Discrimination of Genetic Biomarkers of Disease through Machine-Learning-Based Hypothesis Testing of Direct SERS Spectra of DNA and RNA

Cancer is globally a leading cause of death that would benefit from diagnostic approaches detecting it in its early stages. However, despite much research and investment, cancer early diagnosis is still underdeveloped. Owing to its high sensitivity, surface-enhanced Raman spectroscopy (SERS)-based detection of biomarkers has attracted growing interest in this area. Oligonucleotides are an important type of genetic biomarkers as their alterations can be linked to the disease prior to symptom onset. We propose a machine-learning (ML)-enabled framework to analyze complex direct SERS spectra of short, single-stranded DNA and RNA targets to identify relevant mutations occurring in genetic biomarkers, which are key disease indicators. First, by employing ad hoc-synthesized colloidal silver nanoparticles as SERS substrates, we analyze single-base mutations in ssDNA and RNA sequences using a direct SERS-sensing approach. Then, an ML-based hypothesis test is proposed to identify these changes and differentiate the mutated sequences from the corresponding native ones. Rooted in "functional data analysis," this ML approach fully leverages the rich information and dependencies within SERS spectral data for improved modeling and detection capability. Tested on a large set of DNA and RNA SERS data, including from miR-21 (a known cancer miRNA biomarker), our approach is shown to accurately differentiate SERS spectra obtained from different oligonucleotides, outperforming various data-driven methods across several performance metrics, including accuracy, sensitivity, specificity, and F1-scores. Hence, this work represents a step forward in the development of the combined use of SERS and ML as effective methods for disease diagnosis with real applicability in the clinic.

Improving the sensing sensitivity of silver nanoparticle-based colorimetric biosensors from the point of salt

The sensing sensitivity was improved for silver nanoparticles (AgNPs)-based colorimetric biosensors by using the most suitable salt to induce AgNPs aggregation. As for the salt composed of low-affinity anion and monovalent cation, the cation-dependent charge screening effect was the driving force for AgNPs aggregation. Apart from the charge screening effect, both the bridging of multivalent cation to the surface ligand of AgNP and the interaction between anion and Ag contributed to inducing AgNPs aggregation. Considering the higher aggregation efficiency of AgNPs resulted in a narrower sensing range, salt composed of low-affinity anion and monovalent cation was recommended for AgNPs-based colorimetric analysis, which was confirmed by fourfold higher sensitivity of DNA-21 detection using NaF than NaCl. This work inspires further thinking on improving the sensing performance of metal nanomaterials-based sensors from the point of colloidal surface science.

Application of SERS in the Detection of Fungi, Bacteria and Viruses

In this review, we report the recent advances of SERS in fungi, bacteria, and viruses. Firstly, we briefly introduce the advantage of SERS over fluorescence on virus identification and detection. Secondly, we review the feasibility analysis of Raman/SERS spectrum analysis, identification, and fungal detection on SERS substrates of various nanostructures with a signal amplification mechanism. Thirdly, we focus on SERS spectra for nucleic acid, pathogens for the detection of viruses and bacteria, and furthermore introduce SERS-based microdevices, including SERS-based microfluidic devices, and three-dimensional nanostructured plasmonic substrates.

Accurate assembly and direct characterization of DNA nanogels crosslinked by G-quadruplex, i-motif and duplex with surface-enhanced Raman spectroscopy

The direct characterization of DNA nanogels at the atomic level is desirable and of great significance, however, has been challenging because of structural complexity and the larger size of nanogels. Herein, we demonstrated a simple, sensitive and reliable SERS (Surface-enhanced Raman spectroscopy)-based approach towards direct monitoring microstructures, such as three types of nanogels crosslinked by DNA G-quadruplex, i-motif and GC duplex. The achievement is attributed to the detection of featured Raman bands corresponding to the formation of Watson-Crick and Hoogsteen hydrogen bonds as well as C·C⁺ base pairs. Importantly, this work reveals that the silver nanoparticles attaching on the surface of nanogels can form local 'hotspots' and produce high-quality of Raman spectra under the assistance of iodide, aluminum ions and dichloromethane, therefore, shows great potential for wide applications in accurate characterization of various DNA nanostructures.

Surface enhanced Raman scattering for probing cellular biochemistry

Surface enhanced Raman scattering (SERS) from biomolecules in living cells enables the sensitive, but also very selective, probing of their biochemical composition. This minireview discusses the developments of SERS probing in cells over the past years from the proof-of-principle to observe a biochemical status to the characterization of molecule-nanostructure and molecule-molecule interactions and cellular processes that involve a wide variety of biomolecules and cellular compartments. Progress in applying SERS as a bioanalytical tool in living cells, to gain a better understanding of cellular physiology and to harness the selectivity of SERS, has been achieved by a combination of live cell SERS with several different approaches. They range from organelle targeting, spectroscopy of relevant molecular models, and the optimization of plasmonic nanostructures to the application of machine learning and help us to unify the information from defined biomolecules and from the cell as an extremely complex system.

Positively-charged plasmonic nanostructures for SERS sensing applications

Surface-enhanced Raman (SERS) spectroscopy has been establishing itself as an ultrasensitive analytical technique with a cross-disciplinary range of applications, which scientific growth is triggered by the continuous improvement in the design of advanced plasmonic materials with enhanced multifunctional abilities and tailorable surface chemistry. In this regard, conventional synthetic procedures yield negatively-charged plasmonic materials which can hamper the adhesion of negatively-charged species. To tackle this issue, metallic surfaces have been modified via diverse procedures with a broad array of surface ligands to impart positive charges. Cationic amines have been preferred because of their ability to retain a positive zeta potential even at alkaline pH as well as due to their wide accessibility in terms of structural features and cost. In this review, we will describe and discuss the different approaches for generating positively-charged plasmonic platforms and their applications in SERS sensing.

Integration of ligands equipped with quaternary amines on plasmonic surfaces generates positively-charged nanomaterials suitable for electrostatically binding negatively-charged species paving the way for their application in SERS sensing.

Modification of a SERS-active Ag surface to promote adsorption of charged analytes: effect of Cu2+ ions

This work studies the impact of the electrostatic interaction between analyte molecules and silver nanoparticles (Ag NPs) on the intensity of surface-enhanced Raman scattering (SERS). For this, we fabricated nanostructured plasmonic films by immobilization of Ag NPs on glass plates and functionalized them by a set of differently charged hydrophilic thiols (sodium 2-mercaptoethyl sulfonate, mercaptopropionic acid, 2-mercaptoethanol, 2-(dimethylamino)ethanethiol hydrochloride, and thiocholine) to vary the surface charge of the SERS substrate. We used two oppositely charged porphyrins, cationic copper(II) tetrakis(4-N-methylpyridyl) porphine (CuTMpyP4) and anionic copper(II) 5,10,15,20-tetrakis(4-sulfonatophenyl)porphine (CuTSPP4), with equal charge value and similar structure as model analytes to probe the SERS signal. Our results indicate that the SERS spectrum intensity strongly, up to complete signal disappearance, correlates with the surface charge of the substrate, which tends to be negative. Using the data obtained and our model SERS system, we analyzed the modification of the Ag surface by different reagents (lithium chloride, polyethylenimine, polyhexamethylene guanidine, and multicharged metal ions). Finally, all those surface modifications were tested using a negatively charged oligonucleotide labeled with Black Hole Quencher dye. Only the addition of copper ions into the analyte solution yielded a good SERS signal. Considering the strong interaction of copper ions with the oligonucleotide molecules, we suppose that inversion of the analyte charge played a key role in this case, instead of a change of charge of the substrate surface. Changing the charge of analytes could be a promising way to get clear SERS spectra of negatively charged molecules on Ag SERS-active supports.

New insight into the aptamer conformation and aptamer/protein interaction by surface-enhanced Raman scattering and multivariate statistical analysis

We study the interaction between one aptamer and its analyte (the MnSOD protein) by the combination of surface-enhanced Raman scattering and multivariate statistical analysis. We observe the aptamer structure and its evolution during the interaction under different experimental conditions (in air or in buffer). Through the spectral treatment by principal component analysis of a large set of SERS data, we were able to probe the aptamer conformations and orientations relative to the surface assuming that the in-plane nucleoside modes are selectively enhanced. We demonstrate that the aptamer orientation and thus its flexibility rely strongly on the presence of a spacer of 15 thymines and on the experimental conditions with the aptamer lying on the surface in air and standing in the buffer. We reveal for the first time that the interaction with MnSOD induces a large loss of flexibility and freezes the aptamer structure in a single conformation.

Surface-enhanced Raman spectroscopy for bioanalysis and diagnosis

In recent years, bioanalytical surface-enhanced Raman spectroscopy (SERS) has blossomed into a fast-growing research area. Owing to its high sensitivity and outstanding multiplexing ability, SERS is an effective analytical technique that has excellent potential in bioanalysis and diagnosis, as demonstrated by its increasing applications in vivo. SERS allows the rapid detection of molecular species based on direct and indirect strategies. Because it benefits from the tunable surface properties of nanostructures, it finds a broad range of applications with clinical relevance, such as biological sensing, drug delivery and live cell imaging assays. Of particular interest are early-stage-cancer detection and the fast detection of pathogens. Here, we present a comprehensive survey of SERS-based assays, from basic considerations to bioanalytical applications. Our main focus is on SERS-based pathogen detection methods as point-of-care solutions for early bacterial infection detection and chronic disease diagnosis. Additionally, various promising in vivo applications of SERS are surveyed. Furthermore, we provide a brief outlook of recent endeavours and we discuss future prospects and limitations for SERS, as a reliable approach for rapid and sensitive bioanalysis and diagnosis.

Targets and Tools: Nucleic Acids for Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) merges nanotechnology with conventional Raman spectroscopy to produce an ultrasensitive and highly specific analytical tool that has been exploited as the optical signal read-out in a variety of advanced applications. In this feature article, we delineate the main features of the intertwined relationship between SERS and nucleic acids (NAs). In particular, we report representative examples of the implementation of SERS in biosensing platforms for NA detection, the integration of DNA as the biorecognition element onto plasmonic materials for SERS analysis of different classes of analytes (from metal ions to microorgniasms) and, finally, the use of structural DNA nanotechnology for the precise engineering of SERS-active nanomaterials.

Ultrasensitive Characterization of the Prion Protein by Surface-Enhanced Raman Scattering: Selective Enhancement via Electrostatic Tethering of the Intrinsically Disordered Domain with Functionalized Silver Nanoparticles

Surface-enhanced Raman scattering (SERS) circumvents the inherent insensitivity of Raman spectroscopy and offers a powerful tool for the ultrasensitive detection and characterization of biomolecules at low concentrations. Here we show that SERS via electrostatic tethering between surface-modified negatively charged silver nanoparticles and highly positively charged intrinsically disordered N-terminal domain of the prion protein allows highly sensitive and reproducible protein detection and characterization at as low as hundreds of nanomolar protein concentrations. These measurements preferentially illuminate a selective part of the protein due to a sharp dependence of the near-field intensity on the distance between the nanoparticle surface and the protein. We also demonstrate that by shortening the length of the disordered tail it is possible to achieve a domain-selective Raman enhancement to study the C-terminal globular domain. Our tether-length-dependent SERS methodology will serve as a potent, noninvasive, and label-free strategy to detect and characterize a wide range of proteins possessing disordered segments.

Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy

Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar–phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.

Gold Nanocylinders on Gold Film as a Multi-spectral SERS Substrate

The surface enhanced Raman scattering (SERS) efficiency of gold nanocylinders deposited on gold thin film is studied. Exploiting the specific plasmonic properties of such substrates, we determine the influence of the nanocylinder diameter and the film thickness on the SERS signal at three different excitation wavelengths (532, 638 and 785 nm). We demonstrate that the highest signal is reached for the highest diameter of 250 nm due to coupling between the nanocylinders and for the lowest thickness (20 nm) as the excited plasmon is created at the interface between the gold and glass substrate. Moreover, even if we show that the highest SERS efficiency is obtained for an excitation wavelength of 638 nm, a large SERS signal can be obtained at all excitation wavelengths and on a wide spectral range. We demonstrate that it can be related with the nature of the plasmon (propagative plasmon excited through the nanocylinder grating) and with its angular dependence (tuning of the plasmon position with the excitation angle). Such an effect allows the excitation of plasmon on nearly the whole visible range, and paves the way to multispectral SERS substrates.

Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We?

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

Multiplex SERS Chemosensing of Metal Ions via DNA-Mediated Recognition

The combination of molecular sensors and plasmonic materials is emerging as one of the most promising approaches for ultrasensitive SERS-based detection of metal ions in complex fluids. However, only a very small fraction of the large pool of potential chemosensors described in classical analytical chemistry has been successfully implemented into viable SERS platforms for metal ion determination. This is due to the molecular restrictions that require the chemosensor to adhere onto the plasmonic surface while retaining the capability to undergo large structural alterations upon metal ion binding. In this work, we demonstrate that the structural and functional plasticity of DNA for interacting with small aromatic molecules can be exploited to this end. DNA coating of silver nanoparticles modulates the interaction of the commercially available alizarin red S (ARS) chemosensor with the nanomaterial, translating its recognition capabilities from bulk solution onto the plasmonic surface, while simultaneously directing the particle assembling into highly efficient SERS clusters. The sensing approach was successfully applied to the multiplex, quantitative determination of Al(III) and Fe(III) in tap water in the subppb level.

Amorphous Carbon Generation as a Photocatalytic Reaction on DNA-Assembled Gold and Silver Nanostructures

Background signals from in situ-formed amorphous carbon, despite not being fully understood, are known to be a common issue in few-molecule surface-enhanced Raman scattering (SERS). Here, discrete gold and silver nanoparticle aggregates assembled by DNA origami were used to study the conditions for the formation of amorphous carbon during SERS measurements. Gold and silver dimers were exposed to laser light of varied power densities and wavelengths. Amorphous carbon prevalently formed on silver aggregates and at high power densities. Time-resolved measurements enabled us to follow the formation of amorphous carbon. Silver nanolenses consisting of three differently-sized silver nanoparticles were used to follow the generation of amorphous carbon at the single-nanostructure level. This allowed observation of the many sharp peaks that constitute the broad amorphous carbon signal found in ensemble measurements. In conclusion, we highlight strategies to prevent amorphous carbon formation, especially for DNA-assembled SERS substrates.

Real-time dynamic SERS detection of galectin using glycan-decorated gold nanoparticles

We present the application of surface-enhanced Raman scattering (SERS) spectroscopy for the fast, sensitive and highly specific detection of the galectin-9 (Gal-9) protein in binding buffer (mimicking natural conditions). The method involves the use of specifically designed nanotags comprising glycan-decorated gold nanoparticles encoded with 4-mercaptobenzoic acid. At fast time scales Gal-9 can be detected down to a concentration of 1.2 nM by monitoring the SERS signal of the reporter, driven by aggregation of the functionalized Au NPs tags, induced by Gal-9 recognition. We additionally demonstrate that the sensitivity and concentration working range of the sensor can be tuned via control of aggregation dynamics and cluster size distribution.

Quantitative surface-enhanced Raman spectroscopy of single bases in oligodeoxynucleotides

To address the question of whether the SERS signals of ss-DNA are simply combinations of the signals from the individual bases that comprise the sequence, SERS spectra of unmodified ss-DNA sequences were obtained using a hydroxylamine-reduced Ag colloid aggregated with MgSO₄. Initially, synthetic oligodeoxynucleotides with systematic structural variations were used to investigate the effect of adding single nucleobases to the 3' terminus of 10-mer and 20-mer sequences. It was found that the resulting SERS difference spectra could be used to identify the added nucleobases since they closely matched reference spectra of the same nucleobase. Investigation of the variation in intensity of an adenine probe which was moved along a test sequence showed there was a small end effect where nucleobases near the 3' terminus gave slightly larger signals but the effect was minor (30%). More significantly, in a sample set comprising 25-mer sequences where A, T or G nucleobases were substituted either near the centres of the sequences or the 5' or 3' ends, the SERS difference spectra only matched the expected form in approximately half the cases tested. This variation appeared to be due to changes in secondary structure induced by altering the sequences since uncoiling the sequences in a thermal pre-treatment step gave difference spectra which in all cases matched the expected form. Multivariate analysis of the set of substitution data showed that 99% of the variance could be accounted for in a model with just three factors whose loadings matched the spectra of the A, T, and G nucleobases and which contained no positional information. This suggests that aside from the differences in secondary structure which can be eliminated by thermal pre-treatment, the SERS spectra of the 25-mers studied here are simply the sum of their component parts. Although this means that SERS provides very little information on the primary sequence it should be excellent for the detection of post-transcription modifications to DNA which can occur at multiple positions along a given sequence.

Laser trapping of Ag nanoparticles to enhance Raman spectroscopy in aqueous media

Laser trapping (LT) of metallic nanoparticles (NPs) is an approach that has the potential to enhance Raman spectroscopy in aqueous media. In this paper, we report the LT of multiple 60-nm Ag NPs using a tightly focused 1064-nm Gaussian laser beam. The dynamic process (trapping and escaping) of the individual Ag NPs were recorded using a charge coupled device (CCD) camera in backscattering illumination mode. We found that up to four Ag NPs could be simultaneously trapped; however, they were unstable in the laser trap due to Brownian motion and NP-NP interactions. However, after mixing Ag NPs with Bacillus subtilis, more of the Ag NPs could be trapped together with the bacteria. Furthermore, a 532-nm solid-state laser beam was used to activate Raman scattering of the Ag NPs + Bacillus subtilis sample. Based on repetitive measurements, the Raman spectra of the Ag NPs + Bacillus subtilis sample were enhanced and the results were consistent. Our work suggests that LT of metallic NPs can be used to enhance Raman spectroscopy in aqueous media. We believe that the enhanced Raman spectroscopy will be useful for real-time biological assays.

Effect of structure levels on surface-enhanced Raman scattering of human telomeric G-quadruplexes in diluted and crowded media

Human telomeric G-quadruplexes are emerging targets in anticancer drug discovery since they are able to efficiently inhibit telomerase, an enzyme which is greatly involved in telomere instability and immortalization process in malignant cells. G-quadruplex (G4) DNA is highly polymorphic and can adopt different topologies upon addition of electrolytes, additives, and ligands. The study of G-quadruplex forms under various conditions, however, might be quite challenging. In this work, surface-enhanced Raman scattering (SERS) spectroscopy has been applied to study G-quadruplexes formed by human telomeric sequences, d[A₃G₃(TTAGGG)₃A₂] (Tel26) and d[(TTAGGG)₄T₂] (wtTel26), under dilute and crowding conditions. The SERS spectra distinctive of hybrid-1 and hybrid-2 G-quadruplexes of Tel26 and wtTel26, respectively, were observed for the sequences folded in the presence of K⁺ ions (110 mM) in a buffered solution, representing the diluted medium. Polyethylene glycol (5, 10, 15, 20, and 40% v/v PEG) was used to create a molecular-crowded environment, resulting in the formation of the parallel G-quadruplexes of both studied human telomeric sequences. Despite extensive overlap by the crowding agent bands, the SERS spectral features indicative of parallel G4 form of Tel26 were recognized. The obtained results implied that SERS of G-quadruplexes reflected not only the primary structure of the studied human telomeric sequence, including its nucleobase composition and sequence, but also its secondary structure in the sense of Hoogsteen hydrogen bonds responsible for the guanine tetrad formation, and finally its tertiary structure, defining a three-dimensional DNA shape, positioned close to the enhancing metallic surface. Graphical abstract.

Surface-enhanced Raman spectroscopy (SERS) characterisation of abasic sites in DNA duplexes

Acquisition of the intrinsic SERS spectra of abasic sites containing DNA enables their structural characterisation and discrimination.

Design and Clinical Verification of Surface-Enhanced Raman Spectroscopy Diagnostic Technology for Individual Cancer Risk Prediction

The use of emerging nanotechnologies, such as plasmonic nanoparticles in diagnostic applications, potentially offers opportunities to revolutionize disease management and patient healthcare. Despite worldwide research efforts in this area, there is still a dearth of nanodiagnostics which have been successfully translated for real-world patient usage due to the predominant sole focus on assay analytical performance and lack of detailed investigations into clinical performance in human samples. In a bid to address this pressing need, we herein describe a comprehensive clinical verification of a prospective label-free surface-enhanced Raman scattering (SERS) nanodiagnostic assay for prostate cancer (PCa) risk stratification. This contribution depicts a roadmap of (1) designing a SERS assay for robust and accurate detection of clinically validated PCa RNA targets; (2) employing a relevant and proven PCa clinical biomarker model to test our nanodiagnostic assay; and (3) investigating the clinical performance on independent training ( n = 80) and validation ( n = 40) cohorts of PCa human patient samples. By relating the detection outcomes to gold-standard patient biopsy findings, we established a PCa risk scoring system which exhibited a clinical sensitivity and specificity of 0.87 and 0.90, respectively [area-under-curve of 0.84 (95% confidence interval: 0.81-0.87) for differentiating high- and low-risk PCa] in the validation cohort. We envision that our SERS nanodiagnostic design and clinical verification approach may aid in the individualized prediction of PCa presence and risk stratification and may overall serve as an archetypical strategy to encourage comprehensive clinical evaluation of nanodiagnostic innovations.

Synthesis of uniform Ag nanosponges and its SERS application

With the aid of amino acid, various Ag nanostructures were successfully synthesized via the reaction between silver nitrate and hydrazine hydrate at room temperature. The as-prepared products were characterized by X-ray diffraction and scanning electron microscopy. It was found that the morphology of the as-prepared Ag products depended on the sorts of amino acid and solvents. The uniform Ag nanosponges could be obtained in glycol with aid of glycine. Using rhodamine 6G (R6G) as probe, the surface-enhanced Raman scattering (SERS) performance was also investigated, which showed that the uniform Ag nanosponges exhibited an intensive and enhanced Raman scattering. Pazufloxacin mesilate (PM) were detected conveniently using these uniform nanosponges as SERS substrates. The present work might afford some guidance for the rationally controllable synthesis of other metal nanomaterials.

Paper-Based Surface-Enhanced Raman Spectroscopy for Diagnosing Prenatal Diseases in Women

We report the development of a surface-enhanced Raman spectroscopy sensor chip by decorating gold nanoparticles (AuNPs) on ZnO nanorod (ZnO NR) arrays vertically grown on cellulose paper (C). We show that these chips can enhance the Raman signal by 1.25 × 10⁷ with an excellent reproducibility of <6%. We show that we can measure trace amounts of human amniotic fluids of patients with subclinical intra-amniotic infection (IAI) and preterm delivery (PTD) using the chip in combination with a multivariate statistics-derived machine-learning-trained bioclassification method. We can detect the presence of prenatal diseases and identify the types of diseases from amniotic fluids with >92% clinical sensitivity and specificity. Our technology has the potential to be used for the early detection of prenatal diseases and can be adapted for point-of-care applications.

Facing Challenges in Real-Life Application of Surface-Enhanced Raman Scattering: Design and Nanofabrication of Surface-Enhanced Raman Scattering Substrates for Rapid Field Test of Food Contaminants

Surface-enhanced Raman scattering (SERS) is capable of detecting a single molecule with high specificity and has become a promising technique for rapid chemical analysis of agricultural products and foods. With a deeper understanding of the SERS effect and advances in nanofabrication technology, SERS is now on the edge of going out of the laboratory and becoming a sophisticated analytical tool to fulfill various real-world tasks. This review focuses on the challenges that SERS has met in this progress, such as how to obtain a reliable SERS signal, improve the sensitivity and specificity in a complex sample matrix, develop simple and user-friendly practical sensing approach, reduce the running cost, etc. This review highlights the new thoughts on design and nanofabrication of SERS-active substrates for solving these challenges and introduces the recent advances of SERS applications in this area. We hope that our discussion will encourage more researches to address these challenges and eventually help to bring SERS technology out of the laboratory.

Label-free SERS in biological and biomedical applications: Recent progress, current challenges and opportunities

To achieve an insightful look within biomolecular processes on the cellular level, the development of diseases as well as the reliable detection of metabolites and pathogens, a modern analytical tool is needed that is highly sensitive, molecular-specific and exhibits fast detection. Surface-enhanced Raman spectroscopy (SERS) is known to meet these requirements and, within this review article, the recent progress of label-free SERS in biological and biomedical applications is summarized and discussed. This includes the detection of biomolecules such as metabolites, nucleic acids and proteins. Further, the characterization and identification of microorganisms has been achieved by label-free SERS-based approaches. Eukaryotic cells can be characterized by SERS in order to gain information about the outer cell wall or to detect intracellular molecules and metabolites. The potential of SERS for medically relevant detection schemes is emphasized by the label-free detection of tissue, the investigation of body fluids as well as applications for therapeutic and illicit drug monitoring. The review article is concluded with an evaluation of the recent progress and current challenges in order to highlight the direction of label-free SERS in the future.

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.

Direct surface-enhanced Raman scattering (SERS) spectroscopy of nucleic acids: from fundamental studies to real-life applications

In this tutorial review, we summarize and discuss the most recent cutting-edge research in the field of direct surface-enhanced Raman scattering (SERS) analysis of nucleic acids.

Bioanalytical applications of surface-enhanced Raman spectroscopy: de novo molecular identification

Surface enhanced Raman scattering (SERS) has become a powerful technique for trace analysis of biomolecules. The use of SERS-tags has evolved into clinical diagnostics, the enhancement of the intrinsic signal of biomolecules on SERS active materials shows tremendous promise for the analysis of biomolecules and potential biomedical assays. The detection of the de novo signal from a wide range of biomolecules has been reported to date. In this review, we examine different classes of biomolecules for the signals observed and experimental details that enable their detection. In particular, we survey nucleic acids, amino acids, peptides, proteins, metabolites, and pathogens. The signals observed show that the interaction of the biomolecule with the enhancing nanostructure has a significant influence on the observed spectrum. Additional experiments demonstrate that internal standards can correct for intensity fluctuations and provide quantitative analysis. Experimental methods that control the interaction at the surface are providing for reproducible SERS signals. Results suggest that combining advances in methodology with the development of libraries for SERS spectra may enable the characterization of biomolecules complementary to other existing methods.