10 s. An investigation of TPP⁺ absorption by baker yeast has shown that this device can be successfully used for long term (several hours) measurements with zero signal drift, which was about 1 μV/s. Finally, due to the small dimensions of the electronic circuit (7.5 × 2 × 1.5 cm), this potentiometer can be easily installed at a large apparatus in the laboratory condition (≈25 °C), such as high pulsed electrical generators of magnetic fields that are used in electroporation studies of biological cells.

Tunable Bloch surface waves in anisotropic photonic crystals based on lithium niobate thin films

We present an original type of one-dimensional photonic crystal that includes one anisotropic layer made of a lithium niobate thin film. We demonstrate the versatility of such a device sustaining different Bloch surface waves (BSWs), depending on the orientation of the incident wave. By varying the orientation of the illumination of the multilayer, we measured an angle variation of 7° between the BSWs corresponding to the extraordinary and the ordinary index of the lithium niobate thin film. The potential of such a platform opens the way to novel tunable and active planar optics based on the electro- and thermo-optical properties of lithium niobate.

Synthesis of polypyrrole within the cell wall of yeast by redox-cycling of [Fe(CN)6](3-)/[Fe(CN)6](4-)

Yeast cells are often used as a model system in various experiments. Moreover, due to their high metabolic activity, yeast cells have a potential to be applied as elements in the design of biofuel cells and biosensors. However a wider application of yeast cells in electrochemical systems is limited due to high electric resistance of their cell wall. In order to reduce this problem we have polymerized conducting polymer polypyrrole (Ppy) directly in the cell wall and/or within periplasmic membrane. In this research the formation of Ppy was induced by [Fe(CN)6](3-)ions, which were generated from K4[Fe(CN)6], which was initially added to polymerization solution. The redox process was catalyzed by oxido-reductases, which are present in the plasma membrane of yeast cells. The formation of Ppy was confirmed by spectrophotometry and atomic force microscopy. It was confirmed that the conducting polymer polypyrrole was formed within periplasmic space and/or within the cell wall of yeast cells, which were incubated in solution containing pyrrole, glucose and [Fe(CN)6](4-). After 24h drying at room temperature we have observed that Ppy-modified yeast cell walls retained their initial spherical form. In contrast to Ppy-modified cells, the walls of unmodified yeast have wrinkled after 24h drying. The viability of yeast cells in the presence of different pyrrole concentrations has been evaluated.

Study of antibody/antigen binding kinetics by total internal reflection ellipsometry

Total internal reflection ellipsometry (TIRE) has been applied for the investigation of (i) kinetics of biosensing layer formation, which was based on the immobilization of fragmented and intact antibodies, and (ii) kinetics of antigen interaction with the immobilized antibodies. It has been demonstrated that ellipsometric parameter Δ(t) showed much higher sensitivity at the initial phase of Au-protein and protein-protein interaction, while the parameter Ψ(t) was more sensitive when the steady-state conditions were established. A new method, which taking into consideration this feature and nonlinear change of Δ(t) and Ψ(t) parameters during various stages of biological layer formation process, was used for the calculation of antibody and antigen adsorption/interaction kinetics. The obtained results were analyzed using a model, which took into account partial reversibility during the formation of both antibody and antigen based monolayers. It was shown that the immobilization rate of antibody during the preparation of the sensing layer was similar for the formation of both intact and fragmented antibody based layers; however, the residence time was 25 times longer for intact antibody based layer formation in comparison to that of fragmented antibody based layer formation. On the contrary, residence time of antigen interaction with immobilized antibodies was about 8 times longer for the sensor based on fragmented antibodies. Moreover, it has been determined that the structural differences of immobilized antibodies (fragmented or intact) significantly influence antibody-antigen interaction rate, the major difference being in the residence time of antigen interaction with both types of immobilized antibodies.