A virus-based nanoplasmonic structure as a surface-enhanced Raman biosensor

Viral nanoparticles: Current advances in design and development

Viral nanoparticles (VNPs) are self-assembling, adaptable delivery systems for vaccines and other therapeutic agents used in a variety of biomedical applications. The potential of viruses to invade and infect various hosts and cells renders them suitable as potential nanocarriers, possessing distinct functional characteristics, immunogenic properties, and improved biocompatibility and biodegradability. VNPs are frequently produced through precise genetic or chemical engineering, which involves adding diverse sequences or functional payloads to the capsid protein (CP). Several spherical and helical plant viruses, bacteriophages, and animal viruses are currently being used as VNPs, or non-infectious virus-like particles (VLPs). In addition to their broad use in cancer therapy, vaccine technology, diagnostics, and molecular imaging, VNPs have made important strides in the realms of tissue engineering, biosensing, and antimicrobial prophylaxis. They are also being used in energy storage cells due to their binding and piezoelectric properties. The large-scale production of VNPs for research, preclinical testing, and clinical use is fraught with difficulties, such as those relating to cost-effectiveness, scalability, and purity. Consequently, many plants- and microorganism-based platforms are being developed, and newer viruses are being explored. The goal of the current review is to provide an overview of these advances.

Characterization and discrimination of spike protein in SARS-CoV-2 virus-like particles via surface-enhanced Raman spectroscopy

Non-infectious virus-like particles (VLPs) are excellent structures for development of many biomedical applications such as drug delivery systems, vaccine production platforms, and detection techniques for infectious diseases including SARS-CoV-2 VLPs. The characterization of biochemical and biophysical properties of purified VLPs is crucial for development of detection methods and therapeutics. The presence of spike (S) protein in their structure is especially important since S protein induces immunological response. In this study, development of a rapid, low-cost, and easy-to-use technique for both characterization and detection of S protein in the two VLPs, which are SARS-CoV-2 VLPs and HIV-based VLPs was achieved using surface-enhanced Raman spectroscopy (SERS). To analyze and classify datasets of SERS spectra obtained from the VLP groups, machine learning classification techniques including support vector machine (SVM), k-nearest neighbors (kNN), and random forest (RF) were utilized. Among them, the SVM classification algorithm demonstrated the best classification performance for SARS-CoV-2 VLPs and HIV-based VLPs groups with 87.5% and 92.5% accuracy, respectively. This study could be valuable for the rapid characterization of VLPs for the development of novel therapeutics or detection of structural proteins of viruses leading to a variety of infectious diseases.

Tobacco Mosaic Viral Nanoparticle Inhibited Osteoclastogenesis Through Inhibiting mTOR/AKT Signaling

INTRODUCTION

Tobacco mosaic virus-based nanoparticles (TMV VNPs) were previously shown to promote osteogenic differentiation in vitro. This study aims to investigate whether and how TMV VNPs impact on osteoclastogenesis in vitro and bone injury healing in vivo.

METHODS

Raw264.7 cells were cultured in osteoclastogenic medium in culture plates coated with or without TMV and TMV-RGD1 VNPs, followed by TRAP staining, RT-qPCR and WB assessing expression of osteoclastogenic marker genes, and immunofluorescence assessing NF-κB activation. TMV and TMV-RGD1-modified hyaluronic acid hydrogel were used to treat mouse tibial bone injury. Bone injury healing was checked by micro-CT and Masson staining.

RESULTS

TMV and TMV-RGD1 VNPs significantly inhibited osteoclast differentiation and downregulated the expression of osteoclastogenic marker genes Ctr, Ctsk, Mmp-9, Rank, and Trap. Moreover, TMV and TMV-RGD1 VNPs inhibited NF-κB p65 phosphorylation and nuclear translocation, as well as activation of mTOR/AKT signaling pathway. TMV and TMV-RGD1-modified HA hydrogel strongly promoted mouse tibial bone injury with increased bone mass compared to plain HA hydrogel. The amount of osteoclasts was significantly reduced in TMV and TMV-RGD1 treated mice. TMV-RGD1 was more effective than TMV in inhibiting osteoclast differentiation and promoting bone injury repair.

DISCUSSION

These data demonstrated the great potential of TMV VNPs to be developed into biomaterial for bone injury repair or replacement.

Recent Progress in Plasmonic Biosensing Schemes for Virus Detection

The global burden of coronavirus disease 2019 (COVID-19) to public health and global economy has stressed the need for rapid and simple diagnostic methods. From this perspective, plasmonic-based biosensing can manage the threat of infectious diseases by providing timely virus monitoring. In recent years, many plasmonics’ platforms have embraced the challenge of offering on-site strategies to complement traditional diagnostic methods relying on the polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). This review compiled recent progress on the development of novel plasmonic sensing schemes for the effective control of virus-related diseases. A special focus was set on the utilization of plasmonic nanostructures in combination with other detection formats involving colorimetric, fluorescence, luminescence, or Raman scattering enhancement. The quantification of different viruses (e.g., hepatitis virus, influenza virus, norovirus, dengue virus, Ebola virus, Zika virus) with particular attention to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was reviewed from the perspective of the biomarker and the biological receptor immobilized on the sensor chip. Technological limitations including selectivity, stability, and monitoring in biological matrices were also reviewed for different plasmonic-sensing approaches.

A review on recent advances in the applications of surface-enhanced Raman scattering in analytical chemistry

This review is focused on recent developments of surface-enhanced Raman scattering (SERS) applications in Analytical Chemistry. The work covers advances in the fabrication methods of SERS substrates, including nanoparticles immobilization techniques and advanced nanopatterning with metallic features. Recent insights in quantitative and sampling methods for SERS implementation and the development of new SERS-based approaches for both qualitative and quantitative analysis are discussed. The advent of methods for pre-concentration and new approaches for single-molecule SERS quantification, such as the digital SERS procedure, has provided additional improvements in the analytical figures-of-merit for analysis and assays based on SERS. The use of metal nanostructures as SERS detection elements integrated in devices, such as microfluidic systems and optical fibers, provided new tools for SERS applications that expand beyond the laboratory environment, bringing new opportunities for real-time field tests and process monitoring based on SERS. Finally, selected examples of SERS applications in analytical and bioanalytical chemistry are discussed. The breadth of this work reflects the vast diversity of subjects and approaches that are inherent to the SERS field. The state of the field indicates the potential for a variety of new SERS-based methods and technologies that can be routinely applied in analytical laboratories.

Assembly of gold nanoparticles using turnip yellow mosaic virus as an in-solution SERS sensor

A common challenge in nanotechnology is the conception of materials with well-defined nanoscale structure. In recent years, virus capsids have been used as templates to create a network to organize 3D nano-objects, building thus new functional nanomaterials and then devices. In this work, we synthetized 3D gold nanoclusters and we used them as Surface Enhanced Raman Scattering (SERS) sensor substrates in solution. In practice, gold nanoparticles (AuNPs) were grafted on turnip yellow mosaic virus (TYMV) capsid, an icosahedral plant virus. Two strategies were considered to covalently bind AuNPs of different sizes (5, 10 and 20 nm) to TYMV. After purification by agarose electrophoresis and digestion by agarase, the resulting nano-bio-hybrid AuNP-TYVM was characterized by different tools. Typically, dynamic light scattering (DLS) confirmed the grafting through the hydrodynamic size increase by comparing AuNPs alone to AuNP-TYMV (up to 33, 50 and 68 nm for 5, 10 and 20 nm sized AuNPs, respectively) or capsids alone (28 nm). Transmission electronic microscopy (TEM) observations revealed that AuNPs were arranged with 5-fold symmetry, in agreement with their grafting around icosahedral capsids. Moreover, UV-vis absorption spectroscopy showed a red-shift of the plasmon absorption band on the grafted AuNP spectrum (530 nm) compared to that of the non-grafted one (520 nm). Finally, by recording in solution the Raman spectra of a dissolved probe molecule, namely 1,2-bis(4-pyridyl)ethane (BPE), in the presence of AuNP-TYVM and bare AuNPs or capsids, a net enhancement of the Raman signal was observed when BPE is adsorbed on AuNP-TYVM. The analytical enhancement factor (AEF) value of AuNP-TYMV is 5 times higher than that of AuNPs. These results revealed that AuNPs organized around virus capsid are able to serve as in-solution SERS-substrates, which is very interesting for the conception of ultrasensitive sensors in biological media.

3D-assembly of gold nanoparticles onto turnip yellow mosaic virus.

Improving the SERS signals of biomolecules using a stacked biochip containing Fe2O3/Au nanoparticles and a DC magnetic field

This study proposes a magnetic biochip that uses surface-enhanced Raman scattering (SERS) for antigen detection. The biochip was a sandwich structure containing alternating layers of gold and magnetic Fe₂O₃ nanoparticles. Both single (Au/Fe₂O₃/Au) and multilayer (Au/Fe₂O₃/Au/Fe₂O₃/Au) chips containing Fe₂O₃ nanoparticles were fabricated to detect bovine serum albumin (BSA). The single-layer chip detected the BSA antigen at a signal-to-noise ratio (SNR) of 5.0. Peaks detected between 1000 and 1500 cm^-1 corresponded to various carbon chains. With more Fe₂O₃ layers, bond resonance was enhanced via the Hall effect. The distribution of electromagnetic field enhancement was determined via SERS. The signal from the single-layer chip containing Au nanoparticles was measured in an external magnetic field. Maximum signal strength was recorded in a field strength of 12.5 gauss. We observed peaks due to other carbon-hydrogen molecules in a 62.5-gauss field. The magnetic field could improve the resolution and selectivity of sample observations.

Virus-like nanoparticles as a novel delivery tool in gene therapy

Viruses are considered as natural nanomaterials as they are in the size range of 20-500 nm with a genetical material either DNA or RNA, which is surrounded by a protein coat capsid. Recently, the field of virus nanotechnology is gaining significant attention from researchers. Attention is given to the utilization of viruses as nanomaterials for medical, biotechnology and energy applications. Removal of genetic material from the viral capsid creates empty capsid for drug incorporation and coating the capsid protein crystals with antibodies, enzymes or aptamers will enhance their targeted drug deliver efficiency. Studies reported that these virus-like nanoparticles have been used in delivering drugs for cancer. It is also used in imaging and sensory applications for various diseases. However, there is reservation among researchers to utilize virus-like nanoparticles in targeted delivery of genes in gene therapy, as there is a possibility of using virus-like nanoparticles for targeted gene delivery. In addition, other biomedical applications that are explored using virus-like nanoparticles and the probable mechanism of delivering genes.

Viral-based nanomaterials for plasmonic and photonic materials and devices

Over the last decade, viruses have established themselves as a powerful tool in nanotechnology. Their proteinaceous capsids benefit from biocompatibility, chemical addressability, and a variety of sizes and geometries, while their ability to encapsulate, scaffold, and self-assemble enables their use for a wide array of purposes. Moreover, the scaling up of viral-based nanotechnologies is facilitated by high capsid production yield and speed, which is particularly advantageous when compared with slower and costlier lithographic techniques. These features enable the bottom-up fabrication of photonic and plasmonic materials, which relies on the precise arrangement of photoactive material at the nanoscale to control phenomena such as electromagnetic wave propagation and energy transfer. The interdisciplinary approach required for the fabrication of such materials combines techniques from the life sciences and device engineering, thus promoting innovative research. Materials with applications spanning the fields of sensing (biological, chemical, and physical sensors), nanomedicine (cellular imaging, drug delivery, phototherapy), energy transfer and conversion (solar cells, light harvesting, photocatalysis), metamaterials (negative refraction, artificial magnetism, near-field amplification), and nanoparticle synthesis are considered with exclusive emphasis on viral capsids and protein cages. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Dual-Functionalized Virus-Gold Nanoparticle Clusters for Biosensing

Metallic nanoscale 3D architectures concentrate electromagnetic energy at precise spatial locations to enable sensing and photocatalysis applications. We have developed solution-based methods to reproducibly fabricate 3D gold nanostructures useful as efficient surface-enhanced Raman spectroscopy (SERS) biosensors. Virus capsids were recruited as templates to assemble gold nanoparticles on their surfaces at well-defined locations to prepare the nanoscale 3D structures. Cowpea mosaic virus (CPMV) and its variants were selected as specific templates due to their high symmetry, scalability, and stability, which have proven useful in materials science applications. While the methods described herein were optimized for the CPMV capsids, they also provide a useful starting point for researchers who are working toward the nanoassembly of metal nanoparticles on other protein scaffolds.

Plant Virus Expression Vectors: A Powerhouse for Global Health

Plant-made biopharmaceuticals have long been considered a promising technology for providing inexpensive and efficacious medicines for developing countries, as well as for combating pandemic infectious diseases and for use in personalized medicine. Plant virus expression vectors produce high levels of pharmaceutical proteins within a very short time period. Recently, plant viruses have been employed as nanoparticles for novel forms of cancer treatment. This review provides a glimpse into the development of plant virus expression systems both for pharmaceutical production as well as for immunotherapy.

Self-Assembled Raspberry-Like Core/Satellite Nanoparticles for Anti-Inflammatory Protein Delivery

Functional proteins are very promising for protein therapeutics; however, effective delivery of therapeutic proteins remains challenging. Herein, we developed novel core/satellite nanoparticles by tethering therapeutic proteins to the core/shell polymeric particle surface through cucurbit[8]uril (CB[8])-mediated host-guest interactions. The effectiveness of the core/satellite nanoparticles as protein carrier was demonstrated through the intra-articular delivery of interleukin-1 receptor antagonist (IL-1Ra). We showed that IL-1Ra can effectively self-assemble onto the surface of the polymeric nanoparticles and maintained good protein bioactivity by inhibiting IL-1-mediated signaling. More importantly, in vivo results revealed that IL-1Ra-bounded core/satellite nanoparticles could significantly increase the retention time of IL-1Ra in the rat stifle joint compared to soluble IL-1Ra, which could greatly improve the efficacy of IL-1Ra. These results indicate that the facile host-guest self-assembly can be exploited as an effective approach for realizing the therapeutic potential of proteins.

Plasmonic nanocarrier grid-enhanced Raman sensor for studies of anticancer drug delivery

Targeted drug delivery systems using nanoparticle nanocarriers offer remarkable promise for cancer therapy by discriminating against devastating cytotoxicity of chemotherapeutic drugs to healthy cells. To aid in the development of new drug nanocarriers, we propose a novel plasmonic nanocarrier grid-enhanced Raman sensor which can be applied for studies and testing of drug loading onto the nanocarriers, attachment of targeting ligands, dynamics of drug release, assessment of nanocarrier stability in biological environment, and general capabilities of the nanocarrier. The plasmonic nanogrid sensor offers strong Raman enhancement due to the overlapping plasmonic fields emanating from the nearest-neighbor gold nanoparticle nanocarriers and creating the enhancement "hot spots". The sensor has been tested for immobilization of an anticancer drug gemcitabine (2',2'-difluoro-2'-deoxycytidine, GEM) which is used in treatment of pancreatic tumors. The drawbacks of currently applied treatment include high systemic toxicity, rapid drug decay, and low efficacy (ca. 20%). Therefore, the development of a targeted GEM delivery system is highly desired. We have demonstrated that the proposed nanocarrier SERS sensor can be utilized to investigate attachment of targeting ligands to nanocarriers (attachment of folic acid ligand recognized by folate receptors of cancer cells is described). Further testing of the nanocarrier SERS sensor involved drug release induced by lowering pH and increasing GSH levels, both occurring in cancer cells. The proposed sensor can be utilized for a variety of drugs and targeting ligands, including those which are Raman inactive, since the linkers can act as the Raman markers, as illustrated with mercaptobenzoic acid and para-aminothiophenol.

'Squeezed' interparticle properties for plasmonic coupling and SERS characteristics of duplex DNA conjugated/linked gold nanoparticles of homo/hetero-sizes

The formation of interparticle duplex DNA conjugates with gold nanoparticles constitutes the basis for interparticle plasmonic coupling responsible for surface-enhanced Raman scattering signal amplification, but understanding of its correlation with interparticle spatial properties and particle sizes, especially in aqueous solutions, remains elusive. This report describes findings of an investigation of interparticle plasmonic coupling based on experimental measurements of localized surface plasmon resonance and surface enhanced Raman scattering characteristics for gold nanoparticles in aqueous solutions upon introduction of interparticle duplex DNA conjugates to define the interparticle spatial properties. Theoretical simulations of the interparticle optical properties and electric field enhancement based on a dimer model have also been performed to aid the understanding of the experimental results. The results have revealed a 'squeezed' interparticle spatial characteristic in which the duplex DNA-defined distance is close or shorter than A-form DNA conformation, which are discussed in terms of the interparticle interactions, providing fresh insight into the interparticle double-stranded DNA-defined interparticle spatial properties for the design of highly-sensitive nanoprobes in solutions for biomolecular detection.

Plant virus nanoparticles: new applications and new benefits

For over two decades now, plants have been explored for their potential to act as production platforms for biopharmaceuticals, such as vaccines and monoclonal antibodies. More recently, plant viruses have been designed as nontoxic nanoparticles that can target a variety of cancers and thus empower the immune system to slow or even reverse tumor progression. The following paper describes the employment of plant virus expression vectors for the treatment of some of the most challenging diseases known today. The paper concludes with a projection of the multiple avenues by which virus nanoparticles could impact developing countries.

Protein-Assisted Assembly of Modular 3D Plasmonic Raspberry-like Core/Satellite Nanoclusters: Correlation of Structure and Optical Properties

We present a bottom-up assembly route for a large-scale organization of plasmonic nanoparticles (NPs) into three-dimensional (3D) modular assemblies with core/satellite structure. The protein-assisted assembly of small spherical gold or silver NPs with a hydrophilic protein shell (as satellites) onto larger metal NPs (as cores) offers high modularity in sizes and composition at high satellite coverage (close to the jamming limit). The resulting dispersions of metal/metal nanoclusters exhibit high colloidal stability and therefore allow for high concentrations and a precise characterization of the nanocluster architecture in dispersion by small-angle X-ray scattering (SAXS). Strong near-field coupling between the building blocks results in distinct regimes of dominant satellite-to-satellite and core-to-satellite coupling. High robustness against satellite disorder was proved by UV/vis diffuse reflectance (integrating sphere) measurements. Generalized multiparticle Mie theory (GMMT) simulations were employed to describe the electromagnetic coupling within the nanoclusters. The close correlation of structure and optical property allows for the rational design of core/satellite nanoclusters with tailored plasmonics and well-defined near-field enhancement, with perspectives for applications such as surface-enhanced spectroscopies.

Toward Virus-Like Surface Plasmon Strain Sensors

The strong configuration dependence of collective surface plasmon resonances in an array of metal nanoparticles provides an opportunity to develop a bioinspired tool for sensing mechanical deformations in soft matter at the nanoscale. We study the feasibility of a strain sensor based on an icosahedral array of nanoparticles encapsulated by a virus capsid. When the system undergoes deformation, the optical scattering cross-section spectra as well as the induced electric field profile change. By numerical simulations, we examine how these changes depend on the symmetry and extent of the deformation and on both the propagation direction and polarization of the incident radiation. Such a sensor could prove useful in studies of the mechanisms of nanoparticle or virus translocation in the confines of a host cell.

Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus

Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed.