Nanostructure-based surface-enhanced Raman scattering biosensors for nucleic acids and proteins

Prepared Sandwich structure WS2/ag@MIP composite for ultrasensitive SERS detection of trace 17β-estradiol in food

17β-E2 is used in animal growth regulation and agricultural fertilizer, and even ng L-1 mass concentration levels can show biological effects. In this work, Ag NPs was used as surface-enhanced Raman spectroscopy (SERS) source and WS2 was synthesized by a simple method to provide a uniform distribution platform for Ag NPs. The MIP was the shell, which can selectively enrich the target molecule, pull the distance between the target molecule and SERS source, and protect Ag NPs. A cyclable SERS substrate with high sensitivity for detecting 17β-E2 in food was constructed. The optimized WS2/Ag@MIP as SERS substrate has the advantages of high Enhanced Factor (EF = 2.78 × 109), low detection limit (LOD = 0. 0958 pM), strong anti-interference ability, and good recycling performance. Moreover, the detection of 17β-E2 in real samples still has good accuracy. This work provides a new possibility for the trace detection of 17β-E2 in food.

Applications of Metals and Metal Compounds in Improving the Sensitivity of Microfluidic Biosensors - A Review

The enhancement of detection sensitivity in microfluidic sensors has been a continuously explored field. Initially, many strategies for sensitivity improvement involved introducing enzyme cascade reactions, but enzyme-based reactions posed challenges in terms of cost, stability, and storage. Therefore, there is an urgent need to explore enzyme-free cascade amplification methods, which are crucial for expanding the application range and improving detection stability. Metal or metal compound nanomaterials have gained great attention in the exploitation of microfluidic sensors due to their ease of preparation, storage, and lower cost. The unique physical properties of metallic nanomaterials, including surface plasmon resonance, surface-enhanced Raman scattering, metal-enhanced fluorescence, and surface-enhanced infrared absorption, contribute significantly to enhancing detection capabilities. The metal-based catalytic nanomaterials, exemplified by Fe3O4 nanoparticles and metal-organic frameworks, are considered viable alternatives to biological enzymes due to their excellent performance. Herein, we provide a detailed overview of the applications of metals and metal compounds in improving the sensitivity of microfluidic biosensors. This review not only highlights the current developments but also critically analyzes the challenges encountered in this field. Furthermore, it outlines potential directions for future research, contributing to the ongoing development of microfluidic biosensors with improved detection sensitivity.

Surface-Enhanced Raman Spectroscopy (SERS)-Based Sensors for Deoxyribonucleic Acid (DNA) Detection

Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful technique for the detection and analysis of biomolecules due to its high sensitivity and selectivity. In recent years, SERS-based sensors have received significant attention for the detection of deoxyribonucleic acid (DNA) molecules, offering promising applications in fields such as medical diagnostics, forensic analysis, and environmental monitoring. This paper provides a concise overview of the principles, advancements, and potential of SERS-based sensors for DNA detection. First, the fundamental principles of SERS are introduced, highlighting its ability to enhance the Raman scattering signal by several orders of magnitude through the interaction between target molecules with metallic nanostructures. Then, the fabrication technologies of SERS substrates tailored for DNA detection are reviewed. The performances of SERS substrates previously reported for DNA detection are compared and analyzed in terms of the limit of detection (LOD) and enhancement factor (EF) in detail, with respect to the technical parameters of Raman spectroscopy (e.g., laser wavelength and power). Additionally, strategies for functionalizing the sensor surfaces with DNA-specific capture probes or aptamers are outlined. The collected data can be of help in selecting and optimizing the most suitable fabrication technology considering nucleotide sensing applications with Raman spectroscopy.

Synovial fluid research based on SERS and SERRS for enhanced detection of biomarkers in staged osteoarthritis

Surface-enhanced (resonance) Raman scattering (SER(R)S) can extremely enhance Raman intensity of samples, which is helpful for detecting synovial fluid (SF) that does not show Raman activity under normal conditions. In this study, SER(R)S spectra of SF from three different osteoarthritis (OA) stages were collected and analyzed for OA progress, finding that the content of collagen increased throughout the disease, while non-collagen proteins and polysaccharides decreased sharply at advanced OA stage accompanied by the increase of phospholipid. The spectral features and differences were enhanced by salting-out and centrifugation. Much more information on biomolecules at different OA stages was disclosed by using SERRS for the first time, these main trace components (β-carotene, collagen, hyaluronic acid, nucleotide, and phospholipid) can be used as potential biomarkers. It indicates that SERRS has a more comprehensive ability to assist SERS in seeking micro(trace) biomolecules as biomarkers and facilitating accurate and efficient diagnosis and mechanism research of OA.

17β-estradiol biosensors based on different bioreceptors and their applications

17β-Estradiol (E2) is a critical sex steroid hormone, which has significant effects on the endocrine systems of both humans and animals. E2 is also believed to play neurotrophic and neuroprotective roles in the brain. Biosensors present a powerful tool to detect E2 because of their small, efficient, and flexible design. Furthermore, Biosensors can quickly and accurately obtain detection results with only a small sampling amount, which greatly meets the detection of the environment, food safety, medicine safety, and human body. This review focuses on previous studies of biosensors for detecting E2 and divides them into non-biometric sensors, enzyme biosensors, antibody biosensors, and aptamer biosensors according to different bioreceptors. The advantages, disadvantages, and design points of various bioreceptors for E2 detection are analyzed and summarized. Additionally, applications of different bioreceptors of E2 detection are presented and highlight the field of environmental monitoring, food and medicine safety, and disease detection in recent years. Finally, the development of E2 detection by biosensor is prospected.

A CRISPR/Cas12a-SERS platform for amplification-free detection of African swine fever virus genes

A surface-enhanced Raman scattering (SERS) strategy combined with a CRISPR/Cas12a system is designed for the amplification-free gene detection of African swine fever virus (ASFV). A SERS sensing probe was fabricated by conjugating plasmonic SERS tags on the magnetic bead (MB) surface with an single-stranded DNA (ssDNA) as a linker. The target ASFV gene-activated Cas12a protein starts the trans-cleavage function on the linker ssDNA, which causes the release of SERS tags, leading to a decrease of the SERS signal detected above the collective MBs. Two signal enhancement strategies were adopted to improve the liquid-phase detection sensitivity arriving at the fM level. One is the unlimited trans-cleavage function of the Cas12a protein, and the other is the magnetic-induced collection of probes that can significantly gather the analytes from the solution to the laser spot and provide SERS hotspots during SERS measurement. Detection range is from 100 nM to 10 fM without the gene amplification steps. This sensing method achieved the SERS detection of ASFV gene in the serum system and the extracted nucleic acids in viral samples with high sensitivity and selectivity at a relative standard deviation of <8%. This sensing platform is mainly in use for site inspection and quick testing of gene samples.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications

Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.

Plasmonic Dual-Gap Nanodumbbells for Label-Free On-Particle Raman DNA Assays

Metal nanostructures with a tunable plasmonic gap are useful for photonics, surface-enhanced spectroscopy, biosensing, and bioimaging applications. The use of these structures as chemical and biological sensing/imaging probes typically requires an ultra-precise synthesis of the targeted nanostructure in a high yield, with Raman dye-labeling and complex assay components and procedures. Here, a plasmonic nanostructure with tunable dual nanogaps, Au dual-gap nanodumbbells (AuDGNs), is designed and synthesized via the anisotropic adsorption of polyethyleneimine on Au nanorods to facilitate tip-selective Au growths on nanorod tips for forming mushroom-shaped dumbbell-head structures at both tips and results in dual gaps (intra-head and inter-head gaps) within a single particle. AuDGNs are synthesized in a high yield (>90%) while controlling the inter-head gap size, and the average surface-enhanced Raman scattering (SERS) enhancement factor (EF) value is 7.5 × 10⁸ with a very narrow EF distribution from 1.5 × 10⁸ to 1.5 × 10⁹ for >90% of analyzed particles. Importantly, AuDGNs enable label-free on-particle SERS detection assays through the diffusion of target molecules into the intraparticle gap for different DNA sequences with varying ATGC combinations in a highly specific and sensitive manner without a need for Raman dyes.

Multiplex signal amplification strategy-based early-stage diagnosis of Parkinson's disease on a SERS-enabled LoC system

In this paper, a multiplex signal amplification strategy was developed for the determination of miR-214 and miR-221 on a surface-enhanced Raman scattering (SERS)-enabled lab-on-a-chip (LoC) system to realize the early-stage diagnosis of Parkinson's disease (PD). The gold nanobipyramids (GNBPs) with great monodispersity were functionalized with Raman reporter molecules and hairpin DNA 1, serving as the SERS nanotags. The presence of targets can initial the strand displacement amplification (SDA) reaction and the numerous short-stranded trigger DNA (tDNA) can be released under the action of polymerase and nicking enzyme. Then, the tDNA can trigger the catalytic hairpin assembly (CHA) event between the SERS nanotags and the capture nanoprobes (Magnetic beads (MBs) modified with hairpin DNA 2), resulting in the aggregation of GNBPs on the MBs surface. The multiplex signal amplification contributed by the SDA-CHA strategy and the magnet-induced aggregation effect can ultimately lead to the significant improvement of the detection sensitivity and the limit of detection (LOD) was low to aM level with reproducibility and specificity meanwhile. Furthermore, a MPTP-induced PD mice model was established to verify the practicability and the expression level of miR-214 and miR-221 at different stages analyzed with the LoC system was confirmed by qRT-PCR.

Encoding microcarriers for biomedicine

High throughput biological analysis has become an important topic in modern biomedical research and clinical diagnosis. The flow encoding scheme based on the encoding microcarriers provides a feasible strategy for the multiplexed biological analysis. Different encoding characteristics invest the microcarriers with different encoding mechanisms. Biosensor analysis, drug screening, cell culture, and the construction and evaluation of bionic organ chips can be realized by decoding the microcarriers and quantifying the detection signal intensity. In this review, the encoding strategy of microcarriers was divided into the optical and non-optical encoding approaches according to their encoding elements, and the research progress of the microcarrier encoding strategy was elaborated. Finally, we summarized the biomedical applications and predicted their future prospects.

Detection and Characterization of Nodularin by Using Label-Free Surface-Enhanced Spectroscopic Techniques

Nodularin (NOD) is a potent toxin produced by Nodularia spumigena cyanobacteria. Usually, NOD co-exists with other microcystins in environmental waters, a class of cyanotoxins secreted by certain cyanobacteria species, which makes identification difficult in the case of mixed toxins. Herein we report a complete theoretical DFT-vibrational Raman characterization of NOD along with the experimental drop-coating deposition Raman (DCDR) technique. In addition, we used the vibrational characterization to probe SERS analysis of NOD using colloidal silver nanoparticles (AgNPs), commercial nanopatterned substrates with periodic inverted pyramids (Klarite^TM substrate), hydrophobic Tienta^® SpecTrim^TM slides, and in-house fabricated periodic nanotrenches by nanoimprint lithography (NIL). The 532 nm excitation source provided more well-defined bands even at LOD levels, as well as the best performance in terms of SERS intensity. This was reflected by the results obtained with the Klarite^TM substrate and the silver-based colloidal system, which were the most promising detection approaches, providing the lowest limits of detection. A detection limit of 8.4 × 10^-8 M was achieved for NOD in solution by using AgNPs. Theoretical computation of the complex vibrational modes of NOD was used for the first time to unambiguously assign all the specific vibrational Raman bands.

Selenium-based nanomaterials for biosensing applications

The unique chemical and physical features of nanomaterials make them ideal for developing new and better sensing devices, particularly biosensors. Various types of nanoparticles, including metal, oxide, and semiconductor nanostructures, have been utilized to manufacture biosensors, and each kind of nanoparticle plays a unique role in the sensing system. Nanoparticles provide critical roles such as immobilizing biomolecules, catalyzing electrochemical processes, enhancing electron transport between electrode surfaces and proteins, identifying biomolecules, and even functioning as the reactant for the catalytic reaction. Among all the potential nanosystems to be used in biosensors, selenium nanoparticle (SeNP) features have sparked a growing interest in their use in bridging biological recognition events and signal transduction, as well as in developing biosensing devices with novel applications for identification, quantification, and study of different analytes of biological relevance. The optical, physical, and chemical characteristics of differently shaped SeNPs opened up a world of possibilities for developing biosensors of biomedical interest. The outstanding biocompatibility, conductivity, catalytic characteristics, high surface-to-volume ratio, and high density of SeNPs have enabled their widespread use in developing electrochemical biosensors with superior analytical performance compared to other designs of biosensors. This review summarizes recent and ongoing advances, current challenges, and future research perspectives on real-world applications of Se-based nanobiosensors to detect biologically relevant analytes such as hydrogen peroxide, heavy metals, or glucose. Due to the superior properties and multifunctionality of Se-NPs biosensors, these structures can open up considerable new horizons in the future of healthcare and medicine.

Optical Biosensor Based on Graphene and Its Derivatives for Detecting Biomolecules

Graphene and its derivatives show great potential for biosensing due to their extraordinary optical, electrical and physical properties. In particular, graphene and its derivatives have excellent optical properties such as broadband and tunable absorption, fluorescence bursts, and strong polarization-related effects. Optical biosensors based on graphene and its derivatives make nondestructive detection of biomolecules possible. The focus of this paper is to review the preparation of graphene and its derivatives, as well as recent advances in optical biosensors based on graphene and its derivatives. The working principle of face plasmon resonance (SPR), surface-enhanced Raman spectroscopy (SERS), fluorescence resonance energy transfer (FRET) and colorimetric sensors are summarized, and the advantages and disadvantages of graphene and its derivatives applicable to various types of sensors are analyzed, and the methods of surface functionalization of graphene and its derivatives are introduced; these optical biosensors can be used for the detection of a range of biomolecules such as single cells, cellular secretions, proteins, nucleic acids, and antigen-antibodies; these new high-performance optical sensors are capable of detecting changes in surface structure and biomolecular interactions with the advantages of ultra-fast detection, high sensitivity, label-free, specific recognition, and the ability to respond in real-time. Problems in the current stage of application are discussed, as well as future prospects for graphene and its biosensors. Achieving the applicability, reusability and low cost of novel optical biosensors for a variety of complex environments and achieving scale-up production, which still faces serious challenges.

Sensing gastric cancer exosomes with MoS2-based SERS aptasensor

Exosomes have been widely used in early cancer diagnosis as promising cancer biomarkers due to their abundant tumor-specific molecular information. In this study, we developed a sensitive and straightforward surface-enhanced Raman scattering (SERS) aptasensor to detect exosomes based on gold nanostars-decorated molybdenum disulfide (MoS₂) nanocomposites (MoS₂-AuNSs). ROX-labeled aptamers (ROX-Apt) were assembled on MoS₂-AuNSs surface as recognition probes that specifically bind with transmembrane protein CD63 (a representative surface marker on exosomes). Thus obvious ROX Raman signals were obtained through the synergistic Raman enhancement effect of AuNSs and MoS₂ nanosheet. In presence of exosomes, ROX-Apt is preferentially tethered onto exosomes and released from the surface of nanocomposites, resulting in a decrease of the SERS signal. Expectedly, the as-fabricated SERS aptasensor was capable of detecting exosomes in a wide range from 55 to 5.5 × 10⁵ particles μL^-1 with a detection limit of 17 particles μL^-1. Moreover, the aptasensor exhibited accepted stability and potential clinical applicability.

Multistage nucleic acid amplification induced nano-aggregation for 3D hotspots-improved SERS detection of circulating miRNAs

Circulating miRNAs in the blood can regulate disease development and thus indicate disease states via their various expression levels. For these reasons, circulating miRNAs constitute useful biomarkers, and an approach to the accurate detection of circulating miRNAs is attractive in the diagnosis and treatment of diseases. However, methods for clinical detecting of circulating miRNA that take both sensitivity and practicality into account are still needed. Therefore, we aimed herein to solve some inherent problems in the actual detection using a robust surface-enhanced Raman scattering (SERS) platform with integrated nucleic acid amplification and nanoparticle aggregation to construct 3D hotspots for improving performance of analyzing circulating miRNAs. After target recognition and initial signal amplification by DNAzyme, we observed that release triggered an open hairpin DNA on gold nanoparticles (AuNPs), which then promote AuNP aggregation, causing the accumulation of a large number of hotspots in three-dimention. The SERS biosensor achieved a better performance than the sandwich-type separation detection, with a low detection limit (0.37 fM) and a broad linear range (1 fM–10 nM) in liquids. This SERS platform can be used as a powerful tool for the detection of circulating miRNAs, and it can be used to improve the sensitivity and accuracy of various clinical-disease diagnoses.

Advancement in Nanoparticle-Based Biosensors for Point-of-Care In Vitro Diagnostics

Abstract:

Recently, there has been great progress in the field of extremely sensitive and precise detection of bioanalytes. The importance of the utilization of nanoparticles in biosensors has been recognized due to their unique properties. Specifically, nanoparticles of gold, silver, and magnetic plus graphene, quantum dots, and nanotubes of carbon are being keenly considered for utilizations within biosensors to detect nucleic acids, glucose, or pathogens (bacteria as well as a virus). Taking advantage of nanoparticles, faster and sensitive biosensors can be developed. Here we review the nanoparticles' contribution to the biosensors field and their potential applications.

Graphene-Based Plasmonic Metamaterial Perfect Absorber for Biosensing Applications

Graphene as a mono-atomic sheet has recently grabbed attention as a material with enormous properties. It has also been examined for enhancing absorbance in the current plasmonic structure. This has led to an increment in the sensitivity of the plasmonic sensors. In this paper, we present theoretical investigation of the novel graphene-based plasmonic metamaterial perfect absorber for biosensing applications. The simulation study performs the analysis of the novel plasmonic metamaterial absorber structure by adding coatings of graphene sheets. Each sheet of graphene enhances absorbance of the structure. In this study, we demonstrate three layers of graphene sheets lead to perfect absorbance (100%) for multiple bands in the visible and near-infrared regions. Furthermore, we also computed the sensitivity of the graphene-based proposed structure by varying the refractive index (RI) of the sensing region from 1.33–1.36 with RI change of 0.01. Proposed fabrication steps for realization of the device are also discussed.

Towards a protein-selective Raman enhancement by a glycopolymer-based composite surface

Surface-enhanced Raman scattering (SERS), which is based on the surface plasmon resonance (LSPR) of noble metal nanostructures, is widely used in the biological field due to its advantages of non-damaging samples and detection up to the molecular level. For biological SERS detection, preparation of substrates with biocompatibility and specific adsorption, leading to selective enhancement of the target biomolecules, are important design strategies. Utilizing the specific interaction between a carbohydrate and protein, a glycopolymer-based composite surface is fabricated to realize specific SERS detection of proteins. Herein, we use N-3,4-dihydroxybenzeneethyl methacrylamide (DMA), 2-deoxy-2-(methacrylamido)glucopyranose (MAG) and methacrylic acid (MAA) as monomers in a sunlight-induced RAFT polymerization to synthesize a dopamine-containing glycopolymer. The glycopolymers are used to prepare a SERS substrate. The composite surface shows specific protein adsorption capacity, and the selective Raman enhancement of specific proteins was successfully achieved between the two different proteins Con A and BSA. This provides a feasible approach to design a SERS surface for protein detection and the study of the interaction between sugar and proteins.

RNA interference (RNAi)-based plasmonic nanomaterials for cancer diagnosis and therapy

RNA interference (RNAi) is being extensively investigated as a potential therapeutic strategy for cancer treatment. However, RNAi-based therapeutics have not yet been used to treat cancer because of their instability and the difficulty of microRNA (miRNA) delivery. Plasmonic nanoparticle-based RNAi nanotherapeutics have been developed for accurate and sensitive diagnosis and a strong therapeutic effect on cancers by leveraging their ease-of-use and specific properties such as photothermal conversion. In this review, recent strategies and advances in plasmonic nanoparticle-based miRNA delivery are briefly presented to facilitate the detection and treatment of several cancers. The challenges and potential opportunities afforded by the RNAi-based theragnosis field are discussed. We expect that the RNAi-integrated plasmonic nanotherapeutics discussed in this review can provide insights for the early diagnosis and effective treatment of cancer.

Rapid and Label-Free Prenatal Detection of Down's Syndrome Using Body Fluid Surface Enhanced Raman Spectroscopy

Down's syndrome (DS) is the leading genetic cause of intellectual disability. In this work, the surface enhanced Raman spectroscopy (SERS) was used for the detection of amniotic fluid and plasma from pregnant women with DS fetus for the first time. High-quality and characteristic spectral features of amniotic fluid and plasma samples from DS groups can be obtained in comparison to normal group. Moreover, principal component analysis with linear discriminant analysis was applied to generate the efficient diagnostic model, achieving accuracies of 94.3% and 88.5% for the DS detection with amniotic fluid and plasma samples, respectively. This preliminary study would provide a novel, convenient and accurate prenatal test based on blood SERS technology for clinical DS screening.

Analyte-Induced Desert Rose-like Ag Nanostructures for Surface-Enhanced Raman Scattering-Based Biomolecule Detection and Imaging

Biomolecule detection based on surface-enhanced Raman scattering (SERS) for application to biosensors and bio-imaging requires the fabrication of SERS nanoprobes that can generate strong Raman signals as well as surface modifications for analyte-specific recognition and binding. Such requirements lead to disadvantages in terms of reproducibility and practicality, and thus, it has been difficult to apply biomolecule detection utilizing the advantages of the SERS phenomenon to actual clinically relevant analysis. To achieve reproducible and practical SERS signal generation in a biomolecule-specific manner without requiring the synthesis of nanostructures and their related surface modification to introduce molecules for specific recognition, we developed a new type of SERS probe formed by enzyme reactions in the presence of Raman reporters. By forming unique plasmonic structures, our method achieves the detection of biomolecules on chips with uniform and stable signals over long periods. To test the proposed approach, we applied it to a SERS-based immunohistochemistry assay and found successful multiplexed protein detection in brain tissue from transgenic mice.

CRISPR-/Cas12a-Mediated Liposome-Amplified Strategy for the Surface-Enhanced Raman Scattering and Naked-Eye Detection of Nucleic Acid and Application to Food Authenticity Screening

Surface-enhanced Raman scattering (SERS) has been recognized as a powerful tool for biosensors due to the ultrahigh sensitivity and unique fingerprint information. However, there are some limitations in trace target nucleic acid detection for the restricted signal-transducing and amplification strategies. Inspired by CRISPR/Cas12a with specific target DNA-activated collateral single-strand DNA (ssDNA) cleavage activity and liposome with signal molecule-loading properties, we first proposed a sensitive SERS-based on-site nucleic acid detection strategy mediated by CRISPR/Cas12a with trans-cleavage activity on ssDNA linkers utilized to capture liposomes. Liposomes loading two kinds of signal molecules, 4-nitrothiophenol (4-NTP) and cysteine, could achieve the dual-mode detection of target DNA with SERS and naked eye, respectively. The promptly amplified signals were initiated by the triggered breakdown of signal molecule-loaded liposomes. Emancipated 4-NTP, a biological-silent Raman reporter, would achieve highly selective and sensitive SERS measurement. Released cysteine induced the aggregation of plasmonic gold nanoparticles, leading to an obvious red to blue colorimetric shift to realize portable naked-eye detection. With this strategy, target nucleic acid concentration was dexterously converted into SERS and visualization signals and could be detected as low as 100 aM and 10 pM, respectively. The approach was also successfully applied to determine meat adulteration, achieving the detection of a low adulteration ratio in the complicated food matrix. We anticipate that this strategy will not only be regarded as a universal platform for the on-site detection of food authenticity but also broaden SERS application for the accurate determination of diverse biomarkers.

Micro-Raman Characterization of Structural Features of High-k Stack Layer of SOI Nanowire Chip, Designed to Detect Circular RNA Associated with the Development of Glioma

The application of micro-Raman spectroscopy was used for characterization of structural features of the high-k stack (h-k) layer of "silicon-on-insulator" (SOI) nanowire (NW) chip (h-k-SOI-NW chip), including Al₂O₃ and HfO₂ in various combinations after heat treatment from 425 to 1000 °C. After that, the NW structures h-k-SOI-NW chip was created using gas plasma etching optical lithography. The stability of the signals from the monocrine phase of HfO₂ was shown. Significant differences were found in the elastic stresses of the silicon layers for very thick (>200 nm) Al₂O₃ layers. In the UV spectra of SOI layers of a silicon substrate with HfO₂, shoulders in the Raman spectrum were observed at 480-490 cm^-1 of single-phonon scattering. The h-k-SOI-NW chip created in this way has been used for the detection of DNA-oligonucleotide sequences (oDNA), that became a synthetic analog of circular RNA-circ-SHKBP1 associated with the development of glioma at a concentration of 1.1 × 10^-16 M. The possibility of using such h-k-SOI NW chips for the detection of circ-SHKBP1 in blood plasma of patients diagnosed with neoplasm of uncertain nature of the brain and central nervous system was shown.

Challenges of SERS technology as a non-nucleic acid or -antigen detection method for SARS-CoV-2 virus and its variants

The COVID-19 pandemic has caused a significant burden since December 2019 that has negatively impacted the global economy owing to the fact that the SARS-CoV-2 virus is fast-transmitting and highly contagious. Efforts have been taken to minimize the impact through strict screening measures in country borders in order to isolate potential virus carriers. Effective fast-screening methods are thus needed to identify infected individuals. The standard diagnostic methods for screening SARS-CoV-2 virus have always been to perform nucleic acid-based and serological tests. However, with each having drawbacks on producing false results at very early or later stage after symptoms onset, supplementary techniques are needed to back up these tests. Surface-enhanced Raman spectroscopy (SERS) as a detection technique has continuously advanced throughout the years in terms of sensitivity and capability to detect ultralow concentration of analytes ranging from single molecule to pathogens, to present as a highly potential alternative to known sensing methods. SERS technology as a candidate for an alternative and supplementary diagnostic method for the viral envelope of SARS-CoV-2 virus is presented, comparing its pros and cons to the standard methods and what other aspects it could offer that the other methods are not capable of. Factors that contribute to the detection effectivity of SERS is also discussed to show the advantages and limitations of this technique. Despite its promising capabilities, challenges like sources of SARS-CoV-2 virus and its variations, reliable SERS spectra, mass production of SERS-active substrates, and compliance to regulations for wide-scale testing scenario are highlighted.

Recent progress of SERS optical nanosensors for miRNA analysis

This review focuses on emerging applications of surface-enhanced Raman spectroscopy (SERS) optical nanosensors for miRNA analysis, in which the key enhancement factors of the SERS signal, i.e. SERS-active substrates, SERS nanoprobes and nano-assembly strategy, are emphasized. This article includes many nanomaterials for miRNA analysis by the SERS technique. We summarize these reported nanomaterials mainly according to their function in the miRNA assay biosensor. We also briefly summarize the research progress of these nanomaterials in SERS detection of intracellular miRNA. Finally, we discussed the prospect and limitations of SERS nanosensors for analyzing miRNA.

Advanced Application of Raman Spectroscopy and Surface-Enhanced Raman Spectroscopy in Plant Disease Diagnostics: A Review

Plant diseases result in 20-40% of agricultural loss every year worldwide. Timely detection of plant diseases can effectively prevent the development and spread of diseases and ensure the agricultural yield. High-throughput and rapid methods are in great demand. This review investigates the advanced application of Raman spectroscopy (RS) and surface-enhanced Raman spectroscopy (SERS) in the detection of plant diseases. The determination of bacterial diseases and stress-induced diseases, fungal diseases, viral diseases, pests in beans, and mycotoxins related to plant diseases using RS and SERS are discussed in detail. Then, biomarkers for RS and SERS detection are analyzed with regard to plant disease diagnosis. Finally, the advantages and challenges are further illustrated. Additionally, potential alternatives are proposed for the challenges. The review is expected to provide a reference and guidance for the use of RS and SERS in plant disease diagnostics.

Raman Spectroscopy-Based Quality Control of "Silicon-On-Insulator" Nanowire Chips for the Detection of Brain Cancer-Associated MicroRNA in Plasma

Application of micro-Raman spectroscopy for the monitoring of quality of nanowire sensor chips fabrication has been demonstrated. Nanowire chips have been fabricated on the basis of «silicon-on-insulator» (SOI) structures (SOI-NW chips). The fabrication of SOI-NW chips was performed by optical litography with gas-phase etching. The so-fabricated SOI-NW chips are intended for highly sensitive detection of brain cancer biomarkers in humans. In our present study, two series of experiments have been conducted. In the first experimental series, detection of a synthetic DNA oligonucleotide (oDNA) analogue of brain cancer-associated microRNA miRNA-363 in purified buffer solution has been performed in order to demonstrate the high detection sensitivity. The second experimental series has been performed in order to reveal miRNA-363 itself in real human plasma samples. To provide detection biospecificity, the SOI-NW chip surface was modified by covalent immobilization of probe oligonucleotides (oDNA probes) complementary to the target biomolecules. Using the SOI-NW sensor chips proposed herein, the concentration detection limit of the target biomolecules at the level of 3.3 × 10-17 M has been demonstrated. Thus, the approach employing the SOI-NW chips proposed herein represents an attractive tool in biomedical practice, aimed at the early revelation of oncological diseases in humans.

Nucleic Acids Analysis

Nucleic acids are natural biopolymers of nucleotides that store, encode, transmit and express genetic information, which play central roles in diverse cellular events and diseases in living things. The analysis of nucleic acids and nucleic acids-based analysis have been widely applied in biological studies, clinical diagnosis, environmental analysis, food safety and forensic analysis. During the past decades, the field of nucleic acids analysis has been rapidly advancing with many technological breakthroughs. In this review, we focus on the methods developed for analyzing nucleic acids, nucleic acids-based analysis, device for nucleic acids analysis, and applications of nucleic acids analysis. The representative strategies for the development of new nucleic acids analysis in this field are summarized, and key advantages and possible limitations are discussed. Finally, a brief perspective on existing challenges and further research development is provided.

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.

Surface Imprinted Layer of Cypermethrin upon Au Nanoparticle as a Specific and Selective Coating for the Detection of Template Pesticide Molecules

The detection of specific pesticides on food products is essential as these substances pose health risks due to their toxicity. The use of surface-enhanced Raman spectroscopy (SERS) takes advantage of the straightforward technique to obtain fingerprint spectra of target analytes. In this study, SERS-active substrates are made using Au nanoparticles (NPs) coated with a layer of polymer and followed by imprinting with a pesticide–Cypermethrin, as a molecularly imprinted polymer (MIP). Cypermethrin was eventually removed and formed as template cavities, then denoted as Au NP/MIP, to capture the analogous molecules. The captured molecules situated in-between the areas of high electromagnetic field formed by plasmonic Au NPs result in an effect of SERS. The formation of Au NP/MIP was, respectively, studied through morphological analysis using transmission electron microscopy (TEM) and compositional analysis using X-ray photoelectron spectroscopy (XPS). Two relatively similar pesticides, Cypermethrin and Permethrin, were used as analytes. The results showed that Au NP/MIP was competent to detect both similar molecules despite the imprint being made only by Cypermethrin. Nevertheless, Au NP/MIP has a limited number of imprinted cavities that result in sensing only low concentrations of a pesticide solution. Au NP/MIP is thus a specific design for detecting analogous molecules similar to its template structure.

Single-molecule analysis of nucleic acid biomarkers - A review

Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.

Remote biosensor for the determination of trypsin by using nanoporous anodic alumina as a three-dimensional nanostructured material

The determination of trypsin in the human real sample is a routine medical investigation to assess the pancreatic disease. Herein, we fabricated an interferometric reflectance spectroscopy based biosensor for the determination trypsin. For this purpose, urease and fluorescein 5(6)-isothiocyanate (FLITC) were immobilized on the nanoporous anodic alumina (NAA). The operation principle of the proposed biosensor is based on the change in the pH of the solution during the reaction of urease and urea and therefore change in the light-absorbing ability of FLITC in the presence of trypsin. The reaction of the urease enzyme with urea increased the pH of the solution because of producing ammonia. This increase in the pH of solution increased the light-absorbing ability of the immobilized FLITC on NAA and therefore the intensity of the reflected light from the NAA to the charge-coupled device detector decreased. In the presence of trypsin, the catalytic activity of immobilized urease on NAA decreased. This decrease in the activity of urease enzyme consequent on the decrease in the amount of the generated ammonia. Therefore, the immobilized FLITC on the NAA did not absorb more light and consciously, the intensity of the light reflected light into the detector increased. The proposed biosensor exhibited a good response to the concentration of trypsin in the range of 0.25–20 μg.mL⁻¹ with the limit of detection of 0.06 μg.mL⁻¹.

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

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

Label-free surface-enhanced Raman spectroscopy with artificial neural network technique for recognition photoinduced DNA damage

Taking advantage of surface-enhanced Raman scattering (SERS) methodology with its unique ability to collect abundant intrinsic fingerprint information and noninvasive data acquisition we set up a SERS-based approach for recognition of physically induced DNA damage with further incorporation of artificial neural network (ANN). As a proof-of-concept application, we used the DNA molecules, where the one oligonucleotide (OND) was grafted to the plasmonic surface while complimentary OND was exposed to UV illumination with various exposure doses and further hybridized with the grafted counterpart. All SERS spectra of entrapped DNA were collected by several operators using the portable spectrometer, without any optimization of measurements procedure (e.g., optimization of acquisition time, laser intensity, finding of optimal place on substrate, manual baseline correction, etc.) which usually takes a significant amount of operator's time. The SERS spectra were employed as input data for ANN training, and the performance of the system was verified by predicting the class labels for SERS validation data, using a spectra dataset, which has not been involved in the training process. During that phase, accuracy higher than 98% was achieved with a level of confidence exceeding 95%. It should be noted that utilization of the proposed functional-SERS/ANN approach allows identifying even the minor DNA damage, almost invisible by control measurements, performed with common analytical procedures. Moreover, we introduce the advanced ANN design, which allows not only classifying the samples but also providing the ANN analysis feedback, which associates the spectral changes and chemical transformations of DNA structure.

Advances in surface-enhanced Raman spectroscopy (SERS) substrates for lipid and protein characterization: sensing and beyond

Surface-enhanced Raman spectroscopy (SERS) has become an essential ultrasensitive analytical tool for biomolecular analysis of small molecules, macromolecular proteins, and even cells. SERS enables label-free, direct detection of molecules through their intrinsic Raman fingerprint. In particular, protein and lipid bilayers are dynamic three-dimensional structures that necessitate label-free methods of characterization. Beyond direct detection and quantitation, the structural information contained in SERS spectra also enables deeper biophysical characterization of biomolecules near metallic surfaces. Therefore, SERS offers enormous potential for such systems, although making measurements in a nonperturbative manner that captures the full range of interactions and activity remains a challenge. Many of these challenges have been overcome through advances in SERS substrate development, which have expanded the applications and targets of SERS for direct biomolecular quantitation and biophysical characterization. In this review, we will first discuss different categories of SERS substrates including solution-phase, solid-supported, tip-enhanced Raman spectroscopy (TERS), and single-molecule substrates for biomolecular analysis. We then discuss detection of protein and biological lipid membranes. Lastly, biophysical insights into proteins, lipids and live cells gained through SERS measurements of these systems are reviewed.

Ultrasensitive SERS detection of specific oligonucleotides based on Au@AgAg bimetallic nanorods

We synthesized a novel and sensitive Au/Ag bimetallic SERS-active nanotag, Au-Ag-Ag core-shell-shell nanorod (Au@AgAgNR). The Au@AgAgNR nanotag exhibited a strong SERS signal and was easily assembled from bilayer silver shells on an Au nanorod (AuNR) core with embedded Raman reporter molecules in the core-shell-shell gaps. The SERS activity of the nanotags was investigated with 2-mercaptopyridine (2-Mpy) as a Raman reporter, which could form pyridine/Ag⁺ coordination complexes to mediate the formation of silver shells. Specific enhancement of Raman signals was observed in the following order: AuNR < Au@AgNR < Au@AgAgNR. Then, Au@AgAgNR nanotags were coupled with magnetic beads (MBs) via specific DNA hybridization as a SERS sensor with a detection limit of 1 fM for a segment of the gene HPV-16. Factors affecting sensitivity and selectivity were investigated, including Raman dye concentration, silver nitrate dosage and the response to similar oligonucleotides. The proposed SERS sensor is expected to be a facile and sensitive method for specific gene detection.

Identification and Analysis of Exosomes by Surface-Enhanced Raman Spectroscopy

The concept of liquid biopsy has emerged as a novel approach for cancer screening, which is based on the analysis of circulating cancer biomarkers in body fluids. Among the various circulating cancer biomarkers, including Food and Drug Administration (FDA)-approved circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), exosomes have attracted tremendous attention due to their ability to diagnose cancer in its early stages with high efficiency. Recently, surface-enhanced Raman spectroscopy (SERS) has been applied for the detection of cancer exosomes due to its high sensitivity, specificity, and multiplexing capability. In this article, we review recent progress in the development of SERS-based technologies for in vitro identification of circulating cancer exosomes. The accent is made on the detection strategies and interpretation of the SERS data. The problems of detecting cancer-derived exosomes from patient samples and future perspectives of SERS-based diagnostics are also discussed.

The control of the adsorption of bovine serum albumin on mercaptan-modified gold thin films investigated by SERS spectroscopy

Nanostructured gold thin films were built from deposition of colloidal gold nanoparticles on silanized glass slides, and used to study the adsorption of bovine serum albumin (BSA) after chemical treatment of gold surface with the mercaptans 2-mercaptoethanol, 3-mercaptoproprionic acid, 1,3-propanedithiol and 1-propanethiol. Surface-enhanced Raman scattering (SERS) spectroscopy was used for investigating the chemical interactions of BSA with the modified gold surfaces. In the presence of the surface modifier 2-mercaptoethanol, a promoter of hydrogen bonds, the stable interactions among BSA and gold surfaces led to high reproducibility of the SERS spectral pattern in the most monitored points of the mapped surface. The vibrational assignment endorsed the assumption that lysine residue, majority present in the molecular structure, were the principal anchor site of BSA involved in the interactions with 2-mercaptoethanol-modified gold surface.

Aptasensors as the future of antibiotics test kits-a case study of the aptamer application in the chloramphenicol detection

Antibiotics are a type of antimicrobial drug with the ubiquitous presence in foodstuff that effectively applied to treat the diseases and promote the animal growth worldwide. Chloramphenicol as one of the antibiotics with the broad action spectrum against Gram-positive and Gram-negative bacteria is widely applied for the effective treatment of infectious diseases in humans and animals. Unfortunately, the serious side effects of chloramphenicol, such as aplastic anemia, kidney damage, nausea, and diarrhea restrict its application in foodstuff and biomedical fields. Development of the sufficiently sensitive methods to detect chloramphenicol residues in food and clinical diagnosis seems to be an essential demand. Biosensors have been introduced as the promising tools to overcome the requirement. As one of the newest types of the biosensors, aptamer-based biosensors (aptasensors) are the efficient sensing platforms for the chloramphenicol monitoring. In the present review, we summarize the recent achievements of the accessible aptasensors for qualitative detection and quantitative determination of chloramphenicol as a candidate of the antibiotics. The present chloramphenicol aptasensors can be classified in two main optical and electrochemical categories. Also, the other formats of the aptasensing assays like the high performance liquid chromatography (HPLC) and microchip electrophoresis (MCE) have been reviewed. The enormous interest in utilizing the diverse nanomaterials is also highlighted in the fabrication of the chloramphenicol aptasensors. Finally, some results are presented based on the advantages and disadvantages of the studied aptasensors to achieve a promising perspective for designing the novel antibiotics test kits.