Quantum scale organic semiconductors for SERS detection of DNA methylation and gene expression

Utilizing a synergistic strategy that combines electromagnetic and chemical enhancement to analyze the SERS effect of the Fe3O4@GO@Ag on PAHs detection

A comprehensive understanding of the enhancement mechanism of the substrate material is crucial to ensure the repeatability and functionality of SERS detection technology. Therefore, this study introduces a theoretical analysis method that integrates electromagnetic and chemical enhancement to achieve a comprehensive understanding of the SERS effect on the magnetic composite substrate. The visual model is employed in this study to comprehensively analyze and illustrate the electric field enhancement and optical effects of composite substrate materials. The study also elucidated the adsorption and charge transfer between the substrate material and target molecules. Based on this theory, Fe3O4@GO@Ag material was prepared and used to detect hydrophobic organic molecules such as polycyclic aromatic hydrocarbons (PAHs), with a concentration as low as 0.5 nM. This study comprehensively analyzed the SERS enhancement effect of the composite substrate for the first time, and prepared a magnetic composite substrate material for the detection of hydrophobic organic molecules, opening up a new avenue for theoretical guidance and experimental exploration in SERS detection and analysis.

Tuning Nanographene-Enhanced Raman Scattering for Rapid Label-Free Detection of Amino Acids

The rapid and sensitive detection of amino acids is important not only for fundamental studies but also for the establishment of a healthy society. However, conventional detection methods have been hampered by the difficulties of low sensitivity, long sampling and detection times, and expensive operation and instruments. Here, we report the plasma engineering of bioresource-derived graphene quantum dots (GQDs) as surface-enhanced Raman scattering (SERS)-active materials for the rapid and sensitive detection of amino acids. Surface-functionalized GQDs with tuned structures and band gaps were synthesized from earth-abundant bioresources by using reactive microplasmas under ambient conditions. Detailed microscopy and spectroscopy studies indicate that the SERS properties of the synthesized GQDs can be tuned by controlling the band gaps of synthesized GQDs. The plasma-synthesized metal-free GQDs with surface functionalities showed improved SERS properties for rapid amino acid detection with low detection limits of 10-5 M for tyrosine and phenylalanine. Theoretical calculations suggest that charge transfer between GQDs and amino acids can enhance the SERS response of the GQDs. Our work provides insights into the controlled engineering of SERS-active nanographene-based materials using the plasma-enhanced method.

Photoinduced Charge Transfer Empowers Ta4C3 and Nb4C3 MXenes with High SERS Performance

This study introduces two-dimensional (2D) Ta4C3 and Nb4C3 MXenes as outstanding materials for surface-enhanced Raman scattering (SERS) sensing, marking a significant departure from traditional noble-metal substrates. These MXenes exhibit exceptional SERS capabilities, achieving enhancement factors around 105 and detection limits as low as 10-7 M for various analytes, including environmental pollutants and drugs. The core of their SERS functionality is attributed to the robust interfacial photoinduced charge-transfer interactions between the MXenes and the adsorbed molecules. This deep insight not only advances our understanding of MXene materials in SERS applications but also opens new avenues for developing highly sensitive and selective SERS sensors. The potential of Ta4C3 and Nb4C3 MXenes to revolutionize SERS technology underscores their importance in environmental monitoring, food safety, and beyond.

Versatile self-assembled near-infrared SERS nanoprobes for multidrug-resistant bacterial infection-specific surveillance and therapy

The rise of multidrug-resistant bacteria (MDRB) has made bacterial infection one of the biggest health threats, causing numerous antibiotics to fail. Real-time monitoring of bacterial disease treatment efficacy at the infection site is required. Herein, we report a versatile Raman tag 3,3'-diethylthiatricarbocyanine iodide (DTTC)-conjugated star-shaped Au-MoS2@hyaluronic acid (AMD@HA) nanocomposite as a surface-enhanced Raman scattering (SERS) nanoprobe for quick bacterial identification and in-situ eradication. Localized surface plasmon resonance (LSPR) from the hybrid metallic nanostructure makes AMD@HA highly responsive to the near-infrared laser, enabling it to demonstrate a photothermal (PTT) effect, increased SERS activity, and peroxidase-like catalytic reaction to release reactive oxygen species. The tail vein injection of AMD@HA nanoprobes is invasive, however SERS imaging for bacterial identification is non-invasive and sensitive, making it an efficient residual bacteria monitoring method. The detection limit for methicillin-resistant Staphylococcus aureus (MRSA) is as low as 102 CFU·mL-1, and the substrates allow for taking 120 s to acquire a Raman image of 1600 (40 × 40) pixels. In mouse models of MRSA-induced wound infection and skin abscess, the combination of AMD@HA-mediated PTT and catalytic therapy demonstrates a synergistic effect in promoting wound healing through rapid sterilization. This SERS-guided therapeutic approach exhibits little toxicity and does not cause considerable collateral damage, offering a highly promising intervention for treating diseases caused by MDRB. STATEMENT OF SIGNIFICANCE: This research introduces a SERS nanoprobe, AMD@HA, for the rapid identification and eradication of multidrug-resistant bacteria (MDRB), a critical health threat. The nanoprobe leverages localized surface plasmon resonance for photothermal therapy and enhanced Raman signals, offering a sensitive, non-invasive diagnostic tool. With a low detection limit for MRSA and a synergistic therapeutic effect in mouse models, our approach holds significant promise for treating MDRB-driven infections with minimal toxicity, advancing the field of antimicrobial strategies.

Multiple valence states of Fe boosting SERS activity of Fe3O4 nanoparticles and enabling effective SERS-MRI bimodal cancer imaging

Developing novel nanoparticle-based bioprobes utilized in clinical settings with imaging resolutions ranging from cell to tissue levels is a major challenge for tumor diagnosis and treatment. Herein, an optimized strategy for designing a Fe3O4-based bioprobe for dual-modal cancer imaging based on surface-enhanced Raman scattering (SERS) and magnetic resonance imaging (MRI) is introduced. Excellent SERS activity of ultrasmall Fe3O4 nanoparticles (NPs) was discovered, and a 5 × 10-9 M limit of detection for crystal violet molecules was successfully obtained. The high-efficiency interfacial photon-induced charge transfer in Fe3O4 NPs was promoted by multiple electronic energy levels ascribed to the multiple valence states of Fe, which was observed using ultraviolet-visible diffuse reflectance spectroscopy. Density functional theory calculations were utilized to reveal that the narrow band gap and high electron density of states of ultrasmall Fe3O4 NPs significantly boosted the vibronic coupling resonances in the SERS system upon illumination. The subtypes of cancer cells were accurately recognized via high-resolution SERS imaging in vitro using the prepared Fe3O4-based bioprobe with high sensitivity and good specificity. Notably, Fe3O4-based bioprobes simultaneously exhibited T1 -weighted MRI contrast enhancement with an active targeting capability for tumors in vivo. To the best of our knowledge, this is the first report on the use of pure semiconductor-based SERS-MRI dual-modal nanoprobes in tumor imaging in vivo and in vitro, which has been previously realized only using semiconductor-metal complex materials. The non-metallic materials with SERS-MRI dual-modal imaging established in this report are a promising cancer diagnostic platform, which not only showed excellent performance in early tumor diagnosis but also possesses great potential for image-guided tumor treatment.

New advances in signal amplification strategies for DNA methylation detection in vitro

5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.

SERS biosensors for liquid biopsy towards cancer diagnosis by detection of various circulating biomarkers: current progress and perspectives

Liquid biopsy has emerged as a promising non-invasive strategy for cancer diagnosis, enabling the detection of various circulating biomarkers, including circulating tumor cells (CTCs), circulating tumor nucleic acids (ctNAs), circulating tumor-derived small extracellular vesicles (sEVs), and circulating proteins. Surface-enhanced Raman scattering (SERS) biosensors have revolutionized liquid biopsy by offering sensitive and specific detection methodologies for these biomarkers. This review comprehensively examines the application of SERS-based biosensors for identification and analysis of various circulating biomarkers including CTCs, ctNAs, sEVs and proteins in liquid biopsy for cancer diagnosis. The discussion encompasses a diverse range of SERS biosensor platforms, including label-free SERS assay, magnetic bead-based SERS assay, microfluidic device-based SERS system, and paper-based SERS assay, each demonstrating unique capabilities in enhancing the sensitivity and specificity for detection of liquid biopsy cancer biomarkers. This review critically assesses the strengths, limitations, and future directions of SERS biosensors in liquid biopsy for cancer diagnosis.

Deciphering biomolecular complexities: the indispensable role of surface-enhanced Raman spectroscopy in modern bioanalytical research

Surface-enhanced Raman spectroscopy (SERS) has emerged as an indispensable analytical tool in biomolecular research, providing unmatched sensitivity critical for the elucidation of biomolecular structures. This review presents a thorough examination of SERS, outlining its fundamental principles, cataloging its varied applications within the biomolecular sphere, and contemplating its future developmental trajectories. We begin with a detailed analysis of SERS's mechanistic principles, emphasizing both the phenomena of surface enhancement and the complexities inherent in Raman scattering spectroscopy. Subsequently, we delve into the pivotal role of SERS in the structural analysis of diverse biomolecules, including proteins, nucleic acids, lipids, carbohydrates, and biochromes. The remarkable capabilities of SERS extend beyond mere detection, offering profound insights into biomolecular configurations and interactions, thereby enriching our comprehension of intricate biological processes. This review also sheds light on the application of SERS in real-time monitoring of various bio-relevant compounds, from enzymes and coenzymes to metal ion-chelate complexes and cellular organelles, thereby providing a holistic view and empowering researchers to unravel the complexities of biological systems. We also address the current challenges faced by SERS, such as enhancing sensitivity and resolution, developing stable and reproducible substrates, and conducting thorough analyses in complex biological matrices. Nonetheless, the continual advancements in nanotechnology and spectroscopy solidify the standing of SERS as a formidable force in biomolecular research. In conclusion, the versatility and robustness of SERS not only deepen our understanding of biomolecular intricacies but also pave the way for significant developments in medical research, therapeutic innovation, and diagnostic approaches.

Single-Atom Site SERS Chip for Rapid, Ultrasensitive, and Reproducible Direct-Monitoring of RNA Binding

Ribonucleic acids (RNA) play active roles within cells or viruses by catalyzing biological reactions, controlling gene expression, and communicating responses to cellular signals. Rapid monitoring RNA variation has become extremely important for appropriate clinical decisions and frontier biological research. However, the most widely used method for RNA detection, nucleic acid amplification, is restricted by a mandatory temperature cycling period of ≈1 h required to reach target detection criteria. Herein, a direct detection approach via single-atom site integrated surface-enhanced Raman scattering (SERS) monitoring nucleic acid pairing reaction, can be completed within 3 min and reaches high sensitivity and extreme reproducibility for COVID-19 and two other influenza viruses' detection. The mechanism is that a single-atom site on SERS chip, enabled by positioning a single-atom oxide coordinated with a specific complementary RNA probe on chip nanostructure hotspots, can effectively bind target RNA analytes to enrich them at designed sites so that the binding reaction can be detected through Raman signal variation. This ultrafast, sensitive, and reproducible single-atom site SERS chip approach paves the route for an alternative technique of immediate RNA detection. Moreover, single-atom site SERS is a novel surface enrichment strategy for SERS active sites for other analytes at ultralow concentrations.

Development of a highly sensitive aptamer-based electrochemical sensor for detecting saxitoxin based on K3Fe(CN)6 regulated silver nanoparticles

BACKGROUND

Saxitoxin (STX) is the most toxic marine toxin, which can pose several adverse effects on human health. High sensitivity, fast response, and low-cost detection of STX contamination are of significance to reducing the fishery and seafood industries' loss. Among the various types of biosensors, the electrochemical biosensors have been extensively studied in the detection of STX, but the electrode surface modification material is easy to fall off, resulting in unstable electrochemical signals and poor reproducibility. It is imperative to have a ratiometric electrochemical biosensor for STX.

RESULTS

In this study, we developed a novel aptamer-based electrochemical sensor (AECs) for the sensitive detection of STX based on a K3Fe(CN)6 regulated silver nanoparticles (Ag NPs) modified with aptamer. The AECs was constructed by immobilizing aptamer on Ag NPs surfaces. Under optimized conditions, the AECs showed a linear response towards STX in the range from 0.04 to 0.15 μM with the regression equation of Y = -8.0 + 233.7 X (R2 = 0.9956). The limit of detection (LOD) was calculated to be 1 nM (based on 3 N/S), which is significantly lower than the regulatory limits for STX in seafood. Moreover, the AECs showed excellent sensitivity, reproducibility and stability, as well as the detection in samples with acceptable recovery ranged from 71.2 % to 93.8 %, demonstrating its broad application prospects in detection of STX in seafood samples.

SIGNIFICANCE

This work proposed an AECs to achieve sensitive detection of STX. A reaction system of K3Fe(CN)6 etched Ag NPs was introduced and used as the signal source to avoid the instability of the electrochemical signal, which can produce a ratiometric electrochemical signal output mode, improving the stability and sensitivity of electrochemical detection of STX.

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

Noble metal-free SERS: mechanisms and applications

Surface-enhanced Raman scattering (SERS) is a very important tool in vibrational spectroscopy. The coupling of nanomaterials induces local surface plasmon resonance (LSPR), which contributes greatly to SERS. Due to its remarkable sensitivity in trace detection, SERS has gained prominence in the fields of catalysis, biosensors, drug tracking, and optoelectronic devices. SERS activity is believed to be closely related to the LSPR and charge transfer (CT) of the material. Noble metal nanostructures have been commonly used as SERS-active substrates due to their strong local electric fields and relatively mature preparation, application, and enhancement mechanisms. In recent years, SERS research based on semiconductor materials has attracted significant attention because semiconductor materials have advantages such as repeatable preparation, simple pretreatment, stable SERS spectra and superior biocompatibility, stability, and reproducibility. Semiconductor-based SERS has the potential to enrich SERS theory and applications. Thus, the development of semiconductor materials will introduce a new epoch for SERS-based research. In this review, we outline the two main kinds of semiconductor SERS-active substrates: inorganic and organic semiconductor SERS-active substrates. We also provide an overview of the SERS mechanism for different kinds of materials and SERS-based applications.

Directly and ultrasensitivity detecting SARS-CoV-2 spike protein in pharyngeal swab solution by using SERS-based biosensor

The global pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a great disaster to the economy and human society. Nowadays, SARS-CoV-2 is fading away from people's memory but it still exists around us. PCR plays an important role in detecting SARS-CoV-2 but it requires a long detecting time, equipped laboratory, and professional operators. In comparison with polymerase chain reaction (PCR), surface-enhanced Raman scattering (SERS) is a promising method for detecting SARS-CoV-2 due to its fast, easily operated, and high-sensitivity properties. In this study, the monolayer Ag nanoparticles (MAgNPs) covered with single-layer graphene (SLG) are applied as a SERS substrate. The angiotensin converting enzyme 2 (ACE2) is selected as a bio-probes that can specifically bind to the SARS-CoV-2 S protein. The SERS-based biosensor is formed by ACE2 functionalized SLG/MAgNPs and the LODs of detecting SARS-CoV-2 S protein in phosphate-buffered saline (PBS) and in pharyngeal swabs solution (PSS) are 0.1 fg mL-1 and 10 fg mL-1, respectively. This biosensor provides a way of directly detecting SARS-CoV-2 S protein with high sensitivity and specificity. It illustrates a practical potential in the rapid detection of the SARS-CoV-2 virus.

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.

Label-free detection of virus based on surface-enhanced Raman scattering

Due to the background interference from biological samples, detecting viruses using surface-enhanced Raman scattering (SERS) in clinical samples is challenging. This study is based on SERS by reducing sodium borohydride and aggregating silver nanoparticles to develop suitable virus detection "hot spot." The monkeypox virus and human papillomavirus fingerprints were quickly obtained, tested, and identified in serum and artificial vaginal discharge, respectively, by combining the principal component analysis method. Therefore, these viruses were successfully identified in the biological background. In addition, the lowest detection limit was 100 copies/mL showing good reproducibility and signal-to-noise ratio. The concentration-dependent curve of the monkeypox virus had a good linear relationship. This method helps solve the SERS signal interference problem in complex biological samples, with low detection limits and high selectivity in virus characterization and quantitative analysis. Therefore, this method has a reasonable prospect of clinical application.

Deciphering the Potential of Multidimensional Carbon Materials for Surface-Enhanced Raman Spectroscopy through Density Functional Theory

Surface-enhanced Raman spectroscopy (SERS) is a potent analytical tool, particularly for molecular identification and structural analysis. Conventional metallic SERS substrates, however, suffer from low reproducibility and compatibility with biological molecules. Recently, metal-free SERS substrates based on chemical enhancement have emerged as a promising alternative with carbon-based materials offering excellent reproducibility and compatibility. Nevertheless, our understanding of carbon materials in SERS remains limited, which hinders their rational design. Here we systematically explore multidimensional carbon materials, including zero-dimensional fullerenes (C60), one-dimensional carbon nanotubes, two-dimensional graphene, and their B-, N-, and O-doped derivatives, for SERS applications. Using density functional theory, we elucidate the nonresonant polarizability-enhanced and resonant charge-transfer-based chemical enhancement mechanisms of these materials by evaluating their static/dynamic polarizability and electron excitation properties. This work provides a critical reference for the future design of carbon-based SERS substrates, opening a new avenue in this field.

Polyphenolic Carbon Quantum Dots with Intrinsic Reactive Oxygen Species Amplification for Two-Photon Bioimaging and In Vivo Tumor Therapy

Recent studies indicate that mitochondrial dysfunctions and DNA damage have a critical influence on cell survival, which is considered one of the therapeutic targets for cancer therapy. In this study, we demonstrated a comparative study of the effect of polyphenolic carbon quantum dots (CQDs) on in vitro and in vivo antitumor efficacy. Dual emissive (green and yellow) shape specific polyphenolic CQDs (G-CQDs and Y-CQDs) were synthesized from easily available nontoxic precursors (phloroglucinol), and the antitumor property of the as-synthesized probe was investigated as compared to round-shaped blue emissive CQDs (B-CQDs) derived from well-reported precursor citric acid and urea. The B-CQDs had a nuclei-targeting property, and G-CQDs and Y-CQDs had mitochondria-targeting properties. We have found that the polyphenol containing CQDs (at a dose of 100 μg mL-1) specifically attack mitochondria by excess accumulation, altering the metabolism, inhibiting branching pattern, imbalanced Bax/Bcl-2 homeostasis, and ultimately generating oxidative stress levels, leading to oxidative stress-induced cell death in cancer cells in vitro. We show that G-CQDs are the main cause of oxidative stress in cancer cells because of their ability to produce sufficient •OH- and 1O2 radicals, evidenced by electron paramagnetic resonance spectroscopy and a terephthalic acid test. Moreover, the near-infrared absorption properties of the CQDs were exhibited in two-photon (TP) emission, which was utilized for TP cellular imaging of cancer cells without photobleaching. The in vivo antitumor test further discloses that intratumoral injection of G-CQDs can significantly augment the treatment efficacy of subcutaneous tumors without any adverse effects on BalB/c nude mice. We believe that shape-specific polyphenolic CQD-based nanotheranostic agents have a potential role in tumor therapy, thus proving an insight on treatment of malignant cancers.

Self-Functionalized Superlattice Nanosensor Enables Glioblastoma Diagnosis Using Liquid Biopsy

Glioblastoma (GBM), the most aggressive and lethal brain cancer, is detected only in the advanced stage, resulting in a median survival rate of 15 months. Therefore, there is an urgent need to establish GBM diagnosis tools to identify the tumor accurately. The clinical relevance of the current liquid biopsy techniques for GBM diagnosis remains mostly undetermined, owing to the challenges posed by the blood-brain barrier (BBB) that restricts biomarkers entering the circulation, resulting in the unavailability of clinically validated circulating GBM markers. GBM-specific liquid biopsy for diagnosis and prognosis of GBM has not yet been developed. Here, we introduce extracellular vesicles of GBM cancer stem cells (GBM CSC-EVs) as a previously unattempted, stand-alone GBM diagnosis modality. As GBM CSCs are fundamental building blocks of tumor initiation and recurrence, it is desirable to investigate these reliable signals of malignancy in circulation for accurate GBM diagnosis. So far, there are no clinically validated circulating biomarkers available for GBM. Therefore, a marker-free approach was essential since conventional liquid biopsy relying on isolation methodology was not viable. Additionally, a mechanism capable of trace-level detection was crucial to detecting the rare GBM CSC-EVs from the complex environment in circulation. To break these barriers, we applied an ultrasensitive superlattice sensor, self-functionalized for surface-enhanced Raman scattering (SERS), to obtain holistic molecular profiling of GBM CSC-EVs with a marker-free approach. The superlattice sensor exhibited substantial SERS enhancement and ultralow limit of detection (LOD of attomolar 10-18 M concentration) essential for trace-level detection of invisible GBM CSC-EVs directly from patient serum (without isolation). We detected as low as 5 EVs in 5 μL of solution, achieving the lowest LOD compared to existing SERS-based studies. We have experimentally demonstrated the crucial role of the signals of GBM CSC-EVs in the precise detection of glioblastoma. This was evident from the unique molecular profiles of GBM CSC-EVs demonstrating significant variation compared to noncancer EVs and EVs of GBM cancer cells, thus adding more clarity to the current understanding of GBM CSC-EVs. Preliminary validation of our approach was undertaken with a small amount of peripheral blood (5 μL) derived from GBM patients with 100% sensitivity and 97% specificity. Identification of the signals of GBM CSC-EV in clinical sera specimens demonstrated that our technology could be used for accurate GBM detection. Our technology has the potential to improve GBM liquid biopsy, including real-time surveillance of GBM evolution in patients upon clinical validation. This demonstration of liquid biopsy with GBM CSC-EV provides an opportunity to introduce a paradigm potentially impacting the current landscape of GBM diagnosis.

Nano-biosensor for SARS-CoV-2/COVID-19 detection: methods, mechanism and interface design

The epidemic of coronavirus disease 2019 (COVID-19) was a huge disaster to human society. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to COVID-19, has resulted in a large number of deaths. Even though the reverse transcription-polymerase chain reaction (RT-PCR) is the most efficient method for the detection of SARS-CoV-2, the disadvantages (such as long detection time, professional operators, expensive instruments, and laboratory equipment) limit its application. In this review, the different kinds of nano-biosensors based on surface-enhanced Raman scattering (SERS), surface plasmon resonance (SPR), field-effect transistor (FET), fluorescence methods, and electrochemical methods are summarized, starting with a concise description of their sensing mechanism. The different bioprobes (such as ACE2, S protein-antibody, IgG antibody, IgM antibody, and SARS-CoV-2 DNA probes) with different bio-principles are introduced. The key structural components of the biosensors are briefly introduced to give readers an understanding of the principles behind the testing methods. In particular, SARS-CoV-2-related RNA mutation detection and its challenges are also briefly described. We hope that this review will encourage readers with different research backgrounds to design SARS-CoV-2 nano-biosensors with high selectivity and sensitivity.

Cytosine epigenetic modifications and conformational changes in G-quadruplex DNA: An ultraviolet resonance Raman spectroscopy study

Epigenetic modifications of DNA are known to play important regulatory roles in biological systems, especially in regulation of gene expression, and are associated with many types of human diseases, including cancer. Alternative DNA secondary structures, such as G-quadruplexes, can also influence gene transcription, thus suggesting that such structures may represent a distinctive layer of epigenetic information. G-quadruplex structures and DNA epigenetic modifications often go side by side, and recent evidence reveals that cytosine modifications within loops of G-quadruplexes can play a role in modulating their stability and structural polymorphism. Therefore, the development and validation of experimental techniques that can easily and reliably analyse G-quadruplex structures are highly desirable. In the present study, we propose to exploit the advantages of UV resonance Raman (UVRR) spectroscopy to investigate cytosine epigenetic modifications along with conformational changes in G-quadruplex-forming DNA. Our findings show that clear and specific spectral changes occur when there is a change in a G-quadruplex structure. Moreover, UVRR spectral analysis can indirectly distinguish the spectral variations occurring because of modifications in the guanine glycosidic conformations, as well as detect changes in the loops induced by H-bond formation or hydration of nitrogenous bases. The results further underscore the utility of UVRR spectroscopy for G-quadruplex structure elucidation under biologically relevant solution conditions.

Recent development of surface-enhanced Raman scattering for biosensing

Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented.

A novel alternative strategy for monitoring and insight into liver fibrosis progression: The combination of surface-enhanced Raman spectroscopy (SERS) and gut microbiota

Nowadays, the studies on the interaction and relationship between the intestinal microorganisms and liver diseases are increasing. However, it is still a huge challenge for the in-depth investigation and dynamic monitoring of such a complex network. Herein, a significant discovery was made. A strong association between gut microbial structural and functional genomics and SERS spectra of hepatocytes were revealed. Based on the study of gut microbes and SERS spectra, complementary information could be provided for the mechanism analysis of related diseases. Liver fibrosis, a chronic liver disease that lack specific cure was thus comprehensive studied. Liver targeting gold nanoparticle dimers were prepared as the SERS tags, and abundant SERS peak signals were acquired. Meanwhile, the gut microbiomes were also comparative studied. The changes of carbohydrates and lipids in liver cells were observed at the early stages of liver fibrosis, and TLR4 (toll-like receptors 4) was activated to elicit immune responses. Then again, oxidative stress, endotoxin and serum inflammatory factors were the major observations at the late stages. The SERS signals and the microbiome analysis were well confirmed and complemented each other, which suggested that the detection strategy could be another valuable method for the "gut-liver axis" study.

Machine learning-assisted global DNA methylation fingerprint analysis for differentiating early-stage lung cancer from benign lung diseases

DNA methylation plays a critical role in the development of human tumors. However, routine characterization of DNA methylation can be time-consuming and labor-intensive. We herein describe a sensitive, simple surface-enhanced Raman spectroscopy (SERS) approach for identifying the DNA methylation pattern in early-stage lung cancer (LC) patients. By comparing SERS spectra of methylated DNA bases or sequences with their counterparts, we identified a reliable spectral marker of cytosine methylation. To move toward clinical applications, we applied our SERS strategy to detect the methylation patterns of genomic DNA (gDNA) extracted from cell line models as well as formalin-fixed paraffin-embedded tissues of early-stage LC and benign lung diseases (BLD) patients. In a clinical cohort of 106 individuals, our results showed distinct methylation patterns in gDNA between early-stage LC (n = 65) and BLD patients (n = 41), suggesting cancer-induced DNA methylation alterations. Combined with partial least square discriminant analysis, early-stage LC and BLD patients were differentiated with an area under the curve (AUC) value of 0.85. We believe that the SERS profiling of DNA methylation alterations, together with machine learning could potentially offer a promising new route toward the early detection of LC.

Decoding the metabolic response of Escherichia coli for sensing trace heavy metals in water

Heavy metal contamination due to industrial and agricultural waste represents a growing threat to water supplies. Frequent and widespread monitoring for toxic metals in drinking and agricultural water sources is necessary to prevent their accumulation in humans, plants, and animals, which results in disease and environmental damage. Here, the metabolic stress response of bacteria is used to report the presence of heavy metal ions in water by transducing ions into chemical signals that can be fingerprinted using machine learning analysis of vibrational spectra. Surface-enhanced Raman scattering surfaces amplify chemical signals from bacterial lysate and rapidly generate large, reproducible datasets needed for machine learning algorithms to decode the complex spectral data. Classification and regression algorithms achieve limits of detection of 0.5 pM for As³⁺ and 6.8 pM for Cr⁶⁺, 100,000 times lower than the World Health Organization recommended limits, and accurately quantify concentrations of analytes across six orders of magnitude, enabling early warning of rising contaminant levels. Trained algorithms are generalizable across water samples with different impurities; water quality of tap water and wastewater was evaluated with 92% accuracy.

Application of SERS in In-Vitro Biomedical Detection

Surface-enhanced Raman scattering (SERS), as a rapid and nondestructive biological detection method, holds great promise for clinical on spot and early diagnosis. In order to address the challenging demands of on spot detection of biomedical samples, a variety of strategies has been developed. These strategies include substrate structural and component engineering, data processing techniques, as well as combination with other analytical methods. This report summarizes the recent SERS developments for biomedical detection, and their promising applications in cancer detection, virus or bacterial infection detection, miscarriage spotting, neurological disease screening et al. The first part discusses the frequently used SERS substrate component and structures, the second part reports on the detection strategies for nucleic acids, proteins, bacteria, and virus, the third part summarizes their promising applications in clinical detection in a variety of illnesses, and the forth part reports on recent development of SERS in combination with other analytical techniques. The special merits, challenges, and perspectives are discussed in both introduction and conclusion sections.

Nanomaterials meet surface-enhanced Raman scattering towards enhanced clinical diagnosis: a review

Surface-enhanced Raman scattering (SERS) is a very promising tool for the direct detection of biomarkers for the diagnosis of i.e., cancer and pathogens. Yet, current SERS strategies are hampered by non-specific interactions with co-existing substances in the biological matrices and the difficulties of obtaining molecular fingerprint information from the complex vibrational spectrum. Raman signal enhancement is necessary, along with convenient surface modification and machine-based learning to address the former issues. This review aims to describe recent advances and prospects in SERS-based approaches for cancer and pathogens diagnosis. First, direct SERS strategies for key biomarker sensing, including the use of substrates such as plasmonic, semiconductor structures, and 3D order nanostructures for signal enhancement will be discussed. Secondly, we will illustrate recent advances for indirect diagnosis using active nanomaterials, Raman reporters, and specific capture elements as SERS tags. Thirdly, critical challenges for translating the potential of the SERS sensing techniques into clinical applications via machine learning and portable instrumentation will be described. The unique nature and integrated sensing capabilities of SERS provide great promise for early cancer diagnosis or fast pathogens detection, reducing sanitary costs but most importantly allowing disease prevention and decreasing mortality rates.

CanMethdb: a database for genome-wide DNA methylation annotation in cancers

MOTIVATION

DNA methylation within gene body and promoters in cancer cells is well documented. An increasing number of studies showed that cytosine-phosphate-guanine (CpG) sites falling within other regulatory elements could also regulate target gene activation, mainly by affecting transcription factors (TFs) binding in human cancers. This led to the urgent need for comprehensively and effectively collecting distinct cis-regulatory elements and TF-binding sites (TFBS) to annotate DNA methylation regulation.

RESULTS

We developed a database (CanMethdb, http://meth.liclab.net/CanMethdb/) that focused on the upstream and downstream annotations for CpG-genes in cancers. This included upstream cis-regulatory elements, especially those involving distal regions to genes, and TFBS annotations for the CpGs and downstream functional annotations for the target genes, computed through integrating abundant DNA methylation and gene expression profiles in diverse cancers. Users could inquire CpG-target gene pairs for a cancer type through inputting a genomic region, a CpG, a gene name, or select hypo/hypermethylated CpG sets. The current version of CanMethdb documented a total of 38 986 060 CpG-target gene pairs (with 6 769 130 unique pairs), involving 385 217 CpGs and 18 044 target genes, abundant cis-regulatory elements and TFs for 33 TCGA cancer types. CanMethdb might help biologists perform in-depth studies of target gene regulations based on DNA methylations in cancer.

AVAILABILITY AND IMPLEMENTATION

The main program is available at https://github.com/chunquanlipathway/CanMethdb.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Evaluation of classification ability of logistic regression model on SERS data of miRNAs

Logistic regression (LR) is a supervised multiple linear regression model, which uses linear weighted calculation for input to obtain weight coefficients of model. The surface enhanced Raman spectroscopy (SERS) technology greatly enhances the Raman signal of analyte. LR model was used to analyze the data of seven types of pancreatic cancer-related miRNAs obtained from commercial SERS substrate. The classification ability of the model on such data was observed under the configurations of different key parameters (classification mode, regularization method and loss function optimization way), and the effect of the two types of data formats were also evaluated. The results showed that though LR model used to classify this data did not perform well as expected, miRNA-191 and miRNA-4306 still had high recalls (sensitivity), which laid a theoretical foundation for the purpose of using LR model to identify these two miRNAs to jointly diagnose of pancreatic cancer at miRNA level.

A high-performance SERS imprinted membrane based on Ag/CNTs for selective detection of spiramycin

In this test, the eggshell membrane (ESM) is selected as the support membrane for the biocompatibility and anchors CNTs on the surface to increase the mechanical properties. Then Ag NPs are decorated on CNTs-ESM substrate as SERS substrate by twice in-situ reduction. Finally, a layer of imprinted polymers is coated on the surface of the substrate to synthesize the imprinted membrane for selective detection of spiramycin. It is exhibited from the characteristic results that the CNTs significantly increase the mechanical properties and the detection sensitivity, simultaneously. When the concentration of SP changes between 10^-6 ∼ 10^-11 M, there is a linear relationship between SERS intensity and SP concentration. The detection limit is 10^-11 M, and the correlation coefficient R² is 0.9864. The SERS imprinted membrane can be applied into the detection of antibiotics in practical sample, which broadens the research field of antibiotics detection.

An efficient and simple SERS approach for trace analysis of tetrahydrocannabinol and cannabinol and multi-cannabinoid detection

Many countries have legalized cannabis and its derived products for multiple purposes. Consequently, it has become necessary to develop a rapid, effective, and reliable tool for detecting delta-9-tetrahydrocannabinol (THC) and cannabinol (CBN), which are important biologically active compounds in cannabis. Herein, we have fabricated SERS chips by using glancing angle deposition and tuned dimensions of silver nanorods (AgNRs) for detecting THC and CBN at low concentrations. Experimental and computational results showed that the AgNR substrate with film thickness (or nanorod length) of 150 nm, corresponding to nanorod diameter of 79 nm and gap between nanorods of 23 nm, can effectively sense trace THC and CBN with good reproducibility and sensitivity. Due to limited spectral studies of the cannabinoids in previous reports, this work also explored towards identifying characteristic Raman lines of THC and CBN. This information is critical to further reliable data analysis and interpretation. Moreover, multianalyte detection of THC and CBN in a mixture was successfully demonstrated by applying an open-source independent component analysis (ICA) model. The overall method is fast, sensitive, and reliable for sensing trace THC and CBN. The SERS chip-based method and spectral results here are useful for a variety of cannabis testing applications, such as product screening and forensic investigation.

An Epigenetic Role of Mitochondria in Cancer

Mitochondria are not only the main energy supplier but are also the cell metabolic center regulating multiple key metaborates that play pivotal roles in epigenetics regulation. These metabolites include acetyl-CoA, α-ketoglutarate (α-KG), S-adenosyl methionine (SAM), NAD⁺, and O-linked beta-N-acetylglucosamine (O-GlcNAc), which are the main substrates for DNA methylation and histone post-translation modifications, essential for gene transcriptional regulation and cell fate determination. Tumorigenesis is attributed to many factors, including gene mutations and tumor microenvironment. Mitochondria and epigenetics play essential roles in tumor initiation, evolution, metastasis, and recurrence. Targeting mitochondrial metabolism and epigenetics are promising therapeutic strategies for tumor treatment. In this review, we summarize the roles of mitochondria in key metabolites required for epigenetics modification and in cell fate regulation and discuss the current strategy in cancer therapies via targeting epigenetic modifiers and related enzymes in metabolic regulation. This review is an important contribution to the understanding of the current metabolic-epigenetic-tumorigenesis concept.

Recent Advances in Inflammatory Diagnosis with Graphene Quantum Dots Enhanced SERS Detection

Inflammatory diseases are some of the most common diseases in different parts of the world. So far, most attention has been paid to the role of environmental factors in the inflammatory process. The diagnosis of inflammatory changes is an important goal for the timely diagnosis and treatment of various metastatic, autoimmune, and infectious diseases. Graphene quantum dots (GQDs) can be used for the diagnosis of inflammation due to their excellent properties, such as high biocompatibility, low toxicity, high stability, and specific surface area. Additionally, surface-enhanced Raman spectroscopy (SERS) allows the very sensitive structural detection of analytes at low concentrations by amplifying electromagnetic fields generated by the excitation of localized surface plasmons. In recent years, the use of graphene quantum dots amplified by SERS has increased for the diagnosis of inflammation. The known advantages of graphene quantum dots SERS include non-destructive analysis methods, sensitivity and specificity, and the generation of narrow spectral bands characteristic of the molecular components present, which have led to their increased application. In this article, we review recent advances in the diagnosis of inflammation using graphene quantum dots and their improved detection of SERS. In this review study, the graphene quantum dots synthesis method, bioactivation method, inflammatory biomarkers, plasma synthesis of GQDs and SERS GQD are investigated. Finally, the detection mechanisms of SERS and the detection of inflammation are presented.

A bioinspired hollow g-C3N4-CuPc heterostructure with remarkable SERS enhancement and photosynthesis-mimicking properties for theranostic applications

Surface-enhanced Raman scattering (SERS) based on chemical mechanism (CM) has great potential for superior stability and selectivity. Moreover, a bioinspired CM-Raman substrate-Raman reporter system with charge separation and electron transport nature provides thylakoid-mimicking potential for multifunctional applications. Herein, hollow carbon nitride nanospheres hierarchically assembled with a well-oriented copper(ii) phthalocyanine layer and hyaluronic acid (HCNs@CuPc@HA) were designed as a light-harvesting nanocomposite and photosynthesis-mimicking nanoscaffold that enhance both CM-SERS and photoredox catalysis. Remarkable SERS enhancement was achieved due to the strengthened short-range substrate–molecule interaction, enriched CuPc molecule loading and enhanced light–mater interactions. Meanwhile, the uniform CuPc molecule film mimics a photo-pigment to accelerate the near infrared (NIR)-oxygen generation and photodynamic catalysis of photosynthetic membrane-like HCNs. The experimental findings were further validated by numerical theory analysis. The greatly enhanced SERS signal and photosynthetic-mimicking properties of the heterostructure (denoted as HCNCHs) were successfully employed for circulating tumor cell (CTC) diagnosis and SERS imaging-guided cancer catalytic therapy in tumor xenograft models.

Thylakoid-inspired HCNs@CuPc@HA is designed as a light-harvesting nanocomposite and photosynthesis-mimicking nanoscaffold to simultaneously enhance chemical mechanism-based SERS and photosynthesis-mimicking catalysis for theranostics application.

How Surface-Enhanced Raman Spectroscopy Could Contribute to Medical Diagnoses

In the last decade, there has been a rapid increase in the number of surface-enhanced Raman scattering (SERS) spectroscopy applications in medical research. In this article we review some recent, and in our opinion, most interesting and promising applications of SERS spectroscopy in medical diagnostics, including those that permit multiplexing within the range important for clinical samples. We focus on the SERS-based detection of markers of various diseases (or those whose presence significantly increases the chance of developing a given disease), and on drug monitoring. We present selected examples of the SERS detection of particular fragments of DNA or RNA, or of bacteria, viruses, and disease-related proteins. We also describe a very promising and elegant ‘lab-on-chip’ approach used to carry out practical SERS measurements via a pad whose action is similar to that of a pregnancy test. The fundamental theoretical background of SERS spectroscopy, which should allow a better understanding of the operation of the sensors described, is also briefly outlined. We hope that this review article will be useful for researchers planning to enter this fascinating field.

Assembly of long silver nanowires into highly aligned structure to achieve uniform "Hot Spots" for Surface-enhanced Raman scattering detection

Silver nanowires (AgNWs) as a promising surface-enhanced Raman spectroscopy (SERS) substrate could be used in the analytical science due to its high sensitivity. However, it is difficult for the randomly-distributed silver nanowires to offer uniform "hot spots" to achieve the SERS signal reproducibility of small molecules detection. Herein, the evaporation-induced aggregation had been used to assemble long silver nanowires into highly aligned structure to achieve uniform "hot spots" for SERS detection. The normal glass slide with well-aligned silver nanowires could act as a high sensitivity and excellent reproducibility SERS substrate to provide a versatile platform for detecting analytes. Rhodamine 6G (R6G) is used to evaluate the sensitivity and reproducibility of these AgNWs SERS substrates. Even the low concentration of the R6G was 10^-10 mol/L, the SERS features of R6G could be still observed clearly, and the uniform distribution of enhancement factor (EF) was higher than 0.8 × 10⁴ accounting for about 75 % in the observed mapping area. Moreover, the relative standard deviation (RSD) of SERS intensity at the band of 610 cm^-1 was used to estimate the signal reproducibility, and the calculated RSD value of aligned AgNWs substrate was about 3.6%, which was much higher than that of the randomly distributed AgNWs (26.8%) because of the highly aligned structure of silver nanowires with abundant and uniform inherent "hot spots". In addition, potential SERS detection of other small molecule, e.g. melamine was also demonstrated in the micromolar range.

Surface-Enhanced Raman Spectroscopy Substrates for Food Safety and Quality Analysis

Surface-enhanced Raman spectroscopy (SERS) has been identified as a fundamental surface-sensitive technique that boosts Raman scattering by adsorbing target molecules on specific surfaces. The application of SERS highly relies on the development of smart SERS substrates, and thus the fabrication of SERS substrates has been constantly improved. Herein, we investigate the impacts of different substrates on SERS technology including plasmonic metal nanoparticles, semiconductors, and hybrid systems in quantitative food safety and quality analysis. We first discuss the fundamentals, substrate designs, and applications of SERS. We then provide a critical review of the recent progress of SERS in its usage for screening and detecting chemical and biological contaminants including fungicides, herbicides, insecticides, hazardous colorants, and biohazards in food samples to assess the analytical capabilities of this technology. Finally, we investigate the future trends and provide practical techniques that could be used to fulfill the requirements for rapid analysis of food at a low cost.

Cancer Stem Cell DNA Enabled Real-Time Genotyping with Self-Functionalized Quantum Superstructures-Overcoming the Barriers of Noninvasive cfDNA Cancer Diagnostics

Cancer diagnosis and determining its tissue of origin are crucial for clinical implementation of personalized medicine. Conventional diagnostic techniques such as imaging and tissue biopsy are unable to capture the dynamic tumor landscape. Although circulating tumor DNA (ctDNA) shows promise for diagnosis, the clinical relevance of ctDNA remains largely undetermined due to several biological and technical complexities. Here, cancer stem cell-ctDNA is used to overcome the biological complexities like the inability for molecular analysis of ctDNA and dependence on ctDNA concentration rather than the molecular profile. Ultrasensitive quantum superstructures overcome the technical complexities of trace-level detection and rapid diagnosis to detect ctDNA within its short half-life. Activation of multiple surface enhanced Raman scattering mechanisms of the quantum superstructures achieved a very high enhancement factor (1.35 × 10¹¹ ) and detection at ultralow concentration (10^-15 M) with very high reliability (RSD: 3-12%). Pilot validation with clinical plasma samples from an independent validation cohort achieved a diagnosis sensitivity of ≈95% and specificity of 83%. Quantum superstructures identified the tissue of origin with ≈75-86% sensitivity and ≈92-96% specificity. With large scale clinical validation, the technology can develop into a clinically useful liquid biopsy tool improving cancer diagnostics.

Detection and discrimination of SARS-CoV-2 spike protein-derived peptides using THz metamaterials

The development of effective assay techniques for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently received research attention due to its rapid worldwide spread and considerable risk to human health. The receptor-binding domain (RBD) of the spike (S) protein in SARS-CoV-2, a key component for viral entry that has a unique sequence compared to other structural proteins, has been considered an important diagnostic target. In this respect, low-frequency vibrational modes have the advantage of providing information about compositional and structural dependencies at the peptide level. In this study, the sensitive and selective detection of peptides derived from the RBD in SARS-CoV-2 and SARS-CoV was investigated using metamaterial-based sensing chips with a terahertz time-domain spectroscopy (THz-TDS) system. Based on their RBD sequences, two pairs of peptides with 20 residues each were prepared. The sensitivity, specificity, and reproducibility of the proposed system were examined via quantitative analysis using THz metamaterials at three resonance frequencies, and it was found that the species could be discriminated based on their sequences. The THz signals were analyzed with regard to the major amino acid components of the peptides, and the molecular distributions were also investigated based on the hydropathy and net charge of the peptides.

Semiconductor-based surface enhanced Raman scattering (SERS): from active materials to performance improvement

Surface enhanced Raman scattering (SERS) is a powerful spectral analysis technique and has exhibited remarkable application prospects in various fields. The design and fabrication of high-performance SERS substrates is key to promoting the development of SERS technology. Apart from noble metal substrates, non-metal substrates based on semiconductor materials have received increasing attention in recent years owing to their unique physical, chemical, and optical properties. However, compared with noble metal substrates, most semiconductor substrates show weak Raman enhancement ability. Therefore, exploring effective strategies to improve the SERS sensitivity is an urgent task. Numerous reviews have outlined the research progress of semiconductor SERS substrates, which mainly focused on summarizing the material category of semiconductor substrates. However, reviews that systematically summarize the strategies for improving the SERS performance of semiconductor substrates are lacking. In this review, we comprehensively discuss the research on semiconductor SERS from the aspects of mechanism, materials, and modification. Firstly, the Raman enhancement mechanism of semiconductor substrates and the SERS-active materials are discussed. Then, we summarize several effective approaches to boost the SERS performance of semiconductor substrates. In conclusion, we propose some prospects for this field.

Tracking the Evolution of Metastasis with Self-Functionalized 3D Nanoprobes

Despite recent advances in cancer treatment, metastasis is the cause of mortality in 90% of cancer cases. It has now been well-established that dissemination of cancer cells to distant sites occurs very early during tumorigenesis, resulting in the minimal effect of surgical or chemotherapeutic treatments after the detection of metastasis. The underlying reason for this challenge is mostly due to the limited understanding of molecular mechanisms of the metastasis cascade, particularly related to metastatic traits. Therefore, there is an urgent need to investigate this currently invisible evolution of metastasis. The tracking of metastasis evolution has not been addressed yet. Here, we introduce, for the first time, a synchronous approach to unveil the molecular mechanisms of the metastasis cascade. As cancer stem cells (CSCs) demonstrate cancer initiation, drug resistance, metastasis, and tumor relapse and can exist in a quasi-intermediate epithelial-mesenchymal transition state, the tumor-initiating events during a CSCs metamorphosis were monitored with single-cell sensitivity. Because of the invasive and resistive properties of the metastable intermediate CSCs, investigation of the molecular profiles of the quasi-intermediate CSCs was necessary for the detection of metastasis dissemination. For this purpose, the ultrasensitive technique of surface-enhanced Raman scattering (SERS) was adopted. Titanium-based, biocompatible three-dimensional (3D) nanoprobes that were synthesized for multiphoton ionization achieved a substantial SERS enhancement of ∼80-fold due to the oxygen vacancy-enriched composition of the nanoprobes. The 3D interconnected complex nanoarchitecture of the nanoprobes enabled us to entrap the nonadherent CSCs of three metastatic cancer cell lines (triple negative breast adenocarcinoma (MDAMB231), human Caucasian colon adenocarcinoma (COLO 205), and cervical adenocarcinoma (HeLa)─all very aggressive forms of cancer). The nanoprobes not only promoted the CSC proliferation to successfully attain the quasi-intermediate states but also monitored its reprogramming into a cancer cell state. The nanoprobes substantially amplified weak intracellular Raman signals to capture the molecular events during a CSC transformation. The detection of cancer was achieved with 100% accuracy. We experimentally demonstrated that the molecular signatures of CSC reprogramming are cancer-type specific. This observation enabled us to identify the origin of metastasis with 100% accuracy, providing more clarity on the relatively unknown quasi-intermediate states. This first demonstration of CSC-based tracking of metastasis evolution has the potential to provide an insightful perspective of tumorigenesis that could be useful in cancer diagnosis and prognosis as well as in the monitoring of therapeutic interventions.

MoS2-Based Substrates for Surface-Enhanced Raman Scattering: Fundamentals, Progress and Perspective

Surface-enhanced Raman scattering (SERS), as an important tool for interface research, occupies a place in the field of molecular detection and analysis due to its extremely high detection sensitivity and fingerprint characteristics. Substantial efforts have been put into the improvement of the enhancement factor (EF) by way of modifying SERS substrates. Recently, MoS2 has emerged as one of the most promising substrates for SERS, which is also exploited as a complementary platform on the conventional metal SERS substrates to optimize the properties. In this minireview, the fundamentals of MoS2-related SERS are first explicated. Then, the synthesis, advances and applications of MoS2-based substrates are illustrated with special emphasis on their practical applications in food safety, biomedical sensing and environmental monitoring, together with the corresponding challenges. This review is expected to arouse broad interest in nonplasmonic MoS2-related materials along with their mechanisms, and to promote the development of SERS studies.

Defect engineering in semiconductor-based SERS

Semiconductor-based surface enhanced Raman spectroscopy (SERS) platforms take advantage of the multifaceted tunability of semiconductor materials to realize specialized sensing demands in a wide range of applications. However, until quite recently, semiconductor-based SERS materials have generally exhibited low activity compared to conventional noble metal substrates, with enhancement factors (EF) typically reaching 103, confining the study of semiconductor-based SERS to purely academic settings. In recent years, defect engineering has been proposed to effectively improve the SERS activity of semiconductor materials. Defective semiconductors can now achieve noble-metal-comparable SERS enhancement and exceedingly low, nano-molar detection concentrations towards certain molecules. The reason for such success is that defect engineering effectively harnesses the complex enhancement mechanisms behind the SERS phenomenon by purposefully tailoring many physicochemical parameters of semiconductors. In this perspective, we introduce the main defect engineering approaches used in SERS-activation, and discuss in depth the electromagnetic and chemical enhancement mechanisms (EM and CM, respectively) that are influenced by these defect engineering methods. We also introduce the applications that have been reported for defective semiconductor-based SERS platforms. With this perspective we aim to meet the imperative demand for a summary on the recent developments of SERS material design based on defect engineering of semiconductors, and highlight the attractive research and application prospects for semiconductor-based SERS.

SERS-based DNA methylation profiling allows the differential diagnosis of malignant lymphadenopathy

This study highlights the potential of surface-enhanced Raman scattering (SERS) to differentiate between B-cell lymphoma (BCL), T-cell lymphoma (TCL), lymph node metastasis of melanoma (Met) and control (Ctr) samples based on the specific SERS signal of DNA extracted from lymph node tissue biopsy. Differences in the methylation profiles as well as the specific interaction of malignant and non-malignant DNA with the metal nanostructure are captured in specific variations of the band at 1005 cm^-1, attributed to 5-methylcytosine and the band at 730 cm^-1, attributed to adenine. Thus, using the area ratio of these two SERS marker bands as input for univariate classification, an area under the curve (AUC) of 0.70 was achieved in differentiating between malignant and non-malignant DNA. In addition, DNA from the BCL and TCL groups exhibited differences in the area of the SERS band at 730 cm^-1, yielding an AUC of 0.84 in differentiating between these two lymphadenopathies. Lastly, using multivariate data analysis techniques, an overall accuracy of 94.7% was achieved in the differential diagnosis between the BCL, TCL, Met and Ctr groups. These results pave the way towards the implementation of SERS as a novel tool in the clinical setting for improving the diagnosis of malignant lymphadenopathy.

Self-functional gold nanoprobes for intra-nuclear epigenomic monitoring of cancer stem-like cells

Cancer epigenomic-environment is a core center of a tumor's genetic and epigenetic configuration. Surveying epigenomic-environment of cancer stem-like cells (CSC) is vital for developing novel diagnostic methods and improving current therapies since CSCs are among the most challenging clinical hurdles. To date, there exists no technique which can successfully monitor the epigenomics of CSC. Here, we have developed unique sub-10 nm Self-functional Gold Nanoprobes (GNP) as a CSC epigenomic monitoring platform that can easily maneuver into the nucleus while not producing any conformal changes to the genomic DNA. The GNP was synthesized using physical synthesis method of pulsed laser multiphoton ionization, which enabled the shrinking of GNP to 2.69 nm which helped us achieve two critical parameters for epigenomics monitoring: efficient nuclear uptake (98%) without complex functionalization and no conformational nuclear changes. The GNP efficiently generated SERS for structural, functional, molecular epigenetics, and nuclear proteomics in preclinical models of breast and lung CSCs. To the best of knowledge, this study is first to utilize the intranuclear epigenomic signal to distinguish between CSC from different tissues with >99% accuracy and specificity. Our findings are anticipated to help advance real-time epigenomics surveillance technologies such as nucleus-targeted drug surveillance and epigenomic prognosis and diagnostics.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

Applied surface enhanced Raman Spectroscopy in plant hormones detection, annexation of advanced technologies: A review

Plant hormones are the molecules that control the vigorous development of plants and help to cope with the stress conditions efficiently due to vital and mechanized physiochemical regulations. Biologists and analytical chemists, both endorsed the extreme problems to quantify plant hormones due to their low level existence in plants and the technological support is devastatingly required to established reliable and efficient detection methods of plant hormones. Surface Enhanced Raman Spectroscopy (SERS) technology is becoming vigorously favored and can be used to accurately and specifically identify biological and chemical molecules. Subsistence molecular properties with varying excitation wavelength require the pertinent substrate to detect SERS signals from plant hormones. Three typical mechanisms of Raman signal enhancement have been discovered, electromagnetic, chemical and Tip-enhanced Raman spectroscopy (TERS). Though, complex detection samples hinder in consistent and reproducible results of SERS-based technology. However, different algorithmic models applied on preprocessed data enhanced the prediction performances of Raman spectra by many folds and decreased the fluorescence value. By incorporating SERS measurements into the microfluidic platform, further highly repeatable SERS results can be obtained. This review paper tends to study the fundamental working principles, methods, applications of SERS systems and their execution in experiments of rapid determination of plant hormones as well as several ways of integrated SERS substrates. The challenges to develop an SERS-microfluidic framework with reproducible and accurate results for plant hormone detection are discussed comprehensively and highlighted the key areas for future investigation briefly.