SERS Detection of Biomolecules by Highly Sensitive and Reproducible Raman-Enhancing Nanoparticle Array

Reproducible SERS substrates manipulated by interparticle spacing and particle diameter of gold nano-island array using in-situ thermal evaporation

Gold (Au) nano-island arrays were deposited on the glass substrate to fabricate surface-enhanced Raman scattering (SERS) substrates by in-situ thermal evaporation (deposited and annealed samples at the same time). The optimal SERS intensity deposited by various thicknesses and in-situ annealing temperatures of Au nano-island arrays would be investigated. The biomolecules (adenine) were dropped on the well-designed SERS substrate for precise and quantitative SERS detection. The characterization of Au nano-island arrays SERS substrate would be evaluated by scanning electron microscope (SEM) and Raman spectroscopy. The results showed that the optimal deposition thickness and annealing temperature of Au nano-island arrays SERS substrate is about 14 nm and 200 °C respectively, which can construct the smallest interparticle spacing (W)/ particle diameter (D) ratio and the lowest reflection (%) and transmittance (%) to form the strongest SERS intensity. Moreover, finite-difference time-domain (FDTD) simulation of the electromagnetic field distributions on Au nano-island arrays displays the similar trend with the experimental results. The 14 nm deposition with 200 °C in-situ annealing temperature would display the highest density of hot-spots by FDTD simulation. The reproducible Au nano-island arrays SERS substrates with tunable surface roughness, W/D ratio, and lower reflection and transmittance show promising potential for SERS detection of biomolecules, bacteria, and viruses.

Traceability of bilberries (Vaccinium myrtillus L.) of the Baltic-Nordic region using surface-enhanced Raman spectroscopy (SERS): DFT simulation-based DNA analysis

Food traceability is a major issue in the industry. We investigated whether bilberries (Vaccinium myrtillus L.) from 4 different locations within the Baltic-Nordic region could be effectively differentiated using surface-enhanced Raman scattering (SERS) based spectral data and chemometric analyses. Furthermore, we aimed to determine if nucleobase (adenine and cytosine) methylation could be responsible for any observed variation. Our experiment was successful in that both principal component (PCA) and discriminant function analyses (DFA) showed differentiation between bilberry DNA from all 4 geographical regions. Density functional theory (DFT) based simulations allowed us to analyze whether DNA's spectral data dissimilarities may be due to nucleobase methylation. Although results were inconclusive on this, our investigation provides valuable data on simulated versus experimental DNA and DNA component spectra. Further research will be directed towards understanding what other epigenetic changes could be responsible for the observed DNA variation as well as determining the optimal parameters for using DFT simulations in upcoming projects.

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.

Rapid detection of bacteria using gold nanoparticles in SERS with three different capping agents: Thioglucose, polyvinylpyrrolidone, and citrate

The increase in outbreaks of emerging and re-emerging bacterial infections over the last few decades calls for their rapid detection and treatment. Surface-enhanced Raman spectroscopy (SERS) is a technique that can be applied to develop fast screening systems for bacterial presence in biological samples. Optimizing the capping agents in nanoparticle synthesis is important because capping agents are responsible for controlling the morphological features and chemical properties of the nanoparticles that are essential for SERS. To the best of our knowledge, this paper is the first to study the application of gold nanoparticles capped with thioglucose and polyvinylpyrrolidone (PVP) in SERS detection of bacteria as an alternative to the citrate-capped gold nanoparticles that are often used in SERS detection of bacteria. Three different species of bacteria were used in this study: Cutibacterium acnes, Escherichia coli and Staphylococcus aureus (methicillin-sensitive and methicillin-resistant). This study demonstrates that the thioglucose, citrate both show good contribution in bacterial species identification and the thioglucose shows the best among the three capping agents in two types of S. aureus identification. Moreover, although PVP showed high Raman peaks in the SERS spectrum for each type of bacteria, it showed least contribution in identifying species and strains due to its low efficacy in producing responses from different nucleic acid components in the bacteria cells.

Trends in Application of SERS Substrates beyond Ag and Au, and Their Role in Bioanalysis

This article compares the applications of traditional gold and silver-based SERS substrates and less conventional (Pd/Pt, Cu, Al, Si-based) SERS substrates, focusing on sensing, biosensing, and clinical analysis. In recent decades plethora of new biosensing and clinical SERS applications have fueled the search for more cost-effective, scalable, and stable substrates since traditional gold and silver-based substrates are quite expensive, prone to corrosion, contamination and non-specific binding, particularly by S-containing compounds. Following that, we briefly described our experimental experience with Si and Al-based SERS substrates and systematically analyzed the literature on SERS on substrate materials such as Pd/Pt, Cu, Al, and Si. We tabulated and discussed figures of merit such as enhancement factor (EF) and limit of detection (LOD) from analytical applications of these substrates. The results of the comparison showed that Pd/Pt substrates are not practical due to their high cost; Cu-based substrates are less stable and produce lower signal enhancement. Si and Al-based substrates showed promising results, particularly in combination with gold and silver nanostructures since they could produce comparable EFs and LODs as conventional substrates. In addition, their stability and relatively low cost make them viable alternatives for gold and silver-based substrates. Finally, this review highlighted and compared the clinical performance of non-traditional SERS substrates and traditional gold and silver SERS substrates. We discovered that if we take the average sensitivity, specificity, and accuracy of clinical SERS assays reported in the literature, those parameters, particularly accuracy (93-94%), are similar for SERS bioassays on AgNP@Al, Si-based, Au-based, and Ag-based substrates. We hope that this review will encourage research into SERS biosensing on aluminum, silicon, and some other substrates. These Al and Si based substrates may respond efficiently to the major challenges to the SERS practical application. For instance, they may be not only less expensive, e.g., Al foil, but also in some cases more selective and sometimes more reproducible, when compared to gold-only or silver-only based SERS substrates. Overall, it may result in a greater diversity of applicable SERS substrates, allowing for better optimization and selection of the SERS substrate for a specific sensing/biosensing or clinical application.

High Sensitivity SERS Substrate of a Few Nanometers Single-Layer Silver Thickness Fabricated by DC Magnetron Sputtering Technology

Surface-enhanced Raman spectroscopy (SERS) is commonly used for super-selective analysis through nanostructured silver layers in the environment, food quality, biomedicine, and materials science. To fabricate a high-sensitivity but a more accessible device of SERS, DC magnetron sputtering technology was used to realize high sensitivity, low cost, a stable deposition rate, and rapid mass production. This study investigated various thicknesses of a silver film ranging from 3.0 to 12.1 nm by field emission scanning electron microscope, X-ray diffraction, and X-ray photoelectron spectroscopy. In the rhodamine 6G (R6G) testing irradiated by a He-Ne laser beam, the analytical enhancement factor (AEF) of 9.35 × 10⁸, the limit of detection (LOD) of 10^-8 M, and the relative standard deviation (RSD) of 1.61% were better than the other SERS substrates fabricated by the same DC sputtering process because the results showed that the 6 nm thickness silver layer had the highest sensitivity, stability, and lifetime. The paraquat and acetylcholine analytes were further investigated and high sensitivity was also achievable. The proposed SERS samples were evaluated and stored in a low humidity environment for up to forty weeks, and no spectrum attenuation could be detected. Soon, the proposed technology to fabricate high sensitivity, repeatability, and robust SERS substrate will be an optimized process technology in multiple applications.

Structural Transition-Induced Raman Enhancement in Bioinspired Diphenylalanine Peptide Nanotubes

Semiconducting materials are increasingly proposed as alternatives to noble metal nanomaterials to enhance Raman scattering. We demonstrate that bioinspired semiconducting diphenylalanine peptide nanotubes annealed through a reported structural transition can support Raman detection of 10^-7 M concentrations for a range of molecules including mononucleotides. The enhancement is attributed to the introduction of electronic states below the conduction band that facilitate charge transfer to the analyte molecule. These results show that organic semiconductor-based materials can serve as platforms for enhanced Raman scattering for chemical sensing. As the sensor is metal-free, the enhancement is achieved without the introduction of electromagnetic surface-enhanced Raman spectroscopy.

Machine Learning-Based Heavy Metal Ion Detection Using Surface-Enhanced Raman Spectroscopy

Surface-Enhanced Raman Spectroscopy (SERS) is often used for heavy metal ion detection. However, large variations in signal strength, spectral profile, and nonlinearity of measurements often cause problems that produce varying results. It raises concerns about the reproducibility of the results. Consequently, the manual classification of the SERS spectrum requires carefully controlled experimentation that further hinders the large-scale adaptation. Recent advances in machine learning offer decent opportunities to address these issues. However, well-documented procedures for model development and evaluation, as well as benchmark datasets, are missing. Towards this end, we provide the SERS spectral benchmark dataset of lead(II) nitride (Pb(NO3)2) for a heavy metal ion detection task and evaluate the classification performance of several machine learning models. We also perform a comparative study to find the best combination between the preprocessing methods and the machine learning models. The proposed model can successfully identify the Pb(NO3)2 molecule from SERS measurements of independent test experiments. In particular, the proposed model shows an 84.6% balanced accuracy for the cross-batch testing task.

SERSNet: Surface-Enhanced Raman Spectroscopy Based Biomolecule Detection Using Deep Neural Network

Surface-Enhanced Raman Spectroscopy (SERS)-based biomolecule detection has been a challenge due to large variations in signal intensity, spectral profile, and nonlinearity. Recent advances in machine learning offer great opportunities to address these issues. However, well-documented procedures for model development and evaluation, as well as benchmark datasets, are lacking. Towards this end, we provide the SERS spectral benchmark dataset of Rhodamine 6G (R6G) for a molecule detection task and evaluate the classification performance of several machine learning models. We also perform a comparative study to find the best combination between the preprocessing methods and the machine learning models. Our best model, coined as the SERSNet, robustly identifies R6G molecule with excellent independent test performance. In particular, SERSNet shows 95.9% balanced accuracy for the cross-batch testing task.

Surface-enhanced Raman scattering of DNA bases using frozen silver nanoparticle dispersion as a platform

Raman spectroscopy is a powerful method to characterize molecules in various media. Although surface-enhanced Raman scattering (SERS) is often employed to compensate for the intrinsically poor sensitivity of Raman spectroscopy, there remain serious tasks, such as simple preparations of SERS substrates, sensitivity control, and reproducible measurements. Here, we propose freezing as an efficient way to overcome these problems in SERS measurements using DNA bases as model targets. Solutes are expelled from ice crystals and concentrated in the liquid phase upon freezing. Silver nanoparticles (AgNPs) are also concentrated in the liquid phase to aggregate with Raman target analytes. The SERS signal intensity is maximized when the AgNP concentration exceeds the critical aggregation value. Freezing allows up to 5000 times enhancements of the SERS signal. Thus, an efficient SERS platform is prepared by simple freezing. The simultaneous detection of four DNA bases effectively eliminates variations of signal intensities and allows the reliable determination of concentration ratios.

Enhancing Raman signals from bacteria using dielectrophoretic force between conductive lensed fiber and black silicon

An osmium-coated lensed fiber (OLF) probe combined with a silver-coated black silicon (SBS) substrate was used to generate a dielectrophoretic (DEP) force that traps bacteria and enables Raman signal detection from bacteria. The lensed fiber coated with a 2-nm osmium layer was used as an electrode for the DEP force and also as a lens to excite Raman signals. The black silicon coated with a 150-nm silver layer was used both as the surface-enhanced Raman scattering (SERS) substrate and the counter electrode. The enhanced Raman signal was collected by the same OLF probe and further analyzed with a spectrometer. For Raman measurements, a drop of bacterial suspension was placed between the OLF probe and the SBS substrate. By controlling the frequency of an AC voltage on the OLF probe and SBS substrate, a DEP force at 1 MHz concentrated bacteria on the SBS surface and removed the unbound micro-objects in the solution at 1 kHz. A bacteria concentration of 6 × 10⁴ CFU/mL (colony forming units per mL) could be identified in less than 15 min, using a volume of only 1 μL, by recording the variation of the Raman peak at 740 cm^-1.

Advanced Nanoporous Anodic Alumina-Based Optical Sensors for Biomedical Applications

Close-packed hexagonal array nanopores are widely used both in research and industry. A self-ordered nanoporous structure makes anodic aluminum oxide (AAO) one of the most popular nanomaterials. This paper describes the main formation mechanisms for AAO, the AAO fabrication process, and optical sensor applications. The paper is focused on four types of AAO-based optical biosensor technology: surface-Enhanced Raman Scattering (SERS), surface Plasmon Resonance (SPR), reflectometric Interference Spectroscopy (RIfS), and photoluminescence Spectroscopy (PL). AAO-based optical biosensors feature very good selectivity, specificity, and reusability.

Analysis of biomolecules in cochineal dyed archaeological textiles by surface-enhanced Raman spectroscopy

SERS spectroscopy is successfully employed in this work to reveal different components integrating the cochineal colorant employed for dying archaeological textile samples from the Arica Region in North Chile. This analysis was done by in-situ experiments that does not imply the material (colorant and biomolecules) extraction. The spectroscopic analysis of the archaeological textiles by SERS reveals the presence of bands attributed to carminic acid and nucleobases, mainly adenine and guanine. The identification of these biomolecules was also verified in raw cochineal extract and in cochineal dyed replica wool fibers fabricated by us following ancient receipts. The effect of Al on the complexation of carminic acid and other biomolecules was also tested in order to understand the changes induced by the metal interaction on the colorant structure. This study revealed that Al can also complex biomolecules existing in the cochineal extract. In particular, guanine residue seems to interact strongly with the metal, since SERS bands of this residue are enhanced. Furthermore, a theoretical analysis on the interaction of carminic acid and a silver surface was also performed in order to better understand the interaction mechanism between carminic acid and a metal surface that leads to the final SERS spectrum. The results of the present work will be very useful in the identification of different molecules and metal complexes that may be forming part of the cochineal colorant found in archaeological materials.

Selective Fluorescent Sensing of Adenine Via the Emissive Enhancement of a Simple Cobalt Porphyrin

Porphyrins absorb strongly in the visible region and are also excellent fluorophores that emit in the visible region that make them excellent candidates for fluorescence sensing and in vivo imaging. This work describes the fluorescence determination of adenine using cobalt complex of a simple porphyrin. Tetraphenylporphyrin (TPP) and tetraphenylpophyrinatocobalt(II) (CoTPP) were synthesized and characterised. TPP on metallation with cobalt resulted in the red shift of fluorescence emission in the region 652 nm and 716 nm and showed an enhancement in the emission peaks with the addition of the nucleobase, adenine. CoTPP is found to be an efficient fluorescent sensor for adenine in DMF solvent. The fluorescence enhancement is due to the formation of the ground state complex formation between adenine and CoTPP, which is supported by experimental evidences from UV- visible spectra, time resolved fluorescence life time measurements etc. The detection limit of adenine was found to be 4.2 μM using the CoTPP fluorescent probe. The proposed sensor is found to be highly selective for adenine in presence of other nitrogen bases like guanine, cytosine, uracil, thymine, alanine, histidine etc. in 1:1 concentration.

High-sensitivity SERS based sensing on the labeling side of glass slides using low branched gold nanoparticles prepared with surfactant-free synthesis

Surface-enhanced Raman scattering (SERS) has become a more attractive tool for biological and chemical sensing due to having a great detection potential to extremely low concentrations of analyte. Here, we report high-sensitivity SERS detection of low branched gold nanoparticles which are produced by a surfactant-free synthesis method. The effects of the size and branches of nanoparticles on the SERS signal intensity were also investigated. Among the prepared nanoparticles, a new type of nanoparticle with small protrusions produced by using a very low concentration of silver ions (2 μM in final solution) achieved the best enhancement factor of ∼4 × 10⁵ for DTNB used as a probe molecule. SERS measurements were performed on the labeling side of microscope glass slides for the first time. The substrate exhibited a good reproducible SERS signal with a relative standard deviation (RSD) of 1.7%. SERS signal intensity obtained using the labelling side was three times larger compared to that obtained using bare glass. To validate the sensing platform, dopamine, an important modulatory neurotransmitter in the brain, was tested. The reported platform was able to achieve label-free detection of dopamine at picomolar and nanomolar concentration level in aqueous and fetal bovine serum (FBS) solution at pH 8.5 respectively. Due to its surfactant-free preparation and enhanced SERS-based sensing features, our reported platform represents a strong alternative to be used in SERS-based sensing applications.

High-sensitivity dopamine detection on aggregated low branched nanoparticles on labelling side of glass slide as a SERS based sensor.

Effects of cold atmospheric plasma treatment on the morphological and optical properties of plasmonic silver nanoparticles

The use of plasma processes in nanomaterial synthesis is limited by a lack of understanding of the effects of plasma treatment on the morphology and other properties. Here, we studied the effects of atmospheric plasma treatment on the morphology and optical properties of Ag nanoparticles. The Ag nanoparticles were deposited on substrates by injecting an aerosol into flowing argon gas and then treated with a low-temperature atmospheric plasma jet. After plasma treatment, the mean Ag nanoparticle diameter reduced to an average of 5 nm, which was accompanied by a blue shift of ∼70 nm in the peak of the surface plasmon resonance; these results are similar to those obtained by thermal treatment at elevated temperatures. The reduction in nanoparticle size is explained by the redox reaction that occurs on the nanoparticle surface, which is evident from the presence of AgO and Ag₂O Raman peaks in the treated sample. The surface charge changed as a result of plasma treatment, as indicated by a large change in the zeta potential from +25.1 ± 4 mV for the untreated sample to -25.9 ± 6 mV after 15 min of plasma treatment. Surface-enhanced Raman spectroscopy of the plasma-treated films was carried out with the fluorescent dye Rhodamine 6 G, which showed a ∼120-fold enhancement in the signal intensity relative to the untreated substrates. We, therefore, conclude that cold-plasma treatment modified the surface morphology of the Ag nanoparticles, thereby enhancing their optical properties. This technique could be applied to a wide range of nanoparticle systems used in biosensing applications.

Magnetic Assembly Route to Construct Reproducible and Recyclable SERS Substrate

The fabrication of a uniform array film through assembly of colloidal building blocks is of practical interest for the integrated individual and collective functions. Here, a magnetic assembly route was put forward to organize monodisperse noble metal microspheres into a uniform array film for surface-enhanced Raman scattering (SERS) application, which demonstrated the integrated signal sensitivity of single noble metal microspheres and reproducibility of their assembled uniform array film. For this purpose, monodisperse multifunctional Fe3O4@SiO2@TiO2@Ag (FOSTA) colloidal microspheres as building blocks were successfully synthesized through a homemade ultrasonic-assisted reaction system. When used in SERS test, these multifunctional microspheres could firstly bind the analyte (R6G) from solution and then assembled into a uniform film under an external magnetic field, which exhibited high SERS detection sensitivity with good reproducibility. In addition, due to the TiO2 interlayer in FOSTA colloidal microspheres, the building blocks could be recycled and self cleaned through photocatalytic degradation of the adsorbed analyte for recycling SERS application.

APTES Duality and Nanopore Seed Regulation in Homogeneous and Nanoscale-Controlled Reduction of Ag Shell on SiO2 Microparticle for Quantifiable Single Particle SERS

Noble-metal nanoparticles size and packing density are critical for sensitive surface-enhanced Raman scattering (SERS) and controlled preparation of such films required to achieve reproducibility. Provided that they are made reliable, Ag shell on SiO₂ microscopic particles (Ag/SiO₂) are promising candidates for lab-on-a-bead analytical measurements of low analyte concentration in liquid specimen. Here, we selected nanoporous silica microparticles as a substrate for reduction of AgNO₃ with 3-aminopropyltriethoxysilane (APTES). In a single preparation step, homogeneous and continuous films of Ag nanoparticles are formed on SiO₂ surfaces with equimolar concentration of APTES and silver nitrate in ethanol. It is discussed that amine and silane moieties in APTES contribute first to an efficient reduction on the silica and second to capping the Ag nanoparticles. The high density and homogeneity of nanoparticle nucleation is further regulated by the nanoporosity of the silica. The Ag/SiO₂ microparticles were tested for SERS using self-assembled 4-aminothiophenol monolayers, and an enhancement factor of ca. 2 × 10⁶ is measured. Importantly, the SERS relative standard deviation is 36% when a single microparticle is considered and drops to 11% when sets of 10 microparticles are considered. As prepared, the microparticles are highly suitable for state-of-the-art quantitative lab-on-a-bead interrogation of specimens.

Analysis of Biomolecules Based on the Surface Enhanced Raman Spectroscopy

Analyzing biomolecules is essential for disease diagnostics, food safety inspection, environmental monitoring and pharmaceutical development. Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for detecting biomolecules due to its high sensitivity, rapidness and specificity in identifying molecular structures. This review focuses on the SERS analysis of biomolecules originated from humans, animals, plants and microorganisms, combined with nanomaterials as SERS substrates and nanotags. Recent advances in SERS detection of target molecules were summarized with different detection strategies including label-free and label-mediated types. This comprehensive and critical summary of SERS analysis of biomolecules might help researchers from different scientific backgrounds spark new ideas and proposals.

Graphene oxide wrapped with gold nanorods as a tag in a SERS based immunoassay for the hepatitis B surface antigen

A composite consisting of graphene oxide and gold nanorods (GO-GNRs) was designed for the trace determination of hepatitis B surface antigen (HBsAg) using surface enhanced Raman spectroscopy (SERS). GO contains numerous carboxy and hydroxy groups on its surface and therefore can serve as the substrate for decoration with GNRs and for immobilizing antibody against HBsAg. The GNRs (carrying the SERS probe 2-mercaptopyridine) exhibit high SERS activity, and this improves the sensitivity of the biosensor. The antibody on the GO-GNRs binds HBsAg with high specificity, and it results in excellent selectivity. The SERS signal (measured at 1002 cm^-1) increases in the 1-1000 pg·mL^-1 HBsAg concentrations range, and the limit of detection is 0.05 pg·mL^-1 (at an S/N ratio of 3). The immunoassay achieves the sensitive and selective determination of HBsAg in serum and expands the potential application of GO-GNR based SERS tag in clinical research. Graphical abstract A novel graphene oxide-gold nanorod (GO-GNRs) based surface-enhanced Raman scattering (SERS) tag for immunoassay was designed. It allows for sensitive and selective determination of HBsAg in serum. The method is expected to expand the potential application in the environment, in medicine and in food analysis.