Surface-enhanced Raman spectroscopy based quantitative bioassay on aptamer-functionalized nanopillars using large-area Raman mapping

Factors that Affect Quantification in Surface-Enhanced Raman Scattering

Surface-enhanced Raman scattering (SERS) is an analytical technique capable of detecting trace amounts of specific species. The uniqueness of vibrational signatures is a major advantage of SERS. This combination of sensitivity and specificity has motivated researchers to develop diverse analytical methodologies leveraging SERS. However, even 50 years after its first observation, SERS is still perceived as an unreliable technique for quantification. This perception has precluded the application of SERS in laboratories that rely on consistent quantification (for regulatory purposes, for instance). In this review, we describe some of the aspects that lead to SERS intensity variations and how those challenges were addressed in the 50 years of the technique. The goal is to identify the sources of variations in SERS intensities and then demonstrate that, even with these pitfalls, the technique can be used for quantification when factors such as nature of the substrate, experimental conditions, sample preparation, surface chemistry, and data analysis are carefully considered and tailored for a particular application.

Highly Tunable, Nanomaterial-Functionalized Structural Templating of Intracellular Protein Structures Within Biological Species

Inside living organisms, proteins are self-assembled into diverse 3D structures optimized for specific functions. This structure-function relationship can be exploited to synthesize functional materials through biotemplating and depositing functional materials onto protein structures. However, conventional biotemplating faces limitations due to the predominantly intracellular existence of proteins and associated challenges in achieving tunability while preserving functionality. In this study, Conversion to Advanced Materials via labeled Biostructures (CamBio), an integrated biotemplating platform that involves labeling target protein structures with antibodies followed by the growth of functional materials, ensuring outstanding nanostructure tunability is proposed. Protein-derived plasmonic nanostructures created by CamBio can serve as precise quantitative tools for assessing target species is demonstrated. The assessment is achieved through highly tunable and efficient surface-enhanced Raman spectroscopy (SERS). CamBio enables the formation of dense nanogap hot spots among metal nanoparticles, templated by diverse fibrous proteins comprising densely repeated monomers. Furthermore, iterative antibody labeling strategies to adjust the antibody density surrounding targets, amplifying the number of nanogaps and consequently improving SERS performance are employed. Finally, cell-patterned substrates and whole meat sections as SERS substrates, confirming their easily accessible, cost-effective, scalable preparation capabilities and dimensional tunability are incorporated.

Freshness in Salmon by Hand-Held Devices: Methods in Feature Selection and Data Fusion for Spectroscopy

Salmon fillet was analyzed via hand-held optical devices: fluorescence (@340 nm) and absorption spectroscopy across the visible and near-infrared (NIR) range (400-1900 nm). Spectroscopic measurements were benchmarked with nucleotide assays and potentiometry in an exploratory set of experiments over 11 days, with changes to spectral profiles noted. A second enlarged spectroscopic data set, over a 17 day period, was then acquired, and fillet freshness was classified ±1 day via four machine learning (ML) algorithms: linear discriminant analysis, Gaussian naïve, weighted K-nearest neighbors, and an ensemble bagged tree method. Dual-mode data fusion returned almost perfect accuracies (mean = 99.5 ± 0.51%), while single-mode ML analyses (fluorescence, visible absorbance, and NIR absorbance) returned lower mean accuracies at greater spread (77.1 ± 10.1%). Single-mode fluorescence accuracy was especially poor; however, via principal component analysis, we found that a truncated fluorescence data set of four variables (wavelengths) could predict "fresh" and "spoilt" salmon fillet based on a subtle peak redshift as the fillet aged, albeit marginally short of statistical significance (95% confidence ellipse). Thus, whether by feature selection of one spectral data set, or the combination of multiple data sets through different modes, this study lays the foundation for better determination of fish freshness within the context of rapid spectroscopic analyses.

Surface-Enhanced Raman Spectroscopy at the Interface between Drug Discovery and Personalized Medicine

Personalized medicine and drug discovery are different, yet overlapping, fields, and information from each field is exchanged to improve the other. The current methods used for devising personalized therapeutic plans and developing drug discovery applications are costly, time-consuming, and complex; thus, their applicability is limited in both fields. However, surface-enhanced Raman spectroscopy (SERS) offers potential solutions to current challenges. This Mini-Review explores the utility of SERS in drug discovery and personalized medicine. The Mini-Review starts with a brief overview of these fields, including the main challenges and current methods, and then explores examples where SERS has been used to overcome some of the main challenges in both fields. It ends with brief conclusions, perspectives, and current challenges limiting the practical application of SERS.

An Internally Attached Aptameric Graphene Nanosensor for Sensitive Vasopressin Measurement in Critical Patient Monitoring

This paper presents an aptameric graphene nanosensor for rapid and sensitive measurement of arginine vasopressin (AVP) toward continuous monitoring of critical care patients. The nanosensor is a field-effect transistor (FET) with monolayer graphene as the conducting channel and is functionalized with a new custom-designed aptamer for specific AVP recognition. Binding between the aptamer and AVP induces a change in the carrier density in the graphene and resulting in measurable changes in FET characteristics for determination of the AVP concentration. The aptamer, based on the natural enantiomer D-deoxyribose, possess optimized kinetic binding properties and is attached at an internal position to the graphene for enhanced sensitivity to low concentrations of AVP. Experimental results show that this aptameric graphene nanosensor is highly sensitive (with a limit of detection of 0.3 pM and a resolution of 0.1 pM) to AVP, and rapidly responsive (within 90 s) to both increasing and decreasing AVP concentration changes. The device is also reversable (within 4%), repeatable (within 4%) and reproducible (within 5%) in AVP measurements.

Determination of latent tuberculosis infection from plasma samples via label-free SERS sensors and machine learning

Effective diagnostic tools for screening of latent tuberculosis infection (LTBI) are lacking. We aim to investigate the performance of LTBI diagnostic approaches using label-free surface-enhanced Raman spectroscopy (SERS). We used 1000 plasma samples from Northeast Thailand. Fifty percent of the samples had tested positive in the interferon-gamma release assay (IGRA) and 50 % negative. The SERS investigations were performed on individually prepared protein specimens using the Raman-mapping technique over a 7 × 7 grid area under measurement conditions that took under 10 min to complete. The machine-learning analysis approaches were optimized for the best diagnostic performance. We found that the SERS sensors provide 81 % accuracy according to train-test split analysis and 75 % for LOOCV analysis from all samples, regardless of the batch-to-batch variation of the sample sets and SERS chip. The accuracy increased to 93 % when the logistic regression model was used to analyze the last three batches of samples, following optimization of the sample collection, SERS chips, and database. We demonstrated that SERS analysis with machine learning is a potential diagnostic tool for LTBI screening.

Detection of SARS-CoV-2 N protein using AgNPs-modified aligned silicon nanowires BioSERS chip

The SARS-CoV-2 (COVID-19) pandemic had a strong impact on societies and economies worldwide and tests for high-performance detection of SARS-CoV-2 biomarkers are still needed for potential future outbreaks of the disease. In this paper, we present the different steps for the design of an aptamer-based surface-enhanced Raman scattering (BioSERS) sensing chip capable of detecting the coronavirus nucleocapsid protein (N protein) in spiked phosphate-buffered solutions and real samples of human blood serum. Optimization of the preparation steps in terms of the aptamer concentration used for the functionalization of the silver nanoparticles, time for affixing the aptamer, incubation time with target protein, and insulation of the silver active surface with cysteamine, led to a sensitive BioSERS chip, which was able to detect the N protein in the range from 1 to 75 ng mL-1 in spiked phosphate-buffered solutions with a detection limit of 1 ng mL-1 within 30 min. Furthermore, the BioSERS chip was used to detect the target protein in scarcely spiked human serum. This study demonstrates the possibility of a clinical application that can improve the detection limit and accuracy of the currently commercialized SARS-CoV-2 immunodiagnostic kit. Additionally, the system is modular and can be applied to detect other proteins by only changing the aptamer.

Nitroaromatic explosives' detection and quantification using an attention-based transformer on surface-enhanced Raman spectroscopy maps

Rapidly and accurately detecting and quantifying the concentrations of nitroaromatic explosives is critical for public health and security. Among existing approaches, explosives' detection with Surface-Enhanced Raman Spectroscopy (SERS) has received considerable attention due to its high sensitivity. Typically, a preprocessed single spectrum that is the average of the entire or a selected subset of a SERS map is used to train various machine learning models for detection and quantification. Designing an appropriate averaging and preprocessing procedure for SERS maps across different concentrations is time-consuming and computationally costly, and the averaging of spectra may lead to the loss of crucial spectral information. We propose an attention-based vision transformer neural network for nitroaromatic explosives' detection and quantification that takes raw SERS maps as the input without any preprocessing. We produce two novel SERS datasets, 2,4-dinitrophenols (DNP) and picric acid (PA), and one benchmark SERS dataset, 4-nitrobenzenethiol (4-NBT), which have repeated measurements down to concentrations of 1 nM to illustrate the detection limit. We experimentally show that our approach outperforms or is on par with the existing methods in terms of detection and concentration prediction accuracy. With the produced attention maps, we can further identify the regions with a higher signal-to-noise ratio in the SERS maps. Based on our findings, the molecule of interest detection and concentration prediction using raw SERS maps is a promising alternative to existing approaches.

SERS immuno- and apta-assays in biosensing/bio-detection: Performance comparison, clinical applications, challenges

Surface Enhanced Raman Spectroscopy is increasingly used as a sensitive bioanalytical tool for detection of variety of analytes ranging from viruses and bacteria to cancer biomarkers and toxins, etc. This comprehensive review describes principles of operation and compares the performance of immunoassays and aptamer assays with Surface Enhanced Raman scattering (SERS) detection to each other and to some other bioassay methods, including ELISA and fluorescence assays. Both immuno- and aptamer-based assays are categorized into assay on solid substrates, assays with magnetic nanoparticles and assays in laminar flow or/and strip assays. The best performing and recent examples of assays in each category are described in the text and illustrated in the figures. The average performance, particularly, limit of detection (LOD) for each of those methods reflected in 9 tables of the manuscript and average LODs are calculated and compared. We found out that, on average, there is some advantage in terms of LOD for SERS immunoassays (0.5 pM median LOD of 88 papers) vs SERS aptamer-based assays (1.7 pM median LOD of 51 papers). We also tabulated and analyzed the clinical performance of SERS immune and aptamer assays, where selectivity, specificity, and accuracy are reported, we summarized the best examples. We also reviewed challenges to SERS bioassay performance and real-life application, including non-specific protein binding, nanoparticle aggregation, limited nanotag stability, sometimes, relatively long time to results, etc. The proposed solutions to those challenges are also discussed in the review. Overall, this review may be interesting not only to bioanalytical chemist, but to medical and life science researchers who are interested in improvement of bioanalyte detection and diagnostics.

Giving Gold Wings: Ultrabright and Fragmentation Free Mass Spectrometry Reporters for Barcoding, Bioconjugation Monitoring, and Data Storage

The widespread application of laser desorption/ionization mass spectrometry (LDI-MS) highlights the need for a bright and multiplexable labeling platform. While ligand-capped Au nanoparticles (AuNPs) have emerged as a promising LDI-MS contrast agent, the predominant thiol ligands suffer from low ion yields and extensive fragmentation. In this work, we develop a N-heterocyclic carbene (NHC) ligand platform that enhances AuNP LDI-MS performance. NHC scaffolds are tuned to generate barcoded AuNPs which, when benchmarked against thiol-AuNPs, are bright mass tags and form unfragmented ions in high yield. To illustrate the transformative potential of NHC ligands, the mass tags were employed in three orthogonal applications: monitoring a bioconjugation reaction, performing multiplexed imaging, and storing and reading encoded information. These results demonstrate that NHC-nanoparticle systems are an ideal platform for LDI-MS and greatly broaden the scope of nanoparticle contrast agents.

Ultrasensitive Optical Fingerprinting of Biorelevant Molecules by Means of SERS-Mapping on Nanostructured Metasurfaces

The most relevant technique for portable (on-chip) sensors is Surface Enhanced Raman Scattering (SERS). This strategy crashes in the case of large (biorelevant) molecules and nano-objects, whose SERS spectra are irreproducible for "homeopathic" concentrations. We suggested solving this problem by SERS-mapping. We analyzed the distributions of SERS parameters for relatively "small" (malachite green (MG)) and "large" (phthalocyanine, H₂Pc*) molecules. While fluctuations of spectra for "small" MG were negligible, noticeable distribution of spectra was observed for "large" H₂Pc*. We show that the latter is due to a random arrangement of molecules with respect to "hot spot" areas, which have limited sizes, thus amplifying the lines corresponding to vibrations of different molecule parts. We have developed a method for engineering low-cost SERS substrates optimized for the best enhancement efficiency and a measurement protocol to obtain a reliable Raman spectrum, even for a countable number of large molecules randomly distributed over the substrate.

Effect of the Combination of Gold Nanoparticles and Polyelectrolyte Layers on SERS Measurements

In this study, polyelectrolyte (PE) layers are deposited on substrates made by glass covered with an array of gold nanoparticles (GNPs). In particular, the samples studied have 0 PE layers (GGPE0), 3 PE layers (GGPE3), 11 PE layers (GGPE11), and 21 PE layers (GGPE21). All samples have been studied by micro-Raman spectroscopy. An acetic acid solution (10% v/v) has been used as a standard solution in order to investigate the SERS effect induced by different numbers of PE layers in each sample. The Surface Enhancement Raman Spectroscopy (SERS) effect correlating to the number of PE layers deposited on the samples has been shown. This effect is explained in terms of an increase in the interaction between the photon of the laser source and the plasmonic band of the GNPs due to a change of the permittivity of the surrounding medium around the GNPs. The trends of the ratios of the intensities of the Raman bands of the acetic acid solution (acetic acid and water molecules) on the band at 1098 cm-1 ascribed to the substrates increase, and the number of PE layers increases.

Towards Label-free detection of viral disease agents through their cell surface proteins: Rapid screening SARS-CoV-2 in biological specimens

Current methods for the screening of viral infections in clinical settings, such as reverse transcription polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA), are expensive, time-consuming, require trained personnel and sophisticated instruments. Therefore, novel sensors that can save time and cost are required specially in remote areas and developing countries that may lack the advanced scientific infrastructure for this task. In this work, we present a sensitive, and highly specific biosensing approach for the detection of harmful viruses that have cysteine residues within the structure of their cell surface proteins. We utilized new method for the rapid screening of SARS-CoV-2 virus in biological fluids through its S1 protein by surface enhanced Raman spectroscopy (SERS). The protein is captured from aqueous solutions and biological specimens using a target-specific extractor substrate. The structure of the purified protein is then modified to convert it into a bio-thiol by breaking the disulfide bonds and freeing up the sulfhydryl (SH) groups of the cysteine residues. The formed biothiol chemisorbs favourably onto a highly sensitive plasmonic sensor and probed by a handheld Raman device in few seconds. The new method was used to screen the S1 protein in aqueous medium, spiked human blood plasma, mucus, and saliva samples down to 150 fg/L. The label-free SERS biosensing method has strong potential for the fingerprint identification many viruses (e.g. the human immunodeficiency virus, the human polyomavirus, the human papilloma virus, the adeno associated viruses, the enteroviruses) through the cysteine residues of their capsid proteins. The new method can be applied at points of care (POC) in remote areas and developing countries lacking sophisticated scientific infrastructure.

An antigen-targeting assay for Lyme disease: Combining aptamers and SERS to detect the OspA protein

Lyme disease is the fastest growing vector-borne disease in the United States. However, current testing modalities are ill suited to detection of Lyme disease, leading to the diagnosis of many cases after treatment is effective. We present an improved, direct method Lyme disease diagnosis, where the Lyme specific biomarker Outer Surface Protein A (OspA) in clinical serum samples is identified using a diagnostic platform combining surface enhanced Raman scattering (SERS) and aptamers. Employing orthogonal projections to latent structures discriminant analysis, the system accurately identified 91% of serum samples from Lyme patients, and 96% of serum samples from symptomatic controls. In addition, the OspA limit-of-detection, determined to be 1 × 10^-4 ng/mL, is greater than four orders of magnitude lower than that found in serum samples from early Lyme disease patients. The application of this platform to detect this difficult-to-diagnose disease suggests its potential for detecting other diseases that present similar difficulties.

Prospects of Surface-Enhanced Raman Spectroscopy for Biomarker Monitoring toward Precision Medicine

Future precision medicine will be undoubtedly sustained by the detection of validated biomarkers that enable a precise classification of patients based on their predicted disease risk, prognosis, and response to a specific treatment. Up to now, genomics, transcriptomics, and immunohistochemistry have been the main clinically amenable tools at hand for identifying key diagnostic, prognostic, and predictive biomarkers. However, other molecular strategies, including metabolomics, are still in their infancy and require the development of new biomarker detection technologies, toward routine implementation into clinical diagnosis. In this context, surface-enhanced Raman scattering (SERS) spectroscopy has been recognized as a promising technology for clinical monitoring thanks to its high sensitivity and label-free operation, which should help accelerate the discovery of biomarkers and their corresponding screening in a simpler, faster, and less-expensive manner. Many studies have demonstrated the excellent performance of SERS in biomedical applications. However, such studies have also revealed several variables that should be considered for accurate SERS monitoring, in particular, when the signal is collected from biological sources (tissues, cells or biofluids). This Perspective is aimed at piecing together the puzzle of SERS in biomarker monitoring, with a view on future challenges and implications. We address the most relevant requirements of plasmonic substrates for biomedical applications, as well as the implementation of tools from artificial intelligence or biotechnology to guide the development of highly versatile sensors.

Fluorescence and electrochemical detection of iodine vapor in the presence of high humidity using Ln-based MOFs

Efficient detection of toxic radioiodine species emitted by nuclear-related activities and accidents is crucial for the health of the human body and safety of the environment. Herein we report that a series of stable Ln-based MOFs with BTC linkers (Ln-BTCs) could provide dual fluorescence and electrochemical response of iodine vapor in the presence of humidity. Iodine molecules could be attracted by the oxygen sites of carboxylate linkers and confined in the cavities of Ln-BTCs. Due to the photoinduced electron transfer effect, the fluorescence of Ln-BTCs is quenched drastically in the presence of iodine. Meanwhile, the conductivity of Ln-BTCs could reach an increase of 107 fold in magnitude after iodine trapping. Water molecules could also be trapped in Ln-BTCs, having interacted with the frameworks via hydrogen bonds, and reduce the iodine uptake capacity, but they cannot alter the fluorescence and conductive properties of Ln-BTCs as distinctly as iodine molecules could. Besides, Raman mapping suggests a diffusion coefficient of 1.5 × 10-14 m2 s-1 for iodine transport in the porous Eu-BTC. The dual fluorescence and electrochemical signal outputs show high sensitivity and attractive ability to reduce false positives, which could be useful for potential integration for sensing radioiodine vapor.

Quantification of Methotrexate in Human Serum Using Surface-Enhanced Raman Scattering-Toward Therapeutic Drug Monitoring

Therapeutic drug monitoring (TDM) can improve clinical care when using drugs with pharmacokinetic variability and a narrow therapeutic window. Rapid, reliable, and easy-to-use detection methods are required in order to decrease the time of analysis and can also enable TDM in resource-limited settings or even at bedside. Monitoring methotrexate (MTX), an anticancer drug, is critical since it is needed to follow the drug clearance rate and decide how to administer the rescue drug, leucovorin (LV), in order to avoid toxicity and even death. We show that with the optimized nanopillar-assisted separation (NPAS) method using surface-enhanced Raman scattering, we were able to measure MTX in PBS and serum in the linear range of 5-150 μM and confirmed that MTX detection can be carried out even in the presence of LV. Additionally, when NPAS was combined with centrifugal filtration, a quantification limit of 2.1 μM for MTX in human serum sample was achieved. The developed detection method enables fast detection (10 min) and quantification of MTX from human serum (>90% accuracy). Furthermore, we show the potential of the developed method for TDM, when quantifying MTX from clinical samples, collected from patients who are undergoing high-dose MTX therapy.

Nucleation and Growth-Controlled Facile Fabrication of Gold Nanoporous Structures for Highly Sensitive Surface-Enhanced Raman Spectroscopy Applications

The fabrication of porous metal structures usually involves complicated processes such as lithography or etching. In this study, a facile and clean method based on thermal evaporation at high pressure is introduced, by which a highly porous, black colored structure of Au can be formed through the control of homogeneous nucleation and growth during evaporation. The deposited films have different morphologies, from columnar to nanoporous structures, depending on the working pressure. These porous structures consist of Au nanoparticle aggregates, and a large number of nano-gaps are found among the nanoparticles. Thus, these structures indicate a much higher intensity of surface-enhanced Raman spectroscopy (SERS) when compared with commercial SERS substrates. The SERS intensity depends on the working pressure and thickness. Even circumstances that can induce agglomeration of nanoparticle aggregates do not deteriorate the sensitivity of SERS. These nanoporous structures based on high-pressure thermal evaporation are expected to provide a new platform for the development of low-cost and highly sensitive chemical sensors.

Recent developments on gold nanostructures for surface enhanced Raman spectroscopy: Particle shape, substrates and analytical applications. A review

Surface enhanced Raman spectroscopy (SERS) is a powerful technique for sensitive analysis which is attracting great attention in the last decades. In this review, different gold nanostructures that have been exploited for SERS analysis are described, ranging from gold nanospheres to anisotropic and complex-shaped gold nanostructures, in which the presence of high aspect ratio features leads to an increment of the electromagnetic field at the surface of the nanomaterial, resulting in enhanced SERS response. In addition to the shape of the nanostructure, the interparticle nanogaps play a prominent role in the SERS efficiency. In this sense, different approaches such as nanoaggregation and formation of assemblies and ordered structures lead to the creation of the so-called hot spots. SERS measurements may be performed in solution, while usually the nanostructures are deposited building a SERS substrate, which can be created via attachment of chemically prepared gold nanostructures, as well as via top-down physical methods. Among the classical supports for creating the SERS substrates, in the last years there is a trend towards the development of flexible supports based on polymers as well as paper. Finally, some recent applications of gold nanostructures-based SERS substrates within the analytical field are discussed to spotlight the potential of this technique in real-world analytical scenarios.

A sensitive spectrophotometric ellipsometry based Aptasensor for the vascular endothelial growth factor detection

A sensitive and selective, aptamer and spectroscopic ellipsometry based sensor is reported here for the early diagnosis of breast cancer, which is a common type of cancer following lung cancer. It was aimed to develop a single-step and label-free assay for the sensitive and selective detection of VEGF₁₆₅. To this end, two different aptamers and spectroscopic ellipsometry were used. In the presented study, by determining the appropriate aptamer immobilization conditions, the spectroscopic ellipsometry technique was successfully applied for the detection of VEGF₁₆₅ at the range of 1 pM-1000 pM in the buffer. Aptasensors have a detection limit of 5.81 pM and 4.29 pM, respectively.

SERS imaging-based aptasensor for ultrasensitive and reproducible detection of influenza virus A

Surface-enhanced Raman scattering (SERS)-based aptasensors display high sensitivity for influenza A/H1N1 virus detection but improved signal reproducibility is required. Therefore, in this study, we fabricated a three-dimensional (3D) nano-popcorn plasmonic substrate using the surface energy difference between a perfluorodecanethiol (PFDT) spacer and the Au layer. This energy difference led to Au nanoparticle self-assembly; neighboring nanoparticles then created multiple hotspots on the substrate. The localized surface plasmon effects at the hot spots dramatically enhanced the incident field. Quantitative evaluation of A/H1N1 virus was achieved using the decrease of Raman peak intensity resulting from the release of Cy3-labeled aptamer DNAs from nano-popcorn substrate surfaces via the interaction between the aptamer DNA and A/H1N1 virus. The use of a Raman imaging technique involving the fast mapping of all pixel points enabled the reproducible quantification of A/H1N1 virus on nano-popcorn substrates. Average ensemble effects obtained by averaging all randomly distributed hot spots mapped on the substrate made it possible to reliably quantify target viruses. The SERS-based imaging aptasensor platform proposed in this work overcomes the issues inherent in conventional approaches (the time-consuming and labor-intensiveness of RT-PCR and low sensitivity and quantitative analysis limits of lateral flow assay kits). Our SERS-based assay for detecting A/H1N1 virus had an estimated limit of detection of 97 PFU mL-1 (approximately three orders of magnitude more sensitive than that determined by the enzyme-linked immunosorbent assay) and the approximate assay time was estimated to be 20 min. Thus, this approach provides an ultrasensitive, reliable platform for detecting viral pathogens.

A SERS-colorimetric dual-mode aptasensor for the detection of cancer biomarker MUC1

Human mucin-1 (MUC1) has attracted considerable attention owing to its overexpression in diverse malignancies. Here, for the rapid and efficient detection of MUC1, we present a SERS-colorimetric dual-mode aptasensor, by integrating SERS probes with magnetic separation, which has several distinctive advantages. Using such a dual-mode aptasensor, the colorimetric functionality is distinguishable by the naked eye, providing a fast and straightforward screening ability for the detection of MUC1. Moreover, SERS-based detection greatly improves the detection sensitivity, reaching a limit of detection of 0.1 U/mL. In addition, the combination of SERS and colorimetric method holds the advantages of these two techniques and thereby increases the reliability and efficiency of MUC1 detection. On the one hand, the magnetic nanobeads functionalized with MUC1-specific aptamer were utilized as an efficient capturing substrate for separating MUC1 from biological complex medium. On the other hand, the gold-silver core-shell nanoparticles modified with Raman reporters and the complementary sequences of MUC1 were used as the signal indicator, which could simultaneously report the SERS signal and colorimetric change. This strategy can achieve a good detection range and realize MUC1 analysis in real patients' samples. Thus, we anticipate that this kind of aptasensor would provide promising potential applications in the diagnosis and prognosis of cancers. Graphical abstract.

Block Copolymer Derived Vertically Coupled Plasmonic Arrays for Surface-Enhanced Raman Spectroscopy

A surface-enhanced Raman spectroscopy sensing template consisting of gold-covered nanopillars is developed. The plasmonic slab consists of a perforated gold film at the base of the nanopillars and a Babinet complementary dot array on top of the pillars. The nanopillars were fabricated by the incorporation of an iron salt precursor into a self-assembled block copolymer thin film and subsequent reactive ion etching. The preparation is easy, scalable, and cost-effective. We report on the increase in surface-enhanced Raman scattering efficiency for smaller pillar heights and stronger coupling between the dot array and perforated gold film with average enhancement factors as high as 10⁷. In addition, the block copolymer-derived templates show an excellent relative standard deviation of 8% in the measurement of the Raman intensity. Finite difference time domain simulations were performed to investigate the nature of the electromagnetic near-field enhancement and to identify plasmonic hot spots.

Phosphorylation-Dependent SERS Readout for Activity Assay of Protein Kinase A in Cell Extracts

Protein kinases are key regulators of cell function, the abnormal activity of which may induce several human diseases, including cancers. Therefore, it is of great significance to develop a sensitive and reliable method for assaying protein kinase activities in real biological samples. Here, we report the phosphorylation-dependent surface-enhanced Raman scattering (SERS) readout of spermine-functionalized silver nanoparticles (AgNPs) for protein kinase A (PKA) activity assay in cell extracts. In this assay, the presence of PKA would phosphorylate and alter the net charge states of Raman dye-labeled substrate peptides, and the resulting anionic products could absorb onto the AgNPs with cationic surface charge through electrostatic attraction. Meanwhile, the Raman signals of dyes labeled on peptides were strongly enhanced by the aggregated AgNPs with interparticle hot spots formed in assay buffer. The SERS readout was directly proportional to the PKA activity in a wide range of 0.0001-0.5 U·μL^-1 with a detection limit as low as 0.00003 U·μL^-1. Moreover, the proposed SERS-based assay for the PKA activity was successfully applied to monitoring the activity and inhibition of PKA in real biological samples, particularly in cell extracts, which would be beneficial for kinase-related disease diagnostics and inhibitor screening.

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.

Engineering State-of-the-Art Plasmonic Nanomaterials for SERS-Based Clinical Liquid Biopsy Applications

Precision oncology, defined as the use of the molecular understanding of cancer to implement personalized patient treatment, is currently at the heart of revolutionizing oncology practice. Due to the need for repeated molecular tumor analyses in facilitating precision oncology, liquid biopsies, which involve the detection of noninvasive cancer biomarkers in circulation, may be a critical key. Yet, existing liquid biopsy analysis technologies are still undergoing an evolution to address the challenges of analyzing trace quantities of circulating tumor biomarkers reliably and cost effectively. Consequently, the recent emergence of cutting-edge plasmonic nanomaterials represents a paradigm shift in harnessing the unique merits of surface-enhanced Raman scattering (SERS) biosensing platforms for clinical liquid biopsy applications. Herein, an expansive review on the design/synthesis of a new generation of diverse plasmonic nanomaterials, and an updated evaluation of their demonstrated SERS-based uses in liquid biopsies, such as circulating tumor cells, tumor-derived extracellular vesicles, as well as circulating cancer proteins, and tumor nucleic acids is presented. Existing challenges impeding the clinical translation of plasmonic nanomaterials for SERS-based liquid biopsy applications are also identified, and outlooks and insights into advancing this rapidly growing field for practical patient use are provided.

Raman Spectroscopy and Aptamers for a Label-Free Approach: Diagnostic and Application Tools

Raman spectroscopy is a powerful optical technique based on the inelastic scattering of incident light to assess the chemical composition of a sample, including biological ones. Medical diagnostic applications of Raman spectroscopy are constantly increasing to provide biochemical and structural information on several specimens, being not affected by water interference, and potentially avoiding the constraint of additional labelling procedures. New strategies have been recently developed to overcome some Raman limitations related, for instance, to the need to deal with an adequate quantity of the sample to perform a reliable analysis. In this regard, the use of metallic nanoparticles, the optimization of fiber optic probes, and other approaches can actually enhance the signal intensity compared to spontaneous Raman scattering. Moreover, to further increase the potential of this investigation technique, aptamers can be considered as a valuable means, being synthetic, short, single, or double-stranded oligonucleotides (RNAs or DNAs) that fold up into unique 3D structures to specifically bind to selected molecules, even at very low concentrations, and thus allowing an early diagnosis of a possible disease. Due to the paramount relevance of the topic, this review focuses on the main Raman spectroscopy techniques combined with aptamer arrays in the label-free mode, providing an overview on different applications to support healthcare management.

Highly Sensitive and Selective Nanogap-Enhanced SERS Sensing Platform

This paper reports a highly sensitive and selective surface-enhanced Raman spectroscopy (SERS) sensing platform. We used a simple fabrication method to generate plasmonic hotspots through a direct maskless plasma etching of a polymer surface and the surface tension-driven assembly of high aspect ratio Ag/polymer nanopillars. These collapsed plasmonic nanopillars produced an enhanced near-field interaction via coupled localized surface plasmon resonance. The high density of the small nanogaps yielded a high plasmonic detection performance, with an average SERS enhancement factor of 1.5 × 10⁷. More importantly, we demonstrated that the encapsulation of plasmonic nanostructures within nanofiltration membranes allowed the selective filtration of small molecules based on the degree of membrane swelling in organic solvents and molecular size. Nanofiltration membrane-encapsulated SERS substrates do not require pretreatments. Therefore, they provide a simple and fast detection of toxic molecules using portable Raman spectroscopy.

Multimeric Rhodamine Dye-Induced Aggregation of Silver Nanoparticles for Surface-Enhanced Raman Scattering

Isotopic variants of Rhodamine 6G (R6G) have previously been used as a method of multiplexed detection for Surface Enhanced Raman Spectroscopy (SERS), including protein detection and quantification. Challenges exist, however, with producing long-term stable SERS signals with exposure to silver or gold metal surfaces without the use of additional protective coatings of nanomaterials. Here, novel rhodamine "dimers" and "trimers" have been created that demonstrate a higher avidity for metal nanoparticles and induce aggregation to create plasmonic "hotspots" as indicated by enhanced Raman scattering in situ. These aggregates can be formed in a colloid, on surfaces, or membrane substrates such as poly(vinylidene fluoride) for applications in biosciences. The integrity of the materials and Raman signals are maintained for months of time on different substrates. These dye materials should provide avenues for simplified in situ generation of sensors for Raman-based assays especially in settings requiring highly robust performance.

Nanopillar-Assisted SERS Chromatography

Practical implementation of surfaced enhanced Raman spectroscopy (SERS) sensing is hindered by complexity of real-life samples, which often requires long and costly pretreatment and purification. Here, we present a novel nanopillar-assisted SERS chromatography (NPC-SERS) method for simultaneous quantitation of target molecules and analysis of complex, multicomponent fluids, e.g., human urine spiked with a model drug paracetamol (PAR). Gold-coated silicon nanopillar (AuNP) SERS substrates and a centrifugal microfluidic platform are tactfully combined, which allows (i) a precise and fully automated sample manipulation and (ii) spatial separation of different molecular species on the AuNP substrate. The NPC-SERS technique provides a novel approach for wetting the stationary phase (AuNP) using the "wicking effect", and thus minimizes dilution of analytes. Separation of PAR and the main human urine components (urea, uric acid, and creatinine) has been demonstrated. Quantitative detection of PAR with ultrawide linear dynamic range (0-500 ppm) is achieved by analyzing the spreading profiles of PAR on the AuNP surface. NPC-SERS transforms SERS into a sensing technique with general applicability, facilitating rapid and quantitative detection of analytes in complex biofluids, such as saliva, blood, and urine.

Sensitive and Reproducible Immunoassay of Multiple Mycotoxins Using Surface-Enhanced Raman Scattering Mapping on 3D Plasmonic Nanopillar Arrays

A surface-enhanced Raman scattering-based mapping technique is reported for the highly sensitive and reproducible analysis of multiple mycotoxins. Raman images of three mycotoxins, ochratoxin A (OTA), fumonisin B (FUMB), and aflatoxin B1 (AFB1) are obtained by rapidly scanning the surface-enhanced Raman scattering (SERS) nanotags-anchoring mycotoxins captured on a nanopillar plasmonic substrate. In this system, the decreased gap distance between nanopillars by their leaning effects as well as the multiple hot spots between SERS nanotags and nanopillars greatly enhances the coupling of local plasmonic fields. This strong enhancement effect makes it possible to perform a highly sensitive detection of multiple mycotoxins. In addition, the high uniformity of the densely packed nanopillar substrate minimizes the spot-to-spot fluctuations of the Raman peak intensity in the scanned area when Raman mapping is performed. Consequently, this makes it possible to gain a highly reproducible quantitative analysis of mycotoxins. The limit of detections (LODs) are determined to be 5.09, 5.11, and 6.07 pg mL^-1 for OTA, FUMB, and AFB1, and these values are approximately two orders of magnitude more sensitive than those determined by the enzyme-linked immunosorbent assays. It is believed that this SERS-based mapping technique provides a facile tool for the sensitive and reproducible quantification of various biotarget molecules.

Flexible, transparent and highly sensitive SERS substrates with cross-nanoporous structures for fast on-site detection

A flexible and transparent film assembled from the cross-nanoporous structures of Au on PET (CNS of Au@PET) is developed as a versatile and effective SERS substrate for rapid, on-site trace analysis with high sensitivity. The fabrication of the CNS of Au can be achieved on a large scale at low cost by employing an etching process with super-aligned carbon nanotubes as a mask, followed by metal deposition. A strongly enhanced Raman signal with good uniformity can be obtained, which is attributed to the excitation of "hot spots" around the metal nanogaps and sharp edges. Using the CNS of Au@PET film as a SERS platform, real-time and on-site SERS detection of the food contaminant crystal violet (CV) is achieved, with a detection limit of CV solution on a tomato skin of 10-7 M. Owing to its ability to efficiently extract trace analytes, the resulting substrate also achieves detection of 4-ATP contaminants and thiram pesticides by swabbing the skin of an apple. A SERS detection signal for 4-ATP has a relative standard deviation of less than 10%, revealing the excellent reproducibility of the substrate. The flexible, transparent and highly sensitive substrates fabricated using this simple and cost-effective strategy are promising for practical application in rapid, on-site SERS-based detection.

Dual-Excitation Nanocellulose Plasmonic Membranes for Molecular and Cellular SERS Detection

We demonstrate that cellulose nanofiber (CNF) biomaterials with high transparency and mechanical robustness can be combined with gold nanorods to form a multifunctional porous membrane for dual-mode surface-enhanced Raman scattering (SERS) detection of both small molecules and cells. The nanoporous nature of the nanofiber membranes allows for effective molecular filtration and preconcentration of the analytes, further boosting the SERS performance. Specifically, because of the low fluorescence and Raman background of the CNF matrix, extremely low loading density of gold nanorods can be used. The nanorod assemblies within the CNF network can be resonantly driven by a 532 nm laser (transverse plasmonic mode) and near resonantly driven at by a 785 nm laser (longitudinal mode), facilitating dual operational modes at two excitation wavelengths. The shorter wavelength excitation mode yields better Raman scattering efficiency and has been demonstrated to be capable of detecting rhodamine 6G (R6G) dyes down to picomolar concentrations. On the other hand, the longer wavelength excitation mode provides autofluorescence suppression for the better detection of microorganisms such as Escherichia coli, shortening the required integration time from hours to minutes. Upon drastically lowering the spectral background noise and utilizing nanofiltration, the plasmonic CNF membranes reported here show significantly improved SERS sensitivity and detection fidelity as compared to traditional metal, metal oxide, synthetic polymer, and paper SERS substrates.

Progress in the Development of SERS-Active Substrates Based on Metal-Coated Porous Silicon

The present work gives an overview of the developments in surface-enhanced Raman scattering (SERS) with metal-coated porous silicon used as an active substrate. We focused this review on the research referenced to SERS-active materials based on porous silicon, beginning from the patent application in 2002 and enclosing the studies of this year. Porous silicon and metal deposition technologies are discussed. Since the earliest studies, a number of fundamentally different plasmonic nanostructures including metallic dendrites, quasi-ordered arrays of metallic nanoparticles (NPs), and metallic nanovoids have been grown on porous silicon, defined by the morphology of this host material. SERS-active substrates based on porous silicon have been found to combine a high and well-reproducible signal level, storage stability, cost-effective technology and handy use. They make it possible to identify and study many compounds including biomolecules with a detection limit varying from milli- to femtomolar concentrations. The progress reviewed here demonstrates the great prospects for the extensive use of the metal-coated porous silicon for bioanalysis by SERS-spectroscopy.

Thrombin Assessment on Nanostructured Label-Free Aptamer-Based Sensors: A Mapping Investigation via Surface-Enhanced Raman Spectroscopy

Aptamers, synthetic single-stranded DNA or RNA molecules, can be regarded as a valuable improvement to develop novel ad hoc sensors to diagnose several clinical pathologies. Their intrinsic potential is related to the high specificity and sensitivity to the selected target biomarkers, being capable of detecting very low concentrations and thus allowing an early diagnosis of a possible disease. This kind of probe can be usefully integrated into a number of different devices in order to provide a reliable acquisition of the analyte and properly elaborate the related signal. The study presents the fabrication and characterization of a label-free aptamer sensor designed using a gold-coated silicon nanostructured substrate to map the target molecule by means of surface-enhanced Raman spectroscopy (SERS). As a proof, thrombin was used as a model at four different concentrations (i.e., 0.0873, 0.873, 8.73, and 87.3 nM). SERS mapping analysis was carried out considering each representative band of the aptamer-thrombin complex (centered at 822, 1140, and 1558 cm⁻¹) and then combining them in order to acquire a comprehensive and unambiguous measure of the target. In both cases, a valuable correlation was evaluated, even if the first approach can suffer from some limitations in the third band related to lower definition of the characteristic peak compared to those in the other two bands.

Culture-Free Detection of Bacterial Pathogens on Plasmonic Nanopillar Arrays Using Rapid Raman Mapping

We utilized a fast Raman spectral mapping technique for fast detection of bacterial pathogens. Three-dimensional (3D) plasmonic nanopillar arrays were fabricated using the nanolithography-free process consisting of maskless Ar plasma treatment of a polyethylene terephthalate substrate and subsequent metal deposition. Bacterial pathogens were immobilized on the positively charged poly(l-lysine)-coated 3D plasmonic substrate through electrostatic interactions. Then, the bacterial surfaces were selectively labeled with antibody-conjugated surface-enhanced Raman scattering (SERS) nanotags, and Raman mapping images were collected and statistically analyzed for quantitative analysis of bacteria. Salmonella typhimurium was selected as a model pathogen bacterium to confirm the efficacy of our SERS imaging technique. Minimum number of Raman mapping points with statistical reliability was determined to reduce assay time. It was possible to get a statistically reliable standard calibration curve for 529 pixels (laser spot with 60 μm interval), which required a total mapping time of 45 min to get a standard calibration curve for five different concentrations of bacteria in the 0 to 10⁶ CFU/mL range. No amplification step was necessary for quantification because low-abundance target bacteria could be measured using the Raman spectral mapping technique. Therefore, this approach allows accurate quantification of bacterial pathogens without any culturing or enrichment process.

3D ZnO/Ag Surface-Enhanced Raman Scattering on Disposable and Flexible Cardboard Platforms

In the present study, zinc oxide (ZnO) nanorods (NRs) with a hexagonal structure have been synthesized via a hydrothermal method assisted by microwave radiation, using specialized cardboard materials as substrates. Cardboard-type substrates are cost-efficient and robust paper-based platforms that can be integrated into several opto-electronic applications for medical diagnostics, analysis and/or quality control devices. This class of substrates also enables highly-sensitive Raman molecular detection, amiable to several different operational environments and target surfaces. The structural characterization of the ZnO NR arrays has been carried out by X-ray diffraction (XRD), scanning electron microscopy (SEM) and optical measurements. The effects of the synthesis time (5–30 min) and temperature (70–130 °C) of the ZnO NR arrays decorated with silver nanoparticles (AgNPs) have been investigated in view of their application for surface-enhanced Raman scattering (SERS) molecular detection. The size and density of the ZnO NRs, as well as those of the AgNPs, are shown to play a central role in the final SERS response. A Raman enhancement factor of 7 × 10⁵ was obtained using rhodamine 6 G (R6G) as the test analyte; a ZnO NR array was produced for only 5 min at 70 °C. This condition presents higher ZnO NR and AgNP densities, thereby increasing the total number of plasmonic “hot-spots”, their volume coverage and the number of analyte molecules that are subject to enhanced sensing.

Chemical Functionalization of Plasmonic Surface Biosensors: A Tutorial Review on Issues, Strategies, and Costs

In an ideal plasmonic surface sensor, the bioactive area, where analytes are recognized by specific biomolecules, is surrounded by an area that is generally composed of a different material. The latter, often the surface of the supporting chip, is generally hard to be selectively functionalized, with respect to the active area. As a result, cross talks between the active area and the surrounding one may occur. In designing a plasmonic sensor, various issues must be addressed: the specificity of analyte recognition, the orientation of the immobilized biomolecule that acts as the analyte receptor, and the selectivity of surface coverage. The objective of this tutorial review is to introduce the main rational tools required for a correct and complete approach to chemically functionalize plasmonic surface biosensors. After a short introduction, the review discusses, in detail, the most common strategies for achieving effective surface functionalization. The most important issues, such as the orientation of active molecules and spatial and chemical selectivity, are considered. A list of well-defined protocols is suggested for the most common practical situations. Importantly, for the reported protocols, we also present direct comparisons in term of costs, labor demand, and risk vs benefit balance. In addition, a survey of the most used characterization techniques necessary to validate the chemical protocols is reported.