Label-Free Surface-Enhanced Raman Spectroscopy Detection of DNA with Single-Base Sensitivity

Novel non-invasive method for urine mapping: Deep-learning-enabled SERS spectroscopy for the rapid differential detection of kidney allograft injury

The kidney allograft has been under continuous attack from diverse injuries since the very beginning of organ procurement, leading to a gradual decline in function, chronic fibrosis, and allograft loss. It is vital to routinely and precisely monitor the risk of injuries after renal transplantation, which is difficult to achieve because the traditional laboratory tests lack sensitivity and specificity, and graft biopsies are invasive with the risk of many complications and time-consuming. Herein, a novel method for the diagnosis of graft injury is demonstrated, using deep learning-assisted surface-enhanced Raman spectroscopy (SERS) of the urine analysis. Specifically, we developed a hybrid SERS substrate composed of gold and silver with high sensitivity to the urine composition under test, eliminating the need for labels, which makes measurements easy to perform and meanwhile results in extremely abundant and complex Raman vibrational bands. Deep learning algorithms were then developed to improve the interpretation of the SERS spectral fingerprints. The deep learning model was trained with SERS signals of urine samples of recipients with different injury types including delayed graft function (DGF), calcineurin-inhibitor toxicity (CNIT), T cell-mediated rejection (TCMR), antibody-mediated rejection (AMR), and BK virus nephropathy (BKVN), which explored the features of these types and achieved the injury differentiation with an overall accuracy of 93.03%. The results highlight the potential of combining label-free SERS spectroscopy with deep learning as a method for liquid biopsy of kidney allograft injuries, which can provide great potential to diagnose and evaluate allograft injuries, and thus extend the life of kidney allografts.

Capillarity-Driven Enrichment and Hydrodynamic Trapping of Trace Nucleic Acids by Plasmonic Cavity Membrane for Rapid and Sensitive Detections

Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.

Evaluation of Ilex guayusa and Piper marginatum Extract Cytotoxicity on Human Dental Pulp Mesenchymal Stem Cells

BACKGROUND

Amelogenesis imperfecta is a hereditary disorder affecting dental enamel. Among its phenotypes, hypocalcified AI is characterized by mineral deficiency, leading to tissue wear and, consequently, dental sensitivity. Excessive fluoride intake (through drinking water, fluoride supplements, toothpaste, or by ingesting products such as pesticides or insecticides) can lead to a condition known as dental fluorosis, which manifests as stains and teeth discoloration affecting their structure. Our recent studies have shown that extracts from Colombian native plants, Ilex guayusa and Piper marginatum, deposit mineral ions such as phosphate and orthophosphate into the dental enamel structure; however, it is unknown whether these extracts produce toxic effects on the dental pulp.

OBJECTIVE

To assess cytotoxicity effects on human dental pulp stem cells (hDPSCs) exposed to extracts isolated from I. guayusa and P. marginatum and, hence, their safety for clinical use.

METHODS

Raman spectroscopy, fluorescence microscopy, and flow cytometry techniques were employed. For Raman spectroscopy, hDPSCs were seeded onto nanobiochips designed to provide surface-enhanced Raman spectroscopy (SERS effect), which enhances their Raman signal by several orders of magnitude. After eight days in culture, I. guayusa and P. marginatum extracts at different concentrations (10, 50, and 100 ppm) were added. Raman measurements were performed at 0, 12, and 24 h following extract application. Fluorescence microscopy was conducted using an OLIMPUS fv1000 microscope, a live-dead assay was performed using a kit employing a BD FACS Canto TM II flow cytometer, and data analysis was determined using a FlowJo program.

RESULTS

The Raman spectroscopy results showed spectra consistent with viable cells. These findings were corroborated using fluorescence microscopy and flow cytometry techniques, confirming high cellular viability.

CONCLUSIONS

The analyzed extracts exhibited low cytotoxicity, suggesting that they could be safely applied on enamel for remineralization purposes. The use of nanobiochips for SERS effect improved the cell viability assessment.

Surface-Enhanced Raman Spectroscopy: Current Understanding, Challenges, and Opportunities

While surface-enhanced Raman spectroscopy (SERS) has experienced substantial advancements since its discovery in the 1970s, it is an opportunity to celebrate achievements, consider ongoing endeavors, and anticipate the future trajectory of SERS. In this perspective, we encapsulate the latest breakthroughs in comprehending the electromagnetic enhancement mechanisms of SERS, and revisit CT mechanisms of semiconductors. We then summarize the strategies to improve sensitivity, selectivity, and reliability. After addressing experimental advancements, we comprehensively survey the progress on spectrum-structure correlation of SERS showcasing their important role in promoting SERS development. Finally, we anticipate forthcoming directions and opportunities, especially in deepening our insights into chemical or biological processes and establishing a clear spectrum-structure correlation.

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.

Surface-Area Enhanced Raman Spectroscopy of DNA in Porous Silica: A Quantitative and Reproducible Alternative to Plasmonic-Based SERS

Despite the success of surface-enhanced Raman spectroscopy (SERS) for detecting DNA immobilized on plasmonic metal surfaces, its quantitative response is limited by the rapid falloff of enhancement with distance from the metal surface and variations in sensitivity that depend on orientation and proximity to plasmonic "hot spots". In this work, we assess an alternative approach for enhancing detection by immobilizing DNA on the interior surfaces of porous silica particles. These substrates provide over a 1000-fold greater surface area for detection compared to a planar support. The porous silica substrate is a purely dielectric material with randomly oriented internal surfaces, where scattering is independent of proximity and orientation of oligonucleotides relative to the silica surface. We characterize the quantitative response of Raman scattering from DNA in porous silica particles with sequences used in previous SERS investigations of DNA for comparison. The results show that Raman scattering of DNA in porous silica is independent of distance of nucleotides from the silica surface, allowing detection of longer DNA strands with constant sensitivity. The surface area enhancement within particles is reproducible (<4% particle-to-particle variation) owing to the uniform internal pore structure and surface chemistry of the silica support. DNA immobilization with a bis-thiosuccinimide linker provides a Raman-active internal standard for quantitative interpretation of Raman scattering results. Despite the high (30 mM) concentrations of immobilized DNA within porous silica particles, they can be used to measure nanomolar binding affinities of target molecules to DNA by equilibrating a very small number of particles with a sufficiently large volume of low-concentration solution of target molecules.

Combinatorial Effect of Tricomponent Dual-Rim Nanoring Building Blocks: Label-Free SERS Detection of Biomolecules

Detecting weakly adsorbing molecules via label-free surface-enhanced Raman scattering (SERS) has presented a significant challenge. To address this issue, we propose a novel approach for creating tricomponent SERS substrates using dual-rim nanorings (DRNs) made of Au, Ag, and CuO, each possessing distinct functionalities. Our method involves depositing different metals on Pt nanoring skeletons to obtain each nanoring with varying surface compositions while maintaining a similar size and shape. Next, the mixture of these nanorings is transferred into a monolayer assembly with homogeneous intermixing on a solid substrate. The surface of the CuO DRNs has dangling bonds (Cu2+) that facilitate the strong adsorption of carboxylates through the formation of chelating bonds, while the combination of Au and Ag DRNs significantly enhances the SERS signal intensity through a strong coupling effect. Notably, the tricomponent assemblies enable the successful SERS-based analysis of biomolecules such as amino acids, proteins, nucleobases, and nucleotides.

Frequency shift Raman-based sensing of serum MicroRNA for ultrasensitive cervical cancer diagnosis

Cervical cancer is the most common gynaecological tumor. The development of a sensor for the ultrasensitive detection of cervical cancer is significant in guaranteeing its prognosis. Herein, we proposed a novel surface-enhanced Raman scattering (SERS) analysis platform using a frequency shifts-based sensing model for rapid and ultrasensitive microRNA (miRNA) assay. During the analysis process, miR-21 can be captured by the single-stranded DNA (ssDNA) modified on the platform which is complementary pairing with miR-21. The connection of miR-21 can lead to the variation of the molecular weight and result in the deformation extent of the Raman report molecule 6Thioguanine (6TG); thus, the peak at 1301 cm-1 due to the ring C-N stretches of 6TG shifts to lower frequency. The detection limit (LOD) of the proposed SERS analysis platform is as low as 8.32 aM. Moreover, the platform also has excellent specificity and repeatability, with the relative standard deviation (RSD) value of 6.53 %. Serum samples of cervical cancer patients and healthy subjects were analyzed via the platform and the accuracy of the detection results was verified by qRT-PCR, revealing that SERS results and qRT-PCR results have high homogeneity. Thus, the platform can serve as a potential tool for clinical diagnosis of cervical cancer.

Characterization of Parallel-Stranded DNA Duplexes by Surface-Enhanced Raman Spectroscopy and Bromide-Modified Gold Nanoparticles

The parallel double-stranded DNA (dsDNA) demonstrates potential utility in molecular biology, diagnosis, therapy, and molecular assembly. However, techniques for the characterization of parallel dsDNA are limited. Here, we demonstrate that a series of intensive characteristic Raman bands of three parallel dsDNAs, which are stabilized by reverse Hoogsteen A+·A+ base pairs or hemiprotonated C+·C, G·G minor groove edge, Hoogsteen A·A base pairs, or Hoogsteen T·A, C+·G base pairs, have been observed by surface-enhanced Raman spectroscopy (SERS) when the gold nanoparticles modified by bromine and magnesium ions (Au BMNPs) were used as substrates. The featured bands can not only accurately discriminate parallel dsDNA from antiparallel one but also identify the strand orientation within dsDNA. The proposed approach will have a significant impact on DNA analysis, especially in the detection and differentiation of various DNA conformations.

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.

Size-dependent toxicity of polystyrene microplastics on the gastrointestinal tract: Oxidative stress related-DNA damage and potential carcinogenicity

Microplastics (MPs) and nanoplastics (NPs) have been generally regarded as emerging pollutants and received worldwide attention in recent years. Water and food consumption are the primary pathways for human exposure to MPs/NPs, thus gastrointestinal tracts may be susceptible to their toxicity. Although the recent report has indicated the presence of MPs/NPs in multiple human organs, little is known about their gastric effects. Therefore, this study focused on the adverse effects of polystyrene microplastics (PS-MPs) on gastric epithelium in vivo and in vitro. Surface-enhanced Raman spectroscopy (SERS) revealed the distribution of PS-MPs was associated with their particle sizes, and predominantly concentrated in gastric tissues. Gastric barrier injury and mitochondrial damage were observed in rats after exposure to PS-MPs. Compared with the larger ones, polystyrene nanoplastics (PS-NPs) more significantly reduced the activity of antioxidant enzymes while enhancing the level of MDA, 8-OhdG and γ-H2AX. Meanwhile, PS-MPs caused upregulation of β-catenin/YAP through redox-dependent regulation of nucleoredoxin (NXN) and dishevelled (Dvl). These findings supported the size-dependent effects of PS-MPs on oxidative stress and DNA damage. Moreover, the redox-dependent activation of the β-catenin/YAP cascade suggested a novel toxic mechanism for PS-MPs and implied the potential carcinogenic effects.

Rapid detection of Pseudomonas syringae pv. actinidiae by electrochemical surface-enhanced Raman spectroscopy

Bacterial cancer caused by Pseudomonas syringae pv. actinidiae (Psa) is a major threat to kiwifruit in the world, and there is still a lack of effective control measures. The field of bacterial detection needs a fast, easy-to-use and sensitive identification platform. The current bacterial identification methods are lack of time efficiency, which brings problems to many sectors of society. Surface-enhanced Raman spectroscopy (SERS) and electrochemistry (EC) have been studied as possible candidates for bacterial detection because of their high sensitivity for the detection of biomolecules. In this work, SERS, EC and electrochemical surface-enhanced Raman spectroscopy (EC-SERS) were used for the first time to study the adsorption and EC behavior of Psa on the surface of nanostructured silver electrodes. Two different Raman spectra of a single analyte were obtained, and this dual detection was realized. Silver nanoparticles with iodide and calcium ions (Ag@ICNPs) were synthesized as SERS substrates significantly enhanced the characteristic signal peaks of Psa, and the limit of detection (LOD) is as low as 1.0 × 102 cfu/mL. Chemical imaging results show that the application of negative voltage can significantly improve the spectrum quality, showing a higher signal at -0.8 V, indicating that Psa molecules may have potential-induced reorientation on the electrode surface. Therefore, EC-SERS has the ability to greatly improve the SERS performance of bacteria in terms of peak intensity and spectral richness.

Machine learning enabled multiplex detection of periodontal pathogens by surface-enhanced Raman spectroscopy

Periodontitis is a chronic inflammation of the periodontium caused by a persistent bacterial infection, resulting in destruction of the supporting structures of teeth. Analysis of microbial composition in saliva can inform periodontal status. Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Streptococcus mutans (Sm) are among reported periodontal pathogens, and were used as model systems in this study. Our atomic force microscopic (AFM) study revealed that these pathogens are biological nanorods with dimensions of 0.6-1.1 μm in length and 500-700 nm in width. Current bacterial detection methods often involve complex preparation steps and require labeled reporting motifs. Employing surface-enhanced Raman spectroscopy (SERS), we revealed cell-type specific Raman signatures of these pathogens for label-free detection. It overcame the complexity associated with spectral overlaps among different bacterial species, relying on high signal-to-noise ratio (SNR) spectra carefully collected from pure species samples. To enable simple, rapid, and multiplexed detection, we harnessed advanced machine learning techniques to establish predictive models based on a large set of raw spectra of each bacterial species and their mixtures. Using these models, given a raw spectrum collected from a bacterial suspension, simultaneous identification of all three species in the test sample was achieved at 95.6 % accuracy. This sensing modality can be applied to multiplex detection of a broader range and a larger set of periodontal pathogens, paving the way for hassle-free detection of oral bacteria in saliva with little to no sample preparation.

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.

DNA induced CTAB-caped gold bipyramidal nanoparticles self-assembly using for Raman detection of DNA molecules

DNA is an indispensable part of metabolism, which affects many important processes in the body, including gene expression, protein synthesis, and drug delivery. Surface-enhanced Raman spectroscopy (SERS) is one of the most important methods used to study the structure and function of DNA and can obtain rich DNA molecular fingerprints. However, it is still a great challenge to use SERS to directly analyze the characteristic Raman signals of the DNA molecule and achieve rapid and simple detection. Hence, a detection platform based on gold bipyramidal nanoparticles (AuNBs) self-assembly that can be directly used for the detection of DNA molecules without the need for additional aggregators and cleaning agents was designed in this study. The original hexadecyltrimethylammonium bromide (CTAB) of AuNBs can be used as the internal standard for DNA quantification without an additional standard. This is the first time that the Raman signals of the analyte molecule can be obtained directly without labels by using the interaction between the molecule and the enhanced substrate. We used this method to capture the original DNA molecules in methylated DNA, serum, and cell metabolites and obtained spectral data processing results using linear discriminant analysis (LDA). This provides new ideas for the digitization of disease treatment and the study of the metabolic processes of life.

Rapidly determining the 3D structure of proteins by surface-enhanced Raman spectroscopy

Despite great advances in protein structure analysis, label-free and ultrasensitive methods to obtain the natural and dynamic three-dimensional (3D) structures are still urgently needed. Surface-enhanced Raman spectroscopy (SERS) can be a good candidate, whereas the complexity originated from the interactions between the protein and the gradient surface electric field makes it extremely challenging to determine the protein structure. Here, we propose a deciphering strategy for accurate determination of 3D protein structure from experimental SERS spectra in seconds by simply summing SERS spectra of isolated amino acids in electric fields of different strength with their orientations in protein. The 3D protein structure can be reconstructed by comparing the experimental spectra obtained in a well-defined gap-mode SERS configuration with the simulated spectra. The gradient electric field endows SERS with a unique advantage to section biomolecules with atomic precision, which makes SERS a competent tool for monitoring biomolecular events under physiological conditions.

Surface-enhanced Raman scattering sensing for detection and mapping of key cellular biomarkers

Cellular biomarkers mainly contain proteins, nucleic acids, glycans and many small molecules including small biomolecule metabolites, reactive oxygen species and other cellular chemical entities. The detection and mapping of the key cellular biomarkers can effectively help us to understand important cellular mechanisms associated with physiological and pathological processes, which greatly promote the development of clinical diagnosis and disease treatment. Surface-enhanced Raman scattering (SERS) possesses high sensitivity and is free from the influence of strong self-fluorescence in living systems as well as the photobleaching of the dyes. It exhibits rich and narrow chemical fingerprint spectra for multiplexed detection, and has become a powerful tool to detect and map cellular biomarkers. In this review, we present an overview of recent advances in the detection and mapping of different classes of cellular biomarkers based on SERS sensing. These advances fully confirm that the SERS-based sensors and sensing methods have great potential for the exploration of biological mechanisms and clinical applications. Additionally, we also discuss the limitations of present research and the future developments of the SERS technology in this field.

Ultralow-background SERS substrates for reliable identification of organic pollutants and degradation intermediates

Chemical methods for preparing SERS substrates have the advantages of low cost and high productivity, but the strong background signals from the substrate greatly limit their applications in characterization and identification of organic compounds. Herein, we developed a one-step synthesis method to prepare silver nanoparticle substrates with ultralow SERS background using anionic ligands as stabilizing agents and applied the SERS substrate for the reliable and reproducible identification of typical organic pollutants and corresponding degradation intermediates. The synthesis method shows excellent universality to different reducing agents cooperating with different anionic ligands (Cl-, Br-, I-, SCN-). As model applications, the machine learning algorithm can realize the precise prediction of six organophosphorus pesticides and eight sulfonamide antibiotics with 100% accuracy based on SERS training data. More importantly, the ultralow-background SERS substrate enables one to detect and identify the time-dependent degradation intermediates of organophosphorus pesticides by combining them with density functional theory (DFT) calculations. All the results indicate that the ultralow-background SERS substrate will greatly push the development of SERS characterization applications.

Deep Learning Assisted Surface-Enhanced Raman Spectroscopy (SERS) for Rapid and Direct Nucleic Acid Amplification and Detection: Toward Enhanced Molecular Diagnostics

Surface-enhanced Raman scattering (SERS) has evolved into a robust analytical technique capable of detecting a variety of biomolecules despite challenges in securing a reliable Raman signal. Conventional SERS-based nucleic acid detection relies on hybridization assays, but reproducibility and signal strength issues have hindered research on directly amplifying nucleic acids on SERS surfaces. This study introduces a deep learning assisted ZnO-Au-SERS-based direct amplification (ZADA) system for rapid, sensitive molecular diagnostics. The system employs a SERS substrate fabricated by depositing gold on uniformly grown ZnO nanorods. These nanorods create hot spots for the amplification of the target nucleic acids directly on the SERS surface, eliminating the need for postamplification hybridization and Raman reporters. The limit of detection of the ZADA system was superior to those of the conventional amplification methods. Clinical validation of the ZADA system with coronavirus disease 2019 (COVID-19) samples from human patients yielded a sensitivity and specificity of 92.31% and 81.25%, respectively. The integration of a deep learning program further enhanced sensitivity and specificity to 100% and reduced SERS analysis time, showcasing the potential of the ZADA system for rapid, label-free disease diagnosis via direct nucleic acid amplification and detection within 20 min.

Long-lived SERS Matrix for Real-Time Biochemical Detection Using "Frozen" Transition State

For the long-time tracking of biological events, maintaining the bioactivity of the analytes during the detection process is essential. Here, we show a versatile surface-enhanced Raman Scattering (SERS) platform, termed a superwettable-omniphobic lubricous porous SERS (SOLP-SERS) substrate. The SOLP-SERS substrate could generate a three-dimensional liquid "hotspots" matrix with an ultra-long lifetime (tens of days) by confining tiny amounts of liquids within the gaps between nanoparticles. Then, the analytes are trapped in the uniform liquid "hotspots", whose bioactivity can be well maintained over a long period of time during SERS detection. Limits of detection down to femtomolar levels were achieved for various molecules. More importantly, SERS signals were uniform within the substrate and remained stable for more than 30 days. As a proof-of-concept experiment, the dynamic detection of the polymerization of Aβ peptides into amyloids was monitored by the SOLP-SERS substrate within 48 h. Moreover, the exosomes secreted by breast cancer cells, an important biomarker of cancer, were also measured. These results demonstrate that the SOLP-SERS platform will provide new insights into the development of real-time biochemical sensors with ultrahigh sensitivity.

Intrinsic SERS Fingerprints of Aptamer-Peptide Conjugates for Direct High-Specific Profiling Abnormal Protein Levels in Cancer Patients

Surface-enhanced Raman spectroscopy (SERS) with ultrasensitive vibrational fingerprints enables quick identification and trace detection of various kinds of molecules. But proteins usually have low Raman cross sections and are difficult to generate recognizable signals in direct SERS detection. Recently, nucleic acid-peptide conjugates are emerging with great potential in structuring, assembling, catalyzing, sensing, etc., and the coupling of aptamers further enables superior biological recognition and programmability. Here, we develop the aptamer-peptide conjugates as a new kind of SERS probe for direct high-specific profiling abnormal protein levels in cancer patients. The aptamer conjugated with glutathione (GSH) functions as both the recognition element and the SERS reporters that can simultaneously generate SERS fingerprints of both peptides and nucleic acids. This kind of biocompatible probe appears to have excellent performance in high-salt environments and realizes rapid, simple, and multisignal detection of thrombin (TB). Data-driven soft independent modeling of class analogy (DD-SIMCA) is used to distinguish SERS profiles of actual blood samples and realize the identification and classification of cancer patients. Furthermore, the effect of low-temperature storage time on blood samples is analyzed by tracking the changes of SERS profiles; the results hint that plasma samples stored under 4 °C for more than 2 days could generate false negative results due to TB hydrolysis, which has important implications for clinical sample analysis. This kind of nucleic acid-peptide conjugate provides new ideas for SERS sensing strategy in the future.

Influence of sandwich-type DNA construction strategy and plasmonic metal on signal generated by SERS DNA sensors

The DNA biosensors are powerful tools in the gene mutation or pathogens detection. That is why there are a lot of DNA detection strategies and methods. Here we present the insight on a slightly overlooked DNA detection technique, surface-enhanced Raman scattering (SERS). The present work is a summary of the influence of the plasmonic metal of the SERS substrate and strategy of the sandwich-type biosensor construction, simply the placement of the Raman reporter and mismatches, on the SERS signal enhancement. We found that, although in general there is an increase in the intensity of the SERS signal when the distance between the Raman scatterer and the SERS-active surface decreases, for this type of DNA SERS sensor a greater intensity of the measured Raman signal is usually observed when the Raman reporter is farther away from the plasmonic substrate. This is probably caused by a significant change in the hybridisation efficiency for the different structures of the sensor analysed due to some steric hindrances.

DNA controllable peroxidase-like activity of Ti3C2 nanosheets for colorimetric detection of microcystin-LR

The peroxidase-like activity of Ti₃C₂ nanosheets (Ti₃C₂ NSs) was evaluated by catalytic oxidation of colorless o-phenylenediamine (OPD) into orange-yellow 2,3-diaminophenazine (DAP) with the aid of H₂O₂. The catalytic behavior followed the typical Michaelis-Menten kinetics. Systematic studies about the catalytic activity of Ti₃C₂ NSs including cytochrome C (Cyt C) electron transfer experiments, radical capture experiments, and fluorescence analysis were conducted, revealing that the catalytic mechanism of Ti₃C₂ NSs was attributed to nanozyme-accelerated electron transfer between substrates and nanozyme-promoted generation of active species (superoxide anion free radical (·O₂^-) and holes (h⁺)). Single-stranded DNA (ssDNA) inhibited the peroxidase-like activity of Ti₃C₂ NSs, and the reduced catalytic activity was ascribed to DNA-hindered substrate accessibility to nanozyme surface. Based on the DNA controllable peroxidase-mimicking activity of Ti₃C₂ NSs, taking microcystin-LR (MC-LR) aptamer as an example, a label-free colorimetric aptasensor was proposed for the sensitive detection of MC-LR. The colorimetric aptasensor showed a wide linear range (0.01-60 ng mL^-1), low limit of detection (6.5 pg mL^-1), and high selectivity. The practicality of the colorimetric aptasensor was demonstrated by detecting different levels of MC-LR in spiked real water samples; satisfactory recoveries (97.2-102.1%) and low relative standard deviations (1.16-3.72%) were obtained.

A visual CRISPR/dCas9-mediated enzyme-linked immunosorbent assay for nucleic acid detection with single-base specificity

Specific and economical nucleic acid detection is crucial for molecular diagnoses in resource-limited settings. Various facile readout approaches have been developed for nucleic acid detection, but they have limited specificity. Herein, nuclease-dead Cas9 (dCas9)/sgRNA was used as an excellent DNA recognition probe system to develop a visual clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9-mediated enzyme-linked immunosorbent assay (ELISA) for specific and sensitive detection of cauliflwer mosaic virus 35s (CaMV35S) promoter in genetically modified (GM) crops. In this work, the CaMV35S promoter was amplified with biotinylated primers, and then precisely bound with dCas9 in the presence of sgRNA. The formed complex was captured by antibody-coated microplate and bound to a streptavidin-labeled horseradish peroxidase probe for the visual detection. Under the optimal conditions, dCas9-ELISA could detect CaMV35s promoter as low as 12.5 copies μL^-1. Moreover, the proposed method was capable to distinguish the target sequence with single-base specificity. Coupled with one-step extraction and recombinase polymerase amplification, dCas9-ELISA can identify actual GM rice seeds within 1.5 h from sampling to results without expensive equipment and technical expertise. Therefore, the proposed method offers a specific, sensitive, rapid and cost-effective detection platform for molecular diagnoses.

Ultra-trace SERS detection of cocaine and heroin using bimetallic gold-silver nanostars (BGNS-Ag)

A rapid, in-field, and reliable method for the detection of illegal drugs of abuse in biological fluids without any sample pretreatment would potentially be helpful for law enforcement, drug control officials, and public healthcare. In this study, we presented a cost-effective and highly reproducible solution-based surface-enhanced Raman scattering (SERS) platform utilizing a portable Raman instrument for fast sensitive SERS detection of illegal drugs, such as cocaine, and heroin in human urine without any sample preprocessing. The SERS platform was constructed for the first time by combining the superior SERS enhancement properties of bimetallic silver-coated gold nanostars (BGNS-Ag) and the advantages of suitable alkaline metal salts such as NaI for SERS signal amplification. The effects of the silver thickness of BGNS-Ag and alkaline salts on the SERS performance were investigated in detail; we observed that the maximum SERS enhancement was obtained for BGNS-Ag with the maximum silver thickness (54 ± 5 nm) in presence of NaI salt. Our SERS platform shows ultra-high sensitivity of cocaine and heroin with a limit of detection (LOD) as low as 10 pg/mL for cocaine and 100 pg/mL for heroin, which was 100 times lower than that of the traditional silver nanoparticle-based illegal drug detection. As a demonstration, the platform was further applied to detect cocaine and heroin spiked in human urine without any sample preprocessing achieving a LOD of 100 pg/mL for cocaine and 1 ng/mL for heroin. Overall, our SERS detection platform shows potential for rapid, onsite, ultra-low-cost portable applications for trace detection of illegal drugs and biomarkers.

Aptamer and Peptide-Engineered Polydopamine Nanospheres for Target Delivery and Tumor Perfusion in Synergistic Chemo-Phototherapy of Pancreatic Cancer

Pancreatic cancer (PC) is the fourth leading cause of cancer death, and the 5 year survival rate is only 4%. Chemotherapy is the treatment option for the majority of PC patients diagnosed at an advanced stage, whereas the desmoplastic stroma of PC could block the perfusion of chemotherapeutic agents to tumor tissues and contribute generally to chemoresistance. Therefore, the clinical status of PC calls for an urgent exploration in the effective treatment strategy. Chemo-phototherapy is an emerging modality against malignant tumors, but owing to the low targeting ability of theranostic agents or unspecific accumulation in the tumor region, majority of chemo-phototherapy techniques have disappointing therapeutic efficiencies. Herein, we have explored CD71-specific targeting aptamers and paclitaxel (PTX)-modified polydopamine (PDA) nanospheres with the conjugation of peptidomimetic AV3 (termed Apt-PDA@PTX/AV3 bioconjugates) to specifically target and combat PC in vivo by synergistic chemo-phototherapy. After the delivery of nanotheranostic agents to the tumor microenvironment (TME) or subsequent endocytic uptake by PC cells, a simultaneous release of AV3 and PTX from Apt-PDA@PTX/AV3 bioconjugates via near-infrared (NIR) irradiation can decrease desmoplastic stroma to enhance tumor perfusion and tumor-killing effects. Meanwhile, PDA cores utilize NIR laser to create unendurable hyperthermia within TME to "cook" tumors. Taken together, the current study finally suggests that our Apt-PDA@PTX/AV3 bioconjugates could act as a novel therapeutic approach by synergistic chemo-phototherapy for the programmable inhibition of PC.

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.

Iodine-Modified Ag NPs for Highly Sensitive SERS Detection of Deltamethrin Residues on Surfaces

It is essential to estimate the indoor pesticides/insecticides exposure risk since reports show that 80% of human exposure to pesticides occurs indoors. As one of the three major contamination sources, surface collected pesticides contributed significantly to this risk. Here, a highly sensitive liquid freestanding membrane (FSM) SERS method based on iodide modified silver nanoparticles (Ag NPs) was developed for quantitative detection of insecticide deltamethrin (DM) residues in solution phase samples and on surfaces with good accuracy and high sensitivity. The DM SERS spectrum from 500 to 2500 cm-1 resembled the normal Raman counterpart of solid DM. Similar bands at 563, 1000, 1165, 1207, 1735, and 2253 cm-1 were observed as in the literature. For the quantitative analysis, the strongest peak at 1000 cm-1 that was assigned to the stretching mode of the benzene ring and the deformation mode of C-C was selected. The peak intensity at 1000 cm-1 and the concentration of DM showed excellent linearity from 39 to 5000 ppb with a regression equation I = 649.428 + 1.327 C (correlation coefficient R2 = 0.991). The limit of detection (LOD) of the DM was found to be as low as 11 ppb. Statistical comparison between the proposed and the HPLC methods for the analysis of insecticide deltamethrin (DM) residues in solution phase samples showed no significant difference. DM residue analysis on the surface was mimicked by dropping DM pesticide on the glass surface. It is found that DM exhibited high residue levels up to one week after exposure. This proposed SERS method could find application in the household pesticide residues analysis.

A direct approach toward investigating DNA-ligand interactions via surface-enhanced Raman spectroscopy combined with molecular dynamics simulations

Small molecules that interfere with DNA replication can trigger genomic instability, which makes these molecules valuable in the search for anticancer drugs. Thus, interactions between DNA and its ligands at the molecular level are of great significance. In the present study, a new method based on surface-enhanced Raman spectroscopy (SERS) combined with molecular dynamics simulations has been proposed for analyzing the interactions between DNA and its ligands. The SERS signals of DNA hairpins (ST: d(CGACCAACGTGTCGCCTGGTCG), AP1: d(CGCACAACGTGTCGCCTGTGCG)), pure argininamide, and their complexes, were obtained, and the characteristic peak sites of the DNA secondary structure and argininamide ligand-binding region were analyzed. Molecular dynamics calculations predicted that argininamide binds to the 8C and 9G bases of AP1 via hydrogen bonding. Our method successfully detected the changes of SERS fingerprint peaks of hydrogen bonds and bases between argininamide and DNA hairpin bases, and their binding sites and action modes were consistent with the predicted results of the molecular dynamics simulations. This SERS technology combined with the molecular dynamics simulation detection platform provides a general analysis tool, with the advantage of effective, rapid, and sensitive detection. This platform can obtain sufficient molecular level conformational information to provide avenues for rapid drug screening and promote progress in several fields, including targeted drug design.

Rapid and robust analysis of aristolochic acid I in Chinese medicinal herbal preparations by surface-enhanced Raman spectroscopy

The use of Chinese herbs containing aristolochic acid can induce the exchange of adenine and thymine in gene mutations and even cause liver cancer. To eliminate the harm of aristolochic acids (AAs) to humans, a rapid and robust method of AAs screening is a prerequisite. In this work, a facile and robust Surface-enhanced Raman spectroscopy (SERS) method was used for the qualitative and quantitative detection of AAs in Chinese medicinal herbal preparations based on the mandelic acid modified Ag nanoparticles SERS substrate. Qualitative and quantitative SERS detection of Aristolochic acid I (AAI) was achieved with a good linear relationship ranging from 0.2 - 120.0 μM and a limit of detection (LOD) of 0.06 μM. The proposed method demonstrates a refined strategy for sensitivity analysis of AAs with the advantages of easy operation, time-saving, high sensitivity, and molecular specificity, making it a preferred platform for the screening of AAI in regular inspections of herbal products and regulatory supervision of the supply chain.

Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis?

Pancreatic cancer (PC) is an aggressive and lethal neoplasm, ranking seventh in the world for cancer deaths, with an overall 5-year survival rate of below 10%. The knowledge about PC pathogenesis is rapidly expanding. New aspects of tumor biology, including its molecular and morphological heterogeneity, have been reported to explain the complicated “cross-talk” that occurs between the cancer cells and the tumor stroma or the nature of pancreatic ductal adenocarcinoma-associated neural remodeling. Nevertheless, currently, there are no specific and sensitive diagnosis options for PC. Vibrational spectroscopy (VS) shows a promising role in the development of early diagnosis technology. In this review, we summarize recent reports about improvements in spectroscopic methodologies, briefly explain and highlight the drawbacks of each of them, and discuss available solutions. The important aspects of spectroscopic data evaluation with multivariate analysis and a convolutional neural network methodology are depicted. We conclude by presenting a study design for systemic verification of the VS-based methods in the diagnosis of PC.

Label-Free Sensing of Biomolecular Adsorption and Desorption Dynamics by Interfacial Second Harmonic Generation

Observing interfacial molecular adsorption and desorption dynamics in a label-free manner is fundamentally important for understanding spatiotemporal transports of matter and energy across interfaces. Here, we report a label-free real-time sensing technique utilizing strong optical second harmonic generation of monolayer 2D semiconductors. BSA molecule adsorption and desorption dynamics on the surface of monolayer MoS₂ in liquid environments have been all-optically observed through time-resolved second harmonic generation (SHG) measurements. The proposed SHG detection scheme is not only interface specific but also expected to be widely applicable, which, in principle, undertakes a nanometer-scale spatial resolution across interfaces.

Highly porous gold supraparticles as surface-enhanced Raman spectroscopy (SERS) substrates for sensitive detection of environmental contaminants

Surface-enhanced Raman spectroscopy (SERS) has great potential as an analytical technique for environmental analyses. In this study, we fabricated highly porous gold (Au) supraparticles (i.e., ∼100 μm diameter agglomerates of primary nano-sized particles) and evaluated their applicability as SERS substrates for the sensitive detection of environmental contaminants. Facile supraparticle fabrication was achieved by evaporating a droplet containing an Au and polystyrene (PS) nanoparticle mixture on a superamphiphobic nanofilament substrate. Porous Au supraparticles were obtained through the removal of the PS phase by calcination at 500 °C. The porosity of the Au supraparticles was readily adjusted by varying the volumetric ratios of Au and PS nanoparticles. Six environmental contaminants (malachite green isothiocyanate, rhodamine B, benzenethiol, atrazine, adenine, and gene segment) were successfully adsorbed to the porous Au supraparticles, and their distinct SERS spectra were obtained. The observed linear dependence of the characteristic Raman peak intensity for each environmental contaminant on its aqueous concentration reveals the quantitative SERS detection capability by porous Au supraparticles. The limit of detection (LOD) for the six environmental contaminants ranged from ∼10 nM to ∼10 μM, which depends on analyte affinity to the porous Au supraparticles and analyte intrinsic Raman cross-sections. The porous Au supraparticles enabled multiplex SERS detection and maintained comparable SERS detection sensitivity in wastewater influent. Overall, we envision that the Au supraparticles can potentially serve as practical and sensitive SERS devices for environmental analysis applications.

Gold nanoparticle decorated blu-ray digital versatile disc as a highly reproducible surface-enhanced Raman scattering substrate for detection and analysis of rotavirus RNA in laboratory environment

Detection and estimation of various biomolecular samples are often required in research and clinical laboratory applications. Present work demonstrates the functioning of a surface-enhanced Raman scattering (SERS) substrate that has been obtained by drop-casting of citrate-reduced gold nanoparticles (AuNPs) of average dimension of 23 nm on a bare blu-ray digital versatile disc (BR-DVD) substrate. The performance of the proposed SERS substrate has been initially evaluated with standard Raman active samples, namely malachite green (MG) and 1,2-bis(4-pyridyl)ethylene (BPE). The designed SERS substrate yields an average enhancement factor of 3.2 × 10⁶ while maintaining reproducibility characteristics as good as 94% over the sensing region of the substrate. The usability of the designed SERS substrate has been demonstrated through the detection and analysis of purified rotavirus double-stranded RNA (dsRNA) samples in the laboratory environment condition. Rotavirus RNA concentrations as low as 10 ng/μL could be detected with the proposed sensing scheme.

A Metallic Niobium Nitride with Open Nanocavities for Surface-Enhanced Raman Spectroscopy

The construction of open hot-spot structures that facilitate the entry of analytes is crucial for surface-enhanced Raman spectroscopy. Here, metallic niobium nitride (NbN) three-dimensional (3D) hierarchical networks with open nanocavity structure are first found to exhibit a strong visible-light localized surface plasmon resonance (LSPR) effect and extraordinary surface-enhanced Raman scattering (SERS) performance. The unique nanocavity structure allows easy entry of molecules, promoting the utilization of electromagnetic hot spots. The NbN substrate has a lowest detection limit of 1.0 × 10^-12 M and a Raman enhancement factor (EF) of 1.4 × 10⁸ for contaminants. Furthermore, the NbN hierarchical networks possess outstanding environmental durability, high signal reproducibility, and detection universality. The remarkable SERS sensitivity of the NbN substrate can be attributed to the joint effect of LSPR and interfacial charge transport (CT).

Halogen ion modified Ag NPs for ultrasensitive SERS detection of nitroaromatic explosives

Trace explosive detection has become one of the hottest topics in scientific communities because homeland security is one of the top priorities for countries all around the world. In this work, Ag NPs prepared with different reducing reagents were modified with various halogen ions for the SERS detection of nitroaromatic explosives (2,4-DNT and 2,4,6-TNT). It was proposed that halogen ions probably replaced the surface adsorbates on Ag NPs, i.e., citrate ions, and gave surface access to target analytes, which in turn enhanced the SERS signal. The LOD values for TNT and 2,4-DNT were found to be only 2 femtomoles. Given its facile and the highly sensitive process, the method that we demonstrated can serve as a promising analytical technology for the ultrasensitive SERS detection of nitroaromatic explosives.

Interaction between Heavy Water and Single-Strand DNA: A SERS Study

The structure and function of biological macromolecules change due to intermolecular deuterium bond formation or deuterium substitution with environmental D₂O. In this study, surface-enhanced Raman spectroscopy (SERS) was used to detect interaction sites between D₂O and ssDNA and their action mechanisms. SERS peaks of ssDNA changed with increasing D₂O proportions, and the site of action mainly involved A and G bases, whose number strengthened the interaction between sequences and D₂O and hence the SERS peak intensities. Fixing the number of A and G bases prevented changes in their positions from significantly altering the map. We also identified the interaction between ssDNA sequences that easily formed a G-quadruplex structure and D₂O. The amplitude of the SERS peak intensity change reflected the ssDNA structural stability and number of active sites. These findings are highly significant for exploring genetic exchanges and mutations and could be used to determine the stability and structural changes of biological macromolecules.

DNA Antiadhesive Layer for Reusable Plasmonic Sensors: Nanostructure Pitch Effect

A long-term reusable sensor that provides the opportunity to easily regenerate the active surface and minimize the occurrence of undesired absorption events is an appealing solution that helps to cut down the costs and improve the device performances. Impressive advances have been made in the past years concerning the development of novel cutting-edge sensors, but the reusability can currently represent a challenge. Direct shielding of the sensor surface is not always applicable, because it can impact the device performance. This study reports an antiadhesive layer (AAL) made of 90 mg/mL DNA sodium salt from salmon testes (ssstDNA) for passivating gold plasmonic sensor surfaces. Our gold two-dimensional (2D) nanostructured plasmonic metasurfaces modified with AAL were used for DNA quantification. AAL is thin enough that the plasmonic sensor remains sensitive to subsequent deposition of DNA, which serves as an analyte. AAL protects the gold surface from unwanted nonspecific adsorption by enabling wash-off of the deposited analyte after analysis and thus recovery of the LSPR peak position (rLSPR). The calibration curve obtained on a single nanostructure (Achiral Octupolar, 100 nm pitch) gave an LOD = 105 ng/mL and an extraordinary dynamic range, performances comparable or superior to those of commercial UV-vis spectrometers for acid nucleic dosage. Two different analytes were tested: ssstDNA (∼2000 bp) in deionized water and double-strand DNA (dsDNA) of 546-1614 bp in 100 mM Tris buffer and 10 mM MgCl₂. The two nanostructures (Achiral Octupolar 25 and 100) were found to have the same sensitivity to DNA in deionized water but different sensitivity to DNA in a salt/buffer solution, opening a potential for solute discrimination. To the best of our knowledge, this is the first report on the use of AAL made of several kilobase-pairs-long dsDNA to produce a reusable plasmonic sensor. The working principle and limitations are drawn based on the LSPR and SERS study.

Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy

Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures.

ATP-Responsive Strand Displacement Coupling with DNA Origami/AuNPs Strategy for the Determination of Microcystin-LR Using Surface-Enhanced Raman Spectroscopy

The DNA origami-mediated self-assembly strategy has emerged as a powerful tool in surface-enhanced Raman spectroscopy (SERS). However, these self-assembly approaches typically do not possess high detection specificity. Herein, a novel strategy based on adenosine triphosphate (ATP)-responsive strand displacement (ARSD) coupling with DNA origami/AuNPs for SERS analysis of microcystin-LR (MC-LR) is presented. In the presence of MC-LR and ATP molecules, nucleic acid sensing structures fabricated with anti-MC-LR aptamer (T1) and ATP aptamer (T2) were triggered to release the remaining ATP. In addition, DNA origami-assisted assembly results in the formation of homogeneous plasmonic nanostructures for Raman enhancement via strong plasmonic coupling. After the binding in the gaps of functionalized DNA origami/AuNPs, the Raman shift of the ATP molecules becomes detectable, leading to increased SERS intensity in 734 cm^-1. A linear response to MC-LR was obtained in the concentration range of 1.56-50 μg·L^-1, and the limit of detection (LOD) was 0.29 μg·L^-1. Combined with the solid-phase extraction sample pretreatment for extraction and 10-fold concentration, this proposed method was successfully used to detect MC-LR type in real lake-water samples with good recoveries of 98.4-116% and relative standard deviations of 1.9-6.7%. Furthermore, for the detection of MC-LR in contaminated lake-water samples, the results of the developed method and ultrahigh-performance liquid chromatography-tandem mass spectrometry were found to be in agreement with relative errors between -12 and 2.4%. The proposed strategy provides a sensitive recognition and signal amplification platform for trace MC-LR analysis as well as innovative nucleic acid sensing structures for toxin analysis more generally.

Identification of Trace Polystyrene Nanoplastics Down to 50 nm by the Hyphenated Method of Filtration and Surface-Enhanced Raman Spectroscopy Based on Silver Nanowire Membranes

Nanoplastics are emerging pollutants that pose potential threats to the environment and organisms. However, in-depth research on nanoplastics has been hindered by the absence of feasible and reliable analytical methods, particularly for trace nanoplastics. Herein, we propose a hyphenated method involving membrane filtration and surface-enhanced Raman spectroscopy (SERS) to analyze trace nanoplastics in water. In this method, a bifunctional Ag nanowire membrane was employed to enrich nanoplastics and enhance their Raman spectra in situ, which omitted sample transfer and avoided losing smaller nanoplastics. Good retention rates (86.7% for 50 nm and approximately 95.0% for 100-1000 nm) and high sensitivity (down to 10^-7 g/L for 50-1000 nm and up to 10⁵ SERS enhancement factor) of standard polystyrene (PS) nanoplastics were achieved using the proposed method. PS nanoplastics with concentrations from 10^-1 to 10^-7 g/L and sizes ranging from 50 to 1000 nm were successfully detected by Raman mapping. Moreover, PS micro- and nanoplastics in environmental water samples collected from the seafood market were also detected at the μg/L level. Consequently, the proposed method provides more possibilities for analyzing low-concentration nanoplastics in aquatic environments with high enrichment efficiency, minimal sample loss, and high sensitivity.

Label-Free Detection of DNA Supramolecular Structure Formation by Surface-Enhanced Raman Spectroscopy

The precise self-assembly of DNA molecules can be used to create nanoprecision supramolecular materials. However, the lack of methods to characterize such supramolecular materials limits their development. Surface-enhanced Raman spectroscopy (SERS) is widely used to detect the secondary structure of simple DNA molecules, but its application in the revealing of complex DNA supramolecular information remains challenging. Herein, we proposed a modified SERS-based platform able to provide structural information on DNA supramolecular materials. The silver nanoparticle-enhanced substrate uses acetonitrile as an internal standard and modifier, and calcium ions are used as an aggregating agent to induce the formation of stable "hotspots" of silver nanoparticles, where the base planes in DNA supramolecules are perpendicular to the surface of the substrate, obtaining enhanced Raman signals of base ring in both single-stranded DNA and DNA supramolecules for the first time. The structure of DNA supramolecules was efficiently characterized using this technique, showing the great application potential of this technique in the structural analysis of nucleic acids and their ligands.

Recent advances in the application of Raman spectroscopy for fish quality and safety analysis

Fish is one of the highly demanded aquatic products, and its quality and safety play a pivotal role in daily diet. However, the possible hazardous substance in perishable fish both in pre- and postharvest periods may decrease their values and pose a threat to public health. Laborious and expensive traditional methods drive the need of developing effective tools for detecting fish quality and safety properties in a rapid, nondestructive, and effective manner. Recent advances in Raman spectroscopy (RS) and surface-enhanced Raman scattering (SERS) have shown enormous potential in various aspects, which largely boost their applications in fish quality and safety evaluation. They have incomparable merits such as providing molecule fingerprint information and allowing for rapid, sensitive, and noninvasive detection with simple sample preparation. This review provides a comprehensive overview focusing on the applications of RS and SERS for fish quality assessment and safety inspection, highlighting the hazardous substance and illegal behavior both in preharvest (veterinary drug residues and environmental pollutants) and postharvest (freshness and illegal behavior) particularly. Moreover, challenges and prospects are also proposed to facilitate the vigorous development of RS and SERS. This review is aimed to emphasize potential opportunities for applying RS and SERS as promising techniques for routine food quality and safety detection. PRACTICAL APPLICATION: With these applications, it can be clearly indicated that RS and SERS are promising and powerful in fish quality and safety surveillance, thereby reducing the occurrence of commercial fraud and food safety issues. More efforts still should be concentrated on exploiting the high-performance Raman instruments, establishing a universal Raman database, developing reproducible SERS substrates and combing RS with other versatile spectral techniques to promote these technologies from laboratory to practice. It is hoped that this review should arouse more research interests in RS and SERS technologies for fish quality and safety surveillance, as well as provide more insights to make a breakthrough.

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

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

Thermoplasmonic Regulation of the Mitochondrial Metabolic State for Promoting Directed Differentiation of Dental Pulp Stem Cells

Regulating stem cell differentiation in a controllable way is significant for regeneration of tissues. Herein, we report a simple and highly efficient method for accelerating the stem cell differentiation of dental pulp stem cells (DPSCs) based on the synergy of the electromagnetic field and the photothermal (thermoplasmonic) effect of plasmonic nanoparticles. By simple laser irradiation at 50 mW/cm² (10 min per day, totally for 5 days), the thermoplasmonic effect of Au nanoparticles (AuNPs) can effectively regulate mitochondrial metabolism to induce the increase of mitochondrial membrane potential and further drive energy increase during the DPSC differentiation process. The proposed method can specifically regulate DPSCs' cell differentiation toward odontoblasts, with the differentiation time reduced to only 5 days. Simultaneously, the molecular profiling change of mitochondria within DPSCs during the cell differentiation process is revealed by in situ surface-enhanced Raman spectroscopy. It clearly demonstrates that the expression of hydroxyproline and glutamate gradually increases with prolonging of the differentiation days. The developed method is simple, robust, and rapid for stem cell differentiation of DPSCs, which would be beneficial to tissue engineering and regenerative medicine.