A manual and an automatic TERS based virus discrimination

Raman spectroscopy for viral diagnostics

Raman spectroscopy offers the potential for fingerprinting biological molecules at ultra-low concentration and therefore has potential for the detection of viruses. Here we review various Raman techniques employed for the investigation of viruses. Different Raman techniques are discussed including conventional Raman spectroscopy, surface-enhanced Raman spectroscopy, Raman tweezer, tip-enhanced Raman Spectroscopy, and coherent anti-Stokes Raman scattering. Surface-enhanced Raman scattering can play an essential role in viral detection by multiplexing nanotechnology, microfluidics, and machine learning for ensuring spectral reproducibility and efficient workflow in sample processing and detection. The application of these techniques to diagnose the SARS-CoV-2 virus is also reviewed.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s12551-023-01059-4.

Length-Controllable Gold-Coated Silver Nanowire Probes for High AFM-TERS Scattering Activity

Tip-enhanced Raman scattering (TERS) microscopy is an advanced technique for investigation at the nanoscale that provides topographic and chemical information simultaneously. The TERS probe plays a crucial role in the microscopic performance. In the recent past, the development of silver nanowire (AgNW) based TERS probes solved the main tip fabrication issues, such as low mechanical strength and reproducibility. However, this fabrication method still suffers from low control of the protruded length of the AgNW. In this work, a simple water-air interface electrocutting method is proposed to achieve wide controllability of the length. This water cutting method was combined with a succedent Au coating on the AgNW surface, and the probe achieved an up to 100× higher enhancement factor (EF) and a 2× smaller spatial resolution compared to pristine AgNW. Thanks to this excellent EF, the water-cut Au-coated AgNW probes were found to possess high TERS activity even in the nongap mode, enabling broad applications.

Contributions of vibrational spectroscopy to virology: A review

Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970 s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review considers the history of the application of vibrational spectroscopic techniques to the characterisation of the morphology and chemical compositions of viruses, their attachment to, uptake by and replication in cells, and their potential for the detection of viruses in population screening, and in infection response monitoring applications. Particular consideration is devoted to recent efforts in the detection of severe acute respiratory syndrome coronavirus 2, and monitoring COVID-19.

Single-Molecule Surface-Enhanced Raman Spectroscopy

Single-molecule surface-enhanced Raman spectroscopy (SM-SERS) has the potential to detect single molecules in a non-invasive, label-free manner with high-throughput. SM-SERS can detect chemical information of single molecules without statistical averaging and has wide application in chemical analysis, nanoelectronics, biochemical sensing, etc. Recently, a series of unprecedented advances have been realized in science and application by SM-SERS, which has attracted the interest of various fields. In this review, we first elucidate the key concepts of SM-SERS, including enhancement factor (EF), spectral fluctuation, and experimental evidence of single-molecule events. Next, we systematically discuss advanced implementations of SM-SERS, including substrates with ultra-high EF and reproducibility, strategies to improve the probability of molecules being localized in hotspots, and nonmetallic and hybrid substrates. Then, several examples for the application of SM-SERS are proposed, including catalysis, nanoelectronics, and sensing. Finally, we summarize the challenges and future of SM-SERS. We hope this literature review will inspire the interest of researchers in more fields.

Gold-coated silver nanowires for long lifetime AFM-TERS probes

Tip-enhanced Raman scattering (TERS) microscopy is an advanced technique for investigation at the nanoscale because of its excellent properties, such as its label-free functionality, non-invasiveness, and ability to simultaneously provide topographic and chemical information. The probe plays a crucial role in TERS technique performance. Widely used AFM-TERS probes fabricated with metal deposition suffer from relatively low reproductivity as well as limited mapping and storage lifetime. To solve the reproducibility issue, silver nanowire (AgNW)-based TERS probes were developed, which, thanks to the high homogeneity of the liquid-phase synthesis of AgNW, can achieve high TERS performance with excellent probe reproductivity, but still present short lifetime due to probe oxidation. In this work, a simple Au coating method is proposed to overcome the limited lifetime and improve the performance of the AgNW-based TERS probe. For the Au-coating, different [Au]/[Ag] molar ratios were investigated. The TERS performance was evaluated in terms of changes in the enhancement factor (EF) and signal-to-noise ratio through multiple mappings and the storage lifetime in air. The Au-coated AgNWs exhibited higher EF than pristine AgNWs and galvanically replaced AgNWs with no remarkable difference between the two molar ratios tested. However, for longer scanning time and multiple mappings, the probes obtained with low Au concentration showed much longer-term stability and maintained a high EF. Furthermore, the Au-coated AgNW probes were found to possess a longer storage lifetime in air, allowing for long and multiple TERS mappings with one single probe.

Nanoscale chemical characterization of biomolecules using tip-enhanced Raman spectroscopy

Nanoscale chemical and structural characterization of single biomolecules and assemblies is of paramount importance for applications in biology and medicine. It aims to describe the molecular structure of biomolecules and their interaction with unprecedented spatial resolution to better comprehend underlying molecular mechanisms of biological processes involved in cell activity and diseases. Tip-enhanced Raman scattering (TERS) spectroscopy appears particularly appealing to reach these objectives. This state-of-the-art TERS technique is as versatile as it is ultrasensitive. To perform a successful TERS experiment, special care and a thorough methodology for the preparation of the TERS system, the TERS probe tip, and sample are needed. Intense efforts have been deployed to characterize nucleic acids, proteins and peptides, lipid membranes, and more complex systems such as cells and viruses using TERS. Although the vast majority of studies have first been performed in dry conditions, they have allowed for several scientific breakthroughs. These include DNA and RNA sequencing, and the determination of relationships between protein structure and biological function by the use of increasingly exploitative chemometric tools for spectral data analysis. The nanoscale determination of the secondary structure of amyloid fibrils, protofibrils and oligomers implicated in neurodegenerative diseases could, for instance, be connected with the toxicity of these species, amyloid formation pathways, and their interaction with phospholipids. Single particles of different viral strains could be distinguished from one another by comparison of their protein and lipid contents. In addition, TERS has allowed for the evermore accurate description of the molecular organization of lipid membranes. Very recent advances also demonstrated the possibility to carry out TERS in aqueous medium, which opens thrilling perspectives for the TERS technique in biological, biomedical, and potential clinical applications.

Real-Time Monitoring of the In Situ Microfluidic Synthesis of Ag Nanoparticles on Solid Substrate for Reliable SERS Detection

A sharpened control over the parameters affecting the synthesis of plasmonic nanostructures is often crucial for their application in biosensing, which, if based on surface-enhanced Raman spectroscopy (SERS), requires well-defined optical properties of the substrate. In this work, a method for the microfluidic synthesis of Ag nanoparticles (NPs) on porous silicon (pSi) was developed, focusing on achieving a fine control over the morphological characteristics and spatial distribution of the produced nanostructures to be used as SERS substrates. To this end, a pSi membrane was integrated in a microfluidic chamber in which the silver precursor solution was injected, allowing for the real-time monitoring of the reaction by UV-Vis spectroscopy. The synthesis parameters, such as the concentration of the silver precursor, the temperature, and the flow rate, were varied in order to study their effects on the final silver NPs' morphology. Variations in the flow rate affected the size distribution of the NPs, whereas both the temperature and the concentration of the silver precursor strongly influenced the rate of the reaction and the particle size. Consistently with the described trends, SERS tests using 4-MBA as a probe showed how the flow rate variation affected the SERS enhancement uniformity, and how the production of larger NPs, as a result of an increase in temperature or of the concentration of the Ag precursor, led to an increased SERS efficiency.

Laser spectroscopic technique for direct identification of a single virus I: FASTER CARS

Surface features of a virus are very important in determining its virility. For example, the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to the ACE2 receptor site of the host cell with a much stronger affinity than did the original SARS virus. Thus, it is clearly important to understand the virion surface structure. To that end, the present paper combines the spatial resolution of atomic force microscopy and the spectral resolution of coherent Raman spectroscopy. This combination of tip-enhanced microscopy using femtosecond adaptive spectroscopic techniques for coherent anti-Stokes Raman scattering (FAST CARS) with enhanced resolution (FASTER CARS) allows us to map a single virus particle with nanometer resolution and chemical specificity.

From the famous 1918 H1N1 influenza to the present COVID-19 pandemic, the need for improved viral detection techniques is all too apparent. The aim of the present paper is to show that identification of individual virus particles in clinical sample materials quickly and reliably is near at hand. First of all, our team has developed techniques for identification of virions based on a modular atomic force microscopy (AFM). Furthermore, femtosecond adaptive spectroscopic techniques with enhanced resolution via coherent anti-Stokes Raman scattering (FASTER CARS) using tip-enhanced techniques markedly improves the sensitivity [M. O. Scully, et al., Proc. Natl. Acad. Sci. U.S.A. 99, 10994–11001 (2002)].

Advances in single cell Raman spectroscopy technologies for biological and environmental applications

The increasing sophistication of single cell Raman spectroscopy (SCRS) via its integrations with other advanced analytical techniques and modern data analytics, enable unprecedented exploration of complex biological and environmental samples with significantly improved specificity, sensitivity, and resolution. Because of the merits of being high-resolution, label-free, non-invasive, molecular-specific, culture-independent, and suitable for in situ, in vitro or in vivo analysis, the SCRS-derived techniques offer abilities superior to conventional bulk measurements for environmental and biological studies. Here, we provide a comprehensive and critical review of the most recent advances in the development and application of SCRS-enabled technologies, with focus on those biomolecular and cellular high-resolution applications in environmental and biological fields. The basic principles, unique advantages, and suitable applications, as well as recognized limitations for each technology are recapitulated. The remaining challenges, research needs and future outlook are discussed. We predict that SCRS-enabled technologies are earning its place as a routine and powerful tool in many and rapidly expanding applications across disciplines.

Present and Future of Surface-Enhanced Raman Scattering

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

Are plasmonic optical biosensors ready for use in point-of-need applications?

Plasmonics has drawn significant attention in the area of biosensors for decades due to the unique optical properties of plasmonic resonant nanostructures. While the sensitivity and specificity of molecular detection relies significantly on the resonance conditions, significant attention has been dedicated to the design, fabrication, and optimization of plasmonic substrates. The adequate choice of materials, structures, and functionality goes hand in hand with a fundamental understanding of plasmonics to enable the development of practical biosensors that can be deployed in real life situations. Here we provide a brief review of plasmonic biosensors detailing most recent developments and applications. Besides metals, novel plasmonic materials such as graphene are highlighted. Sensors based on Surface Plasmon Resonance (SPR), Localized Surface Plasmon Resonance (LSPR), and Surface Enhanced Raman Spectroscopy (SERS) are presented and classified based on their materials and structure. In addition, most recent applications to environment monitoring, health diagnosis, and food safety are presented. Potential problems related to the implementation in such applications are discussed and an outlook is presented.

Volume-Enhanced Raman Scattering Detection of Viruses

Virus detection and analysis are of critical importance in biological fields and medicine. Surface-enhanced Raman scattering (SERS) has shown great promise in small molecule and even single molecule detection, and can provide fingerprint signals of molecules. Despite the powerful detection capabilities of SERS, the size discrepancy between the SERS "hot spots" (generally, <10 nm) and viruses (usually, sub-100 nm) yields poor detection reliability of viruses. Inspired by the concept of molecular imprinting, a volume-enhanced Raman scattering (VERS) substrate composed of hollow nanocones at the bottom of microbowls (HNCMB) is developed. The hollow nanocones of the resulting VERS substrates serve a twofold purpose: 1) extending the region of Raman signal enhancement from the nanocone surface (e.g., surface "hot spots") to the hollow area within the cone (e.g., volume "hot spots")-a novel method of Raman signal enhancement, and 2) directing analyte such as viruses of a wide range of sizes to those VERS "hot spots" while simultaneously increasing the surface area contributing to SERS. Using HNCMB VERS substrates, greatly improved Raman signals of single viruses are demonstrated, an achievement with important implications in disease diagnostics and monitoring, biomedical fields, as well as in clinical treatment.

Advanced Nanoscale Approaches to Single-(Bio)entity Sensing and Imaging

Individual (bio)chemical entities could show a very heterogeneous behaviour under the same conditions that could be relevant in many biological processes of significance in the life sciences. Conventional detection approaches are only able to detect the average response of an ensemble of entities and assume that all entities are identical. From this perspective, important information about the heterogeneities or rare (stochastic) events happening in individual entities would remain unseen. Some nanoscale tools present interesting physicochemical properties that enable the possibility to detect systems at the single-entity level, acquiring richer information than conventional methods. In this review, we introduce the foundations and the latest advances of several nanoscale approaches to sensing and imaging individual (bio)entities using nanoprobes, nanopores, nanoimpacts, nanoplasmonics and nanomachines. Several (bio)entities such as cells, proteins, nucleic acids, vesicles and viruses are specifically considered. These nanoscale approaches provide a wide and complete toolbox for the study of many biological systems at the single-entity level.

Surface-Enhanced Raman Spectroscopy for Bioanalysis: Reliability and Challenges

Surface-enhanced Raman spectroscopy (SERS) inherits the rich chemical fingerprint information on Raman spectroscopy and gains sensitivity by plasmon-enhanced excitation and scattering. In particular, most Raman peaks have a narrow width suitable for multiplex analysis, and the measurements can be conveniently made under ambient and aqueous conditions. These merits make SERS a very promising technique for studying complex biological systems, and SERS has attracted increasing interest in biorelated analysis. However, there are still great challenges that need to be addressed until it can be widely accepted by the biorelated communities, answer interesting biological questions, and solve fatal clinical problems. SERS applications in bioanalysis involve the complex interactions of plasmonic nanomaterials with biological systems and their environments. The reliability becomes the key issue of bioanalytical SERS in order to extract meaningful information from SERS data. This review provides a comprehensive overview of bioanalytical SERS with the main focus on the reliability issue. We first introduce the mechanism of SERS to guide the design of reliable SERS experiments with high detection sensitivity. We then introduce the current understanding of the interaction of nanomaterials with biological systems, mainly living cells, to guide the design of functionalized SERS nanoparticles for target detection. We further introduce the current status of label-free (direct) and labeled (indirect) SERS detections, for systems from biomolecules, to pathogens, to living cells, and we discuss the potential interferences from experimental design, measurement conditions, and data analysis. In the end, we give an outlook of the key challenges in bioanalytical SERS, including reproducibility, sensitivity, and spatial and time resolution.

Tip-enhanced Raman spectroscopy - from early developments to recent advances

An analytical technique operating at the nanoscale must be flexible regarding variable experimental conditions while ideally also being highly specific, extremely sensitive, and spatially confined. In this respect, tip-enhanced Raman scattering (TERS) has been demonstrated to be ideally suited to, e.g., elucidating chemical reaction mechanisms, determining the distribution of components and identifying and localizing specific molecular structures at the nanometre scale. TERS combines the specificity of Raman spectroscopy with the high spatial resolution of scanning probe microscopies by utilizing plasmonic nanostructures to confine the incident electromagnetic field and increase it by many orders of magnitude. Consequently, molecular structure information in the optical near field that is inaccessible to other optical microscopy methods can be obtained. In this general review, the development of this still-young technique, from early experiments to recent achievements concerning inorganic, organic, and biological materials, is addressed. Accordingly, the technical developments necessary for stable and reliable AFM- and STM-based TERS experiments, together with the specific properties of the instruments under different conditions, are reviewed. The review also highlights selected experiments illustrating the capabilities of this emerging technique, the number of users of which has steadily increased since its inception in 2000. Finally, an assessment of the frontiers and new concepts of TERS, which aim towards rendering it a general and widely applicable technique that combines the highest possible lateral resolution and extreme sensitivity, is provided.

Tunable, Liquid Resistant Tip Enhanced Raman Spectroscopy Probes: Toward Label-Free Nano-Resolved Imaging of Biological Systems

Tip enhanced Raman spectroscopy (TERS) has been established as a powerful, noninvasive technique for chemical identification at the nanoscale. However, difficulties, including the degradation of probes, limit its use in liquid systems. Here TERS probes for studies in aqueous environments have been demonstrated using titanium nitride coatings with an alumina protective layer. The probes show enhancement in signal intensity as high as 380% in liquid measurements, and the probe resonance can be tuned by varying deposition conditions to optimize performance for different laser sources and types of samples. This development of inexpensively produced probes suited for studies in aqueous environments enables its wider use for fields such as biology and biomedicine in which aqueous environments are the norm.

Damage-free tip-enhanced Raman spectroscopy for heat-sensitive materials

We report a method to establish experimental conditions for tip-enhanced Raman spectroscopy (TERS) with low thermal and mechanical damage to samples. In this method, we monitor the thermal desorption of thiol molecules from a gold-coated probe of an atomic force microscope (AFM) via TERS spectra. Temperatures for desorption of thiol molecules (60-100 °C) from gold surfaces cover the temperature range for degradation of heat-sensitive biomaterials (e.g. proteins). By monitoring the desorption of the thiols on the probe, we can estimate the power of an excitation laser for the samples to reach their critical temperatures for thermal degradation. Furthermore, we also found that an active oscillation of AFM cantilevers significantly promotes the heat transfer from the probe to the surrounding medium. This enables us to employ a higher power density of the excitation laser, resulting in a stronger Raman signal compared with the signal obtained with a contact mode. We propose that this combinatory method is effective in acquiring strong TERS signals while suppressing thermal and mechanical damage to soft and heat-sensitive samples.

Raman Imaging in Cell Membranes, Lipid-Rich Organelles, and Lipid Bilayers

Raman-based optical imaging is a promising analytical tool for noninvasive, label-free chemical imaging of lipid bilayers and cellular membranes. Imaging using spontaneous Raman scattering suffers from a low intensity that hinders its use in some cellular applications. However, developments in coherent Raman imaging, surface-enhanced Raman imaging, and tip-enhanced Raman imaging have enabled video-rate imaging, excellent detection limits, and nanometer spatial resolution, respectively. After a brief introduction to these commonly used Raman imaging techniques for cell membrane studies, this review discusses selected applications of these modalities for chemical imaging of membrane proteins and lipids. Finally, recent developments in chemical tags for Raman imaging and their applications in the analysis of selected cell membrane components are summarized. Ongoing developments toward improving the temporal and spatial resolution of Raman imaging and small-molecule tags with strong Raman scattering cross sections continue to expand the utility of Raman imaging for diverse cell membrane studies.

Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples

Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.

Towards a correlative approach for characterising single virus particles by transmission electron microscopy and nanoscale Raman spectroscopy

The morphology and structure of biological nanoparticles, such as viruses, can be efficiently analysed by transmission electron microscopy (TEM).

Exploring the Nanoscale: Fifteen Years of Tip-Enhanced Raman Spectroscopy

Spectroscopic methods with high spatial resolution are essential to understand the physical and chemical properties of nanoscale materials including biological and chemical materials. Tip-enhanced Raman spectroscopy (TERS) is a combination of surface-enhanced Raman spectroscopy (SERS) and scanning probe microscopy (SPM), which can provide high-resolution topographic and spectral information simultaneously below the diffraction limit of light. Even examples of sub-nanometer resolution have been demonstrated. This review intends to give an introduction to TERS, focusing on its basic principle and the experimental setup, the strengths followed by recent applications, developments, and perspectives in this field.

Rational fabrication of a gold-coated AFM TERS tip by pulsed electrodeposition

Reproducible fabrication of sharp gold- or silver-coated tips has become the bottleneck issue in tip-enhanced Raman spectroscopy, especially for atomic force microscopy (AFM)-based TERS. Herein, we developed a novel method based on pulsed electrodeposition to coat a thin gold layer over atomic force microscopy (AFM) tips to produce plasmonic TERS tips with high reproducibility. We systematically investigated the influence of the deposition potential and step time on the surface roughness and sharpness. This method allows the rational control of the radii of gold-coated TERS tips from a few to hundreds of nanometers, which allows us to systematically study the dependence of the TERS enhancement on the radius of the gold-coated AFM tip. The maximum TERS enhancement was achieved for the tip radius in the range of 60-75 nm in the gap mode. The coated gold layer has a strong adhesion with the silicon tip surface, which is highly stable in water, showing the great potential for application in the aqueous environment.