Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection

Target-induced nanoparticle assemblies: a comprehensive review of strategies for nucleic acid functionalization, biosensing, and drug delivery applications

Fundamental studies on nanoparticle superstructures or core-satellite assemblies and their interactions with biomolecules have led to advancements in nanobiotechnology. Consequently, some novel nucleic acid (NA) biosensing, diagnostics, and imaging approaches have been developed by functionalizing the surface of nanoparticles with target-specific analytes. For functionalization, multivalent nanoparticles are chosen over monovalent ones because they can enhance the concentration of probes on the nanoparticle surface and simultaneously bind to multiple target sites, leading to specific and sensitive detection, primarily in the case of target NAs with low-abundance target. Selection of appropriate satellite (shell) and core nanoparticles is crucial for building assemblies that can improve the resistance of DNA against serum degradation and nuclease activity by several folds compared with those of un-assembled particles. Structural modification of NPs via covalent ligation with DNA or miRNA using synthetic click chemistry approaches resulted in the formation of dimers/tetramers, which could ease the delivery of DNA-intercalating drugs and simultaneously sense target biomarkers in the cellular environment, showing the synergistic applications of multivalent assemblies. This review provides an overview of the design strategies and chemistries involved in the loading of nucleic acid probes onto the NP surface, synthesis of PEG ligands, and purification and characterization techniques for assemblies (dimer, trimer, and multimer). In addition, the applications of NP assemblies in biosensing miRNA, strategies and challenges involved in the intracellular detection of miRNA, colorimetric, SERS, and electrochemical techniques for bacterial/virus detection, and drug delivery applications are discussed. Finally, the advantages, challenges, and future perspectives in commercializing this technology are comprehensively elucidated.

Targeted molecular rapid SERS diagnosis in clinical human serum through aptamer origami-collapsed nanofingers chip

Surface-Enhanced Raman Scattering (SERS) offers great potential for label-free molecular diagnosis, especially in detecting disease biomarkers. However, the complexity of the biological environment in clinical human serum often significantly impairs detection accuracy. In this study, we present a highly effective SERS strategy utilizing aptamer origami-collapsed nanofingers for the precise qualitative and quantitative detection of specific targeted biomarkers in clinical serum. Here, the biomarker-specific aptamers are anchored to gold nanofingers, which then collapse during liquid evaporation, forming sub-nanometric gaps that enhance near-field strength. The serum is introduced directly into these stabilized nanofingers, where targeted biomarkers are selectively captured in aptamer hotspots, yielding pure Raman spectra of the biomarkers without interference from other serum molecules. The ratio of the biomarker's characteristic Raman peak to that of the aptamer allows for accurate quantification. This approach was validated with alpha-fetoprotein (AFP) for hepatocellular carcinoma and cardiac troponin I (cTnI) for acute myocardial infarction in clinical serum, achieving detection within 3 min. This strategy represents a significant advancement in SERS-based medical diagnostics, offering exceptional sensitivity and specificity in complex biological samples.

Surface Enhanced Raman Scattering for Biomolecular Sensing in Human Healthcare Monitoring

Since the 1980s, surface enhanced Raman scattering (SERS) has been used for the rapid and sensitive detection of biomolecules. Whether a label-free or labeled assay is adopted, SERS has demonstrated low limits of detection in a variety of biological matrices. However, SERS analysis has been confined to the laboratory due to several reasons such as reproducibility and scalability, both of which have been discussed at length in the literature. Another possible issue with the lack of widespread adoption of SERS is that its application in point of use (POU) testing is only now being fully explored due to the advent of portable Raman spectrometers. Researchers are now investigating how SERS can be used as the output on several POU platforms such as lateral flow assays, wearable sensors, and in volatile organic compound (VOC) detection for human healthcare monitoring, with favorable results that rival the gold standard approaches. Another obstacle that SERS faces is the interpretation of the wealth of information obtained from the platform. To combat this, machine learning is being explored and has been shown to provide quick and accurate analysis of the generated data, leading to sensitive detection and discrimination of many clinically relevant biomolecules. This review will discuss the advancements of SERS combined with POU testing and the strength that machine learning can bring to the analysis to produce a powerful combined platform for human healthcare monitoring.

A label-free colorimetric assay for sensitive screening of T4 polynucleotide kinase activity and inhibition based on enzyme-aided cyclic strand displacement amplification and PNA-gold nanoparticle platform

The phosphorylation of nucleic acids mediated by 5'-polynucleotide kinase (PNK) exerts a crucial regulatory function in a wide range of significant cellular activities. Nevertheless, the current approaches for detecting PNK require expensive labeled probes and complex instrumentation, making it impossible to achieve real-time, on-site, and rapid analysis. Here, we take T4 PNK as a model and establish a novel colorimetric strategy for the detection of PNK activity and its inhibition by means of a coupled enzyme-assisted cyclic strand displacement amplification (SDA) and peptide nucleic acid (PNA)-gold nanoparticle (AuNP) based platform. The inspiration for this innovative strategy comes from the high stability, strong binding ability, and potent regulatory effect of PNA probes on AuNPs. Under the catalysis of PNK, the 5'-hydroxyl end of the hairpin-shaped DNA (hpDNA) is initially phosphorylated and subsequently digested by λ exonuclease (λ exo). This results in the release of a single-stranded DNA, which serves as a triggering factor to initiate the strand displacement reaction (SDR). The replaced PNA probe adheres to the surface of AuNPs, inducing their aggregation and causing a remarkable color change. Meanwhile, the double-stranded SDR product releases the SDR trigger with the aid of a nicking enzyme, triggering the next round of the SDR cycle and achieving highly efficient and controllable signal amplification. This assay is simple to operate and does not require bulky and expensive instruments or complex labeled probes. Compared with existing colorimetric methods, the detection sensitivity has been greatly improved, reaching 3.52 × 10-4 U/mL. Additionally, the method has demonstrated satisfactory results when applied to intricate biological matrices and the screening of T4 PNK inhibitors. Therefore, the proposed strategy holds significant potential for real-time analysis, high-throughput detection, and PNK-related drug screening.

Digital microfluidics with integrated Raman sensor for high-sensitivity in-situ bioanalysis

This study introduces an advanced bioanalytical platform that combines digital microfluidics (DMF) with Raman spectroscopy, effectively addressing common issues in bioanalysis such as sample contamination, excessive consumption of samples and reagents, and manual handling. Our innovative system is engineered to handle diverse sample types and enables both sample preparation and in-situ analysis on a single device, utilizing less than 5 μL of samples and reagents. It incorporates a Translucent Raman Enhancement Stack (TRES) sensor, which boosts the detection signal, and includes droplet-driving functionality for automated processing of complex samples in a compact setting. The hydrophilic surface of the TRES sensor draws analytes into the detection zone, expediting sample attachment and enhancing the surface-enhanced Raman scattering (SERS). Moreover, the TRES sensors are cost-effective, straightforward to manufacture, and scalable, making them suitable for widespread production and single-use bioanalytical applications. This integrated and automated approach streamlines the sample preparation and analysis processes, enhances detection efficiency, and achieves high sensitivity, excellent linearity, and effective detection of different biochemical analytes. We validate the system's accuracy through on-device enrichment and analysis of exosomes from serum, demonstrating its capability for real-time, on-site analysis of complex biological samples.

Anisotropically Shaped Plasmonic WO3-x Nanostructure-Driven Ultrasensitive SERS Detection and Machine Learning-Based Differentiation of Nitro-Explosives

Discovery of new surface-enhanced Raman spectroscopy (SERS) substrates consisting of inexpensive and earth-abundant elements is an unmet need for the advancement of future analysis techniques for the ultrasensitive detection and quantification of chemical and biological analytes. Nanostructures (NSs) of noble metals such as Au, Ag, and Cu are the benchmarks for the preparation of highly efficient SERS substrates because of their unique localized surface plasmon resonance (LSPR) properties. Non-noble-metal SERS substrates, e.g., metal chalcogenide semiconductors and transition metal oxides, have been prepared to mitigate the cost; however, their low sensitivity restricts widespread applications. In this article, we report for the first time that the structure of oxygen-deficient, LSPR-active, nonstoichiometric tungsten oxide (i.e., WO3-x) NSs can control the SERS enhancement factor (EF). SERS substrates prepared with colloidally synthesized WO3-x nanowires, nanorods, and nanoplatelets display SERS EF of 2.5 × 106, 3.1 × 107, and 5.5 × 107, respectively, using rhodamine 6G (R6G) molecules as Raman probes. Our experimentally acquired SERS data and spectroscopically determined electronic band structure of LSPR-active WO3-x NSs, and time-domain density functional theory (TDDFT)-based calculations support a dual enhancement scheme involving a strong plasmonic effect controlled electromagnetic field and their oxygen vacancy-induced chemical enhancement mechanisms, respectively. To demonstrate the practical utility of our WO3-x NCs, we are able to detect aromatic nitro-explosives (tetryl, TNT, and DNT) with a very low limit of detection (LOD, 10-9 M). Importantly, machine learning-driven chemometric analysis for SERS-based detection shows excellent classification between these three explosives. Finally, three nonaromatic, nitro-explosives, HMX, RDX, and PETN are also successfully detected utilizing our LSPR-active, WO3-x-based SERS substrates. To the best of our knowledge, this is the first example where LSPR-active, non-noble-metal NSs are used for the detection of both aromatic and aliphatic nitro-explosives. Taken together, our work represents the advancement of the fabrication of non-noble-metal-based SERS substrates, which can be widely employed for the low-cost detection of analytes across forensic science, chemistry, and biomedical fields.

Highly Sensitive and Interference-Free Detection of Multiple Drug Molecules in Serum Using Dual-Modified SERS Substrates Combined with AI Algorithm Analysis

Surface-enhanced Raman spectroscopy (SERS) technology has shown broad potential in drug concentration detection, but its application in blood drug monitoring faces significant challenges. The primary difficulty lies in overcoming the interference caused by various biomolecules present in serum, which can severely obscure the SERS signals of target drug molecules. Traditional enhancement substrates are often limited to detecting single drugs and are prone to interference, making the label-free detection of multiple drugs particularly challenging. To address these issues, we developed a novel SERS substrate based on Au@AgNRs, which undergoes a two-step modification to produce Au@AgDBCNRs. This innovative substrate provides exceptional signal amplification, simultaneously allowing the sensitive detection of multiple drug molecules. Moreover, our method eliminates the need for serum deproteinization, enabling the direct detection of drugs in serum while effectively mitigating interference from blood components. The cetyltrimethylammonium bromide coating on Au@AgDBCNRs is an internal standard for drug quantification without additional standards. The platform significantly improves detection accuracy and efficiency by automatically integrating artificial intelligence to recognize and analyze Raman spectral features. This novel SERS platform provides a new idea for therapeutic drug monitoring and is expected to provide rapid, accurate, and cost-effective drug detection in the clinical environment, which has great potential in improving patient care and optimizing drug dosage strategies.

Digital SERS immunoassay of Interleukin-6 based on Au@Ag-Au nanotags

Interleukin-6 (IL-6) is a crucial cytokine involved in inflammation and immune regulation. However, the detection of IL-6 with ultrasensitivity and high specificity remains a significant challenge due to the inherent complexity of biofluids. Herein, we present a digital surface enhanced Raman scattering (SERS) immunoassay using core-shell Au@Ag-Au nanotags for IL-6 detection with ultrasensitivity and high reliability. A low-cost silicon chip was functionalized as capture substrates, employing novel SERS nanotags that exhibit strong, robust and reproducible signals at single-nanoparticle resolution as the amplification element. We proposed two analytical methods to validate single-molecule events follow a Poisson distribution and to quantify protein biomarkers over a broad linear dynamic range, respectively. The strong alignment between theoretical and experimental results enhances the method's reliability. Our assay provides two readouts: colorimetric analysis by naked eyes for high concentrations (>1 ng/mL) and digital SERS analysis for low concentrations. Following method optimization, we obtained a linear range from 100 fg/mL to 1 ng/mL (R2 = 0.994) with a limit of detection (LOD) of 12.4 fg/mL, suitable for clinical applications. The method was tested for IL-6 quantification in healthy human serum and saliva, with recoveries from 92.4% to 105.3%. Finally, the immunoassay demonstrated strong consistency with the standard clinical laboratory method when tested with clinical serum samples. Thus, our proposed the digital SERS immunoassay is a promising tool for the precision clinical diagnosis of IL-6-related diseases or other conditions.

Surface-enhanced Raman spectroscopy: a half-century historical perspective

Surface-enhanced Raman spectroscopy (SERS) has evolved significantly over fifty years into a powerful analytical technique. This review aims to achieve five main goals. (1) Providing a comprehensive history of SERS's discovery, its experimental and theoretical foundations, its connections to advances in nanoscience and plasmonics, and highlighting collective contributions of key pioneers. (2) Classifying four pivotal phases from the view of innovative methodologies in the fifty-year progression: initial development (mid-1970s to mid-1980s), downturn (mid-1980s to mid-1990s), nano-driven transformation (mid-1990s to mid-2010s), and recent boom (mid-2010s onwards). (3) Illuminating the entire journey and framework of SERS and its family members such as tip-enhanced Raman spectroscopy (TERS) and shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) and highlighting the trajectory. (4) Emphasizing the importance of innovative methods to overcome developmental bottlenecks, thereby expanding the material, morphology, and molecule generalities to leverage SERS as a versatile technique for broad applications. (5) Extracting the invaluable spirit of groundbreaking discovery and perseverant innovations from the pioneers and trailblazers. These key inspirations include proactively embracing and leveraging emerging scientific technologies, fostering interdisciplinary cooperation to transform the impossible into reality, and persistently searching to break bottlenecks even during low-tide periods, as luck is what happens when preparation meets opportunity.

Hierarchical structures of surface-accessible plasmonic gold and silver nanoparticles for SERS detection

Surface-enhanced Raman spectroscopy (SERS) is a highly sensitive analytical technique with excellent molecular specificity. However, separate pristine nanoparticles produce relatively weak Raman signals. It is necessary to focus on increasing the "hot-spot" density generated at the nanogaps between the adjacent nanoparticles (second-generation SERS hotspot), thus significantly boosting the Raman signal by creating an electromagnetic field. This study employed a self-assembly method without using modifiers based on promoter-induced self-assembly to synthesize stable and plasmonically active surfaces from citrate-reduced Ag and Au nanoparticles. Hierarchical structures like Pickering emulsions (PEs) and stable plasmonic aggregates (SPAs) were studied, focusing on controlling their sizes using "promoters" (TBANO3). The sizes of the SPAs were also adjusted from 85.5 nm to 136 nm by regulating the ratio of the water to the oil phase. Furthermore, to understand the distribution of "hot-spots" on these Au or Ag hierarchical structures, the electric field was simulated using the finite difference time domain (FDTD) software. Third-generation hotspots were also created using hybrid structures of plasmonic nanomaterials and surfaces to significantly improve SERS detection by depositing the colloidosome structure on Cu foil (AgSPAs/Cu substrate). The SERS signal was amplified by achieving an enhancement factor of 7 × 107, compared to an enhancement factor of 2 × 106 when using the AgSPA/glass substrate. Significantly, the limits of detection (LOD) and quantification (LOQ) for the colloidosome substrate to detect crystal violet were found to be 4.51 ppb and 13.66 ppb, respectively. The reproducibility of the prepared substrates was demonstrated to be commendably high, characterized by relative standard deviations (RSDs) of 8.00% for the 1177 cm-1 peak, 7.61% for the 1588 cm-1 peak, and 9.35% for the 1619 cm-1 peak. The AgSPAs/Cu substrate's demonstrated reliability made it suitable for detecting and quantifying analytes, potentially for determining trace amounts of pesticide residues. The LOD and LOQ for thiram detection were calculated to be 0.1 ppm and 0.3 ppm, respectively. These findings highlight the effectiveness of increasing electromagnetic field density for SERS enhancement.

Optimal size and PEG coating of gold nanoparticles for prolonged blood circulation: a statistical analysis of published data

This study presents a statistical analysis of how gold nanoparticle (GNP) size and polyethylene glycol (PEG) coating molecular weight (MW) affect the circulation of nanoparticles in blood. We showed a non-linear relationship with interaction between GNP size and PEG MW. The findings revealed a threshold effect, and recommendations for GNP coating are discussed.

Advances, Challenges, and Opportunities in Plasmonic Nanogap-Enhanced Raman Scattering with Nanoparticles

Surface-enhanced Raman scattering has been widely used for molecular/material characterization and chemical and biological sensing and imaging applications. In particular, plasmonic nanogap-enhanced Raman scattering (NERS) is based on the highly localized electric field formed within the nanogap between closely spaced metallic surfaces to more strongly amplify Raman signals than the cases with molecules on metal surfaces. Nanoparticle-based NERS offers extraordinarily strong Raman signals and a plethora of opportunities in sensing, imaging and many different types of biomedical applications. Despite its potential, several challenges still remain for NERS to be widely useful in real-world applications. This Perspective introduces various plasmonic nanogap configurations with nanoparticles, discusses key advances and critical challenges while addressing possible misunderstandings in this field, and provides future directions for NERS to generate stronger, more uniform, and stable signals over a large number of structures for practical applications.

Exploring the charge transfer enhancement mechanism in selective SERS detection with Mo1-xWxS2@Ag2S nanosheets

In order to solve the problem of poor sensitivity and selectivity of conventional SERS substrates, we synthesized Mo1-xWxS2@Ag2S nanosheets in this paper by a two-step hydrothermal method. The structure and morphology of the synthesized Mo1-xWxS2@Ag2S nanosheets were characterized by XRD and SEM,respectively. The results show that the Mo1-xWxS2@Ag2S nanosheet has an irregular layered structure. Further, the SERS properties of Mo1-xWxS2@Ag2S nanosheets were tested by using rhodamine 6G (R6G), crystalline violet (CV), and 4-mercaptobenzoic acid (4-MBA) as probe molecules, respectively. The test results demonstrated that the nanosheets were specific to R6G and CV probe molecules, and the mechanism of selectivity was due to CT enhancement. In addition, Mo1-xWxS2@Ag2S exhibits ultrahigh sensitivity in R6G and CV, with the corresponding detection limit of both reached 10-8 M. And linear fitting of the peak intensities was carried out, with the R2 coefficient of 0.981 and 0.951, respectively. Finally, the relative standard deviations (RSDs) of this Mo1-xWxS2@Ag2S nanosheets was obtained to be 8.56 % by test 1 × 10-4 M R6G at the characteristic peak 613 cm-1, which represents excellent detection repeatability. The Mo1-xWxS2@Ag2S nanosheets are rich in edge-active sites favorable for charge transfer, which can enhance the SERS signals of the target molecules better. Besides, the Raman detection of the surface of Mo1-xWxS2@Ag2S nanosheets using nitrofurantoin (NFT) also reached a detection limit of 10-8 M. Mo1-xWxS2@Ag2S nanosheets substrates can find applications in medicine and provide new strategies for improving the SERS performance.

Surface-enhanced Raman scattering for HSP 70A mRNA detection in live cells using silica nanoparticles and DNA-modified gold nanoparticles

Real-time monitoring of mRNA in living cells is crucial for understanding dynamic biological processes. Traditional methods such as northern blotting, PCR, and sequencing require cell lysis and do not allow for continuous observation. Fluorescence-based techniques have advanced this field, but they are limited by photobleaching, which hinders long-term monitoring. In this study, we designed a dual-probe system combining fluorescence and surface-enhanced Raman scattering (SERS) signals to monitor mRNA in living cells. Our system uses silica nanoparticles (SiNPs) with DNA sequences which are hybridized with fluorescent DNA sequences and DNA-modified gold nanoparticles (AuNPs) to detect heat shock protein 70A mRNA, which can be induced by photothermal damage from laser exposure. Following nanoparticle uptake and induction of heat shock, we observed a time-dependent decrease in fluorescence intensity and increase in SERS intensity, indicating successful mRNA monitoring in living cells. These findings suggest that our dual-probe system with SiNPs and AuNPs is a promising nanotechnological platform for sensitive, long-term monitoring of gene expression in living cells, offering significant potential for future biological and medical research.

Plasmonic nanoparticle sensors: current progress, challenges, and future prospects

Plasmonic nanoparticles (NPs) have played a significant role in the evolution of modern nanoscience and nanotechnology in terms of colloidal synthesis, general understanding of nanocrystal growth mechanisms, and their impact in a wide range of applications. They exhibit strong visible colors due to localized surface plasmon resonance (LSPR) that depends on their size, shape, composition, and the surrounding dielectric environment. Under resonant excitation, the LSPR of plasmonic NPs leads to a strong field enhancement near their surfaces and thus enhances various light-matter interactions. These unique optical properties of plasmonic NPs have been used to design chemical and biological sensors. Over the last few decades, colloidal plasmonic NPs have been greatly exploited in sensing applications through LSPR shifts (colorimetry), surface-enhanced Raman scattering, surface-enhanced fluorescence, and chiroptical activity. Although colloidal plasmonic NPs have emerged at the forefront of nanobiosensors, there are still several important challenges to be addressed for the realization of plasmonic NP-based sensor kits for routine use in daily life. In this comprehensive review, researchers of different disciplines (colloidal and analytical chemistry, biology, physics, and medicine) have joined together to summarize the past, present, and future of plasmonic NP-based sensors in terms of different sensing platforms, understanding of the sensing mechanisms, different chemical and biological analytes, and the expected future technologies. This review is expected to guide the researchers currently working in this field and inspire future generations of scientists to join this compelling research field and its branches.

Defect-Engineered Coordination Compound Nanoparticles Based on Prussian Blue Analogues for Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for label-free chemical analysis. The emergence of nonmetallic materials as SERS substrates, offering chemical signal enhancements, presents an exciting direction for achieving reproducible and biocompatible SERS, a challenge with traditional metallic substrates. Despite the potential, the realm of nonmetallic SERS substrates, particularly nanoparticles, remains largely untapped. Here, we present defect-engineered coordination compounds (DECCs) based on Prussian blue analogues (PBAs) as a class of nonmetallic nanoparticle-based SERS substrates. We demonstrate the utility and flexibility of the DECC template by incorporating various metal (M) elements into PBAs to synthesize nanoparticles that deliver substantial chemical mechanism (CM)-based enhancements to the Raman signal with a ∼ 108-fold increase. The introduction of the M-PBA-based DECC nanoparticles as a class of SERS substrates represents a pioneering stride, enabling the straightforward and systematic exploration of a library of compounds for SERS-based analysis of a wide range of target molecules, especially biomolecules.

Direct Zeptomole Detection of RNA Biomarkers by Ultrabright Fluorescent Nanoparticles on Magnetic Beads

Nucleic acids are important biomarkers in cancer and viral diseases. However, their ultralow concentration in biological/clinical samples makes direct target detection challenging, because it leads to slow hybridization kinetics with the probe and its insufficient signal-to-noise ratio. Therefore, RNA target detection is done by molecular (target) amplification, notably by RT-PCR, which is a tedious multistep method that includes nucleic acid extraction and reverse transcription. Here, a direct method based on ultrabright dye-loaded polymeric nanoparticles in a sandwich-like hybridization assay with magnetic beads is reported. The ultrabright DNA-functionalized nanoparticle, equivalent to ≈10 000 strongly emissive rhodamine dyes, is hybridized with the magnetic bead to the RNA target, providing the signal amplification for the detection. This concept (magneto-fluorescent sandwich) enables high-throughput detection of DNA and RNA sequences of varied lengths from 48 to 1362 nt with the limit of detection down to 0.3 fm using a plate reader (15 zeptomoles), among the best reported for optical sandwich assays. Moreover, it allows semi-quantitative detection of SARS-CoV-2 viral RNA directly in clinical samples without a dedicated RNA extraction step. The developed technology, combining ultrabright nanoparticles with magnetic beads, addresses fundamental challenges in RNA detection; it is expected to accelerate molecular diagnostics of diseases.

Ecofriendly Filtration of Silver Nanoparticles for Ultrasensitive Surface-Enhanced (Resonance) Raman Spectroscopy-Based Detection

In this study, a widely used colloid of Creighton AgNPs (ORI, 1-100 nm, mostly ≤ 40 nm, ∼10 μg mL-1) was rapidly manipulated via tangential flow filtration (TFF) for highly reproducible surface-enhanced (resonance) Raman spectroscopy (SE(R)RS) experiments down to the single-molecule (SM) level. The quasi-spherical AgNPs were size-selected, purified, and concentrated in two TFF fractions of a cutoff diameter of ∼40 nm: AgNP ≤ 40 (∼900 μg mL-1) and AgNP ≥ 40 (∼100 μg mL-1). The SE(R)S-based sensing capabilities of the two TFF fractions were then tested under pre-resonance (632.8 nm) and resonance (532.1 nm) excitation conditions for rhodamine 6G (R6G, 10-6-10-15 M). Both TFF isolates, AgNP ≤ 40 and AgNP ≥ 40, were more effective in adsorbing the R6G analyte (≥91%) than the original colloid (≥78%) at submonolayer coverages. Furthermore, the surface enhancement factors (SEF) of the two TFF fractions were markedly superior to those of ORI under all excitation conditions. SERS at 632.8 nm: only AgNP ≥ 40 enabled the detection of R6G at 10-9 M and produced the largest SEF (2.1 × 106). SE(R)RS and SM-SERRS at 532.1 nm: AgNP ≥ 40 gave rise to the largest SEF values (2.5 × 1010) corresponding to the SM regime down to 10-15 M of R6G. Nevertheless, AgNP ≤ 40 compensated for the size-dependence of the electromagnetic enhancements by an increase in the silver concentration, which led to SEF values comparable to those of AgNP ≥ 40 through additional resonance enhancements. TFF resulted into a ∼100-fold increase (AgNP ≤ 40) in the number of negatively charged AgNPs that were available to electrostatically bridge R6G cations and form SERRS "hot-spots" (AgNP-R6G-AgNP) within the focal volume. Evidently, the interplay between AgNP size, AgNP concentration, and excitation wavelength governs the SE(R)RS enhancements. This study demonstrated that TFF can facilitate the ecofriendly isolation of spherical AgNPs of controlled morphological and plasmonic properties for further enhancing their sensing capabilities as SE(R)RS substrates.

Plasmonic Nanotrenches with 1 nm Nanogaps for Surface-Enhanced Raman Scattering-Based Screening of His-Tagged Proteins

This study represents a highly sensitive and selective approach to protein screening using surface-enhanced Raman scattering (SERS) facilitated by octahedral Au nanotrenches (OANTs). OANTs are a novel class of nanoparticles characterized by narrow, trench-like excavations indented into the eight facets of a Au octahedron. This unique configuration maximizes electromagnetic near-field focusing as the gap distance decreases to ∼1 nm. Owing to geometrical characteristics of the OANTs, near-field focusing can be maximized through the confinement and reflectance of light trapped within the trenches. We used Ni ions and molecular linkers to confer selective binding affinity for His-tagged proteins on the surfaces of the OANTs for SERS-based protein screening. Remarkably, SERS-based protein screening with the surface-modified OANTs yielded outstanding screening capabilities: 100% sensitivity and 100% selectivity in distinguishing His-tagged human serum albumin (HSA) from native HSA. This highlights the significantly enhanced protein screening capabilities achieved through the synergistic combination of SERS and the OANTs.

Efficient and accurate detection of GC-associated miR-96-5p using a competitive lateral flow method based on SERS

To facilitate rapid, efficient, and accurate detection of miR-96-5p associated with gastric cancer (GC), we developed a bioanalytical platform by integrating surface-enhanced Raman spectroscopy with lateral flow assay (SERS-LFA). With these SERS-LFA strips, miR-96-5p within the specimen competed with Au rhombic dodecahedron (AuRD) conjugated single-stranded DNA (ssDNA) to bond to the immobilized hairpin DNA (hpDNA) probe on the T line. Consequently, higher abundance of miR-96-5p led to reduced conjugation of AuRD on the T line, thereby resulting in diminished SERS intensity. The biosensor exhibited a detection time of approximately 30 min and demonstrated a low limit of detection (LOD) for miR-96-5p in PBS buffer solution, down to 3.7 fM. To validate its clinical utility for the early diagnosis of patients with different degrees of gastric lesions, we performed quantitative evaluations in cohorts that included healthy individuals, patients with mild intraepithelial neoplasia, patients with severe intraepithelial neoplasia, as well as patients diagnosed with GC. The results obtained from the SERS-LFA strips were in agreement with those obtained from the quantitative real-time polymerase chain reaction (qRT-PCR). Given the accomplishments, this biosensor has significant potential for the clinical diagnosis of GC, offering a promising avenue for timely detection and improved patient prognoses.

2D Material-Based Surface-Enhanced Raman Spectroscopy Platforms (Either Alone or in Nanocomposite Form)-From a Chemical Enhancement Perspective

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique with molecular fingerprinting capability and high sensitivity, even down to the single-molecule level. As it is 50 years since the observation of the phenomenon, it has now become an important task to discuss the challenges in this field and determine the areas of development. Electromagnetic enhancement has a mature theoretical explanation, while a chemical mechanism which involves more complex interactions has been difficult to elucidate until recently. This article focuses on the 2D material-based platforms where chemical enhancement (CE) is a significant contributor to SERS. In the context of a diverse range (transition metal dichalcogenides, MXenes, etc.) and categories (insulating, semiconducting, semimetallic, and metallic) of 2D materials, the review aims to realize the influence of various factors on SERS response such as substrates (layer thickness, structural phase, etc.), analytes (energy levels, molecular orientation, etc.), excitation wavelengths, molecular resonances, charge-transfer transitions, dipole interactions, etc. Some examples of special treatments or approaches have been outlined for overcoming well-known limitations of SERS and include how CE benefits from the defect-induced physicochemical changes to 2D materials mostly via the charge-transport ability or surface interaction efficiency. The review may help readers understand different phenomena involved in CE and broaden the substrate-designing approaches based on a diverse set of 2D materials.

Development and Application of Surface-Enhanced Raman Scattering (SERS)

Since the discovery of the phenomenon of surface-enhanced Raman scattering (SERS), it has gradually become an important tool for the analysis of material compositions and structures. The applications of SERS have been expanded from the fields of environmental and materials science to biomedicine due to the extremely high sensitivity and non-destructiveness of SERS-based analytical technology that even allows single-molecule detection. This article provides a comprehensive overview of the surface-enhanced Raman scattering (SERS) phenomenon. The content is divided into several main sections: basic principles and the significance of Raman spectroscopy; historical advancements and technological progress in SERS; and various practical applications across different fields. We also discuss how electromagnetic fields contribute to the SERS effect, the role of chemical interactions in enhancing Raman signals, a modeling and computational approaches to understand and predict SERS effects.

From Genotype to Phenotype: Raman Spectroscopy and Machine Learning for Label-Free Single-Cell Analysis

Raman spectroscopy has made significant progress in biosensing and clinical research. Here, we describe how surface-enhanced Raman spectroscopy (SERS) assisted with machine learning (ML) can expand its capabilities to enable interpretable insights into the transcriptome, proteome, and metabolome at the single-cell level. We first review how advances in nanophotonics-including plasmonics, metamaterials, and metasurfaces-enhance Raman scattering for rapid, strong label-free spectroscopy. We then discuss ML approaches for precise and interpretable spectral analysis, including neural networks, perturbation and gradient algorithms, and transfer learning. We provide illustrative examples of single-cell Raman phenotyping using nanophotonics and ML, including bacterial antibiotic susceptibility predictions, stem cell expression profiles, cancer diagnostics, and immunotherapy efficacy and toxicity predictions. Lastly, we discuss exciting prospects for the future of single-cell Raman spectroscopy, including Raman instrumentation, self-driving laboratories, Raman data banks, and machine learning for uncovering biological insights.

Diagnosis and treatment status of inoperable locally advanced breast cancer and the application value of inorganic nanomaterials

Locally advanced breast cancer (LABC) is a heterogeneous group of breast cancer that accounts for 10-30% of breast cancer cases. Despite the ongoing development of current treatment methods, LABC remains a severe and complex public health concern around the world, thus prompting the urgent requirement for innovative diagnosis and treatment strategies. The primary treatment challenges are inoperable clinical status and ineffective local control methods. With the rapid advancement of nanotechnology, inorganic nanoparticles (INPs) exhibit a potential application prospect in diagnosing and treating breast cancer. Due to the unique inherent characteristics of INPs, different functions can be performed via appropriate modifications and constructions, thus making them suitable for different imaging technology strategies and treatment schemes. INPs can improve the efficacy of conventional local radiotherapy treatment. In the face of inoperable LABC, INPs have proposed new local therapeutic methods and fostered the evolution of novel strategies such as photothermal and photodynamic therapy, magnetothermal therapy, sonodynamic therapy, and multifunctional inorganic nanoplatform. This article reviews the advances of INPs in local accurate imaging and breast cancer treatment and offers insights to overcome the existing clinical difficulties in LABC management.

SERS-based microdevices for use as in vitro diagnostic biosensors

Advances in surface-enhanced Raman scattering (SERS) detection have helped to overcome the limitations of traditional in vitro diagnostic methods, such as fluorescence and chemiluminescence, owing to its high sensitivity and multiplex detection capability. However, for the implementation of SERS detection technology in disease diagnosis, a SERS-based assay platform capable of analyzing clinical samples is essential. Moreover, infectious diseases like COVID-19 require the development of point-of-care (POC) diagnostic technologies that can rapidly and accurately determine infection status. As an effective assay platform, SERS-based bioassays utilize SERS nanotags labeled with protein or DNA receptors on Au or Ag nanoparticles, serving as highly sensitive optical probes. Additionally, a microdevice is necessary as an interface between the target biomolecules and SERS nanotags. This review aims to introduce various microdevices developed for SERS detection, available for POC diagnostics, including LFA strips, microfluidic chips, and microarray chips. Furthermore, the article presents research findings reported in the last 20 years for the SERS-based bioassay of various diseases, such as cancer, cardiovascular diseases, and infectious diseases. Finally, the prospects of SERS bioassays are discussed concerning the integration of SERS-based microdevices and portable Raman readers into POC systems, along with the utilization of artificial intelligence technology.

Recent advances in the authentication (geographical origins, varieties and aging time) of tangerine peel (Citri reticulatae pericarpium): A review

The consumption of tangerine peel (Citri reticulatae pericarpium, CRP) has been steadily increasing worldwide due to its proven health benefits and sensory characteristics. However, the price of CRP varies widely based on its origin, variety, and aging time, which has led many manufacturers to offer inferior products by exploiting the sensory similarity of CRP, seriously undermining consumers' interests. Therefore, it is essential to identify the authenticity of the CRP. In this study, the research progress on the authenticity of CRP from different origins, years and varieties over the past 10 years and the application and prospects of the main technologies and techniques were reviewed. The advantages and disadvantages of the commonly used methods were also summarized and compared. Mass spectrometry-based and spectroscopy-based techniques are the most commonly used methods for analyzing CRP authenticity. However, designing fast, non-destructive and green methods for identifying CRP authenticity would be the future trend.

Interface-constrained catalytic hairpin assembly permits highly sensitive SERS signaling of miRNA

The rapid and precise monitoring of peripheral blood miRNA levels holds paramount importance for disease diagnosis and treatment monitoring. In this study, we propose an innovative research strategy that combines the catalytic hairpin assembly reaction with SERS signal congregation and enhancement. This combination can significantly enhance the stability of SERS detection, enabling stable and efficient detection of miRNA. Specifically, our paper-based SERS detection platform incorporates a streptavidin-modified substrate, biotin-labeled catalytic hairpin assembly reaction probes, 4-ATP, and primer-co-modified gold nanoparticles. In the presence of miRNA, the 4-ATP and primer-co-modified gold nanoparticles can specifically recognize the miRNA and interact with the biotin-labeled CHA probes to initiate an interfacial catalytic hairpin assembly reaction. This enzyme-free high-efficiency catalytic process can accumulate a large amount of biotin on the gold nanoparticles, which then bind to the streptavidin on the substrate with the assistance of the driving liquid, forming red gold nanoparticle stripes. These provide a multitude of hotspots for SERS, enabling enhanced signal detection. This innovative design achieves a low detection limit of 3.47 fM while maintaining excellent stability and repeatability. This conceptually innovative detection platform offers new technological possibilities and solutions for clinical miRNA detection.

Oxidative Coupling and Self-Assembly of Polyphenols for the Development of Novel Biomaterials

In recent years, the development of biomaterials from green organic sources with nontoxicity and hyposensitivity has been explored for a wide array of biotherapeutic applications. Polyphenolic compounds have unique structural features, and self-assembly by oxidative coupling allows molecular species to rearrange into complex biomaterial that can be used for multiple applications. Self-assembled polyphenolic structures, such as hollow spheres, can be designed to respond to various chemical and physical stimuli that can release therapeutic drugs smartly. The self-assembled metallic-phenol network (MPN) has been used for modulating interfacial properties and designing biomaterials, and there are several advantages and challenges associated with such biomaterials. This review comprehensively summarizes current challenges and prospects of self-assembled polyphenolic hollow spheres and MPN coatings and self-assembly for biomedical applications.

SERS sensing for cancer biomarker: Approaches and directions

These days, cancer is thought to be more than just one illness, with several complex subtypes that require different screening approaches. These subtypes can be distinguished by the distinct markings left by metabolites, proteins, miRNA, and DNA. Personalized illness management may be possible if cancer is categorized according to its biomarkers. In order to stop cancer from spreading and posing a significant risk to patient survival, early detection and prompt treatment are essential. Traditional cancer screening techniques are tedious, time-consuming, and require expert personnel for analysis. This has led scientists to reevaluate screening methodologies and make use of emerging technologies to achieve better results. Using time and money saving techniques, these methodologies integrate the procedures from sample preparation to detection in small devices with high accuracy and sensitivity. With its proven potential for biomedical use, surface-enhanced Raman scattering (SERS) has been widely used in biosensing applications, particularly in biomarker identification. Consideration was given especially to the potential of SERS as a portable clinical diagnostic tool. The approaches to SERS-based sensing technologies for both invasive and non-invasive samples are reviewed in this article, along with sample preparation techniques and obstacles. Aside from these significant constraints in the detection approach and techniques, the review also takes into account the complexity of biological fluids, the availability of biomarkers, and their sensitivity and selectivity, which are generally lowered. Massive ways to maintain sensing capabilities in clinical samples are being developed recently to get over this restriction. SERS is known to be a reliable diagnostic method for treatment judgments. Nonetheless, there is still room for advancement in terms of portability, creation of diagnostic apps, and interdisciplinary AI-based applications. Therefore, we will outline the current state of technological maturity for SERS-based cancer biomarker detection in this article. The review will meet the demand for reviewing various sample types (invasive and non-invasive) of cancer biomarkers and their detection using SERS. It will also shed light on the growing body of research on portable methods for clinical application and quick cancer detection.

Recent advances in SERS-based bioanalytical applications: live cell imaging

Raman scattering can provide information on molecular fingerprints, which have been widely applied in various fields of material science and nanobiotechnology. Notably, low interference with water molecules in obtaining the Raman spectra between 500 and 2000 cm-1 made it a powerful spectroscopic tool in biology, such as imaging and signaling for a living cell. To be a robust tool for cell biology, the performance of obtaining molecular-specific information with high sensitivity, high resolution in real time, and without inducing cell damage is strongly required. The conventional fluorescence-based method has been suffered from the rapid photobleaching of organic fluorophores and the lack of molecular information. In contrast, Raman scattering is a promising spectroscopic tool to acquire cellular information, and the extremely low signal intensity of Raman scattering could be amplified by incorporating the plasmonic nanomaterials. Along with the fundamental research focus on surface-enhanced Raman scattering (SERS), the practical approaches of SERS for cellular imaging as a new tool for drug screening and monitoring cellular signals have been extensively explored based on new optical setups and new designing strategies for the nanostructures. Diverse nanostructure and surface chemistry for targeting or sensing have been played pivotal roles in acquiring cellular information and high resolution cell imaging. In this regard, this review focused on the recent advances of SERS-based technologies for a live cell imaging investigated such as potential drug screening, signaling for chemicals or biomolecules in cell, in situ sensing, and high spatiotemporal resolution.

Adaptive Gap-Tunable Surface-Enhanced Raman Spectroscopy

Gap plasmon (GP) resonance in static surface-enhanced Raman spectroscopy (SERS) structures is generally too narrow and not tunable. Here, we present an adaptive gap-tunable SERS device to selectively enhance and modulate different vibrational modes via active flexible Au nanogaps, with adaptive optical control. The tunability of GP resonance is up to ∼1200 cm-1 by engineering gap width, facilitated by mechanical bending of a polyethylene terephthalate substrate. We confirm that the tuned GP resonance selectively enhances different Raman spectral regions of the molecules. Additionally, we dynamically control the SERS intensity through the wavefront shaping of excitation beams. Furthermore, we demonstrate simulation results, exhibiting the mechanical and optical properties of a one-dimensional flexible nanogap and their advantage in high-speed biomedical sensing. Our work provides a unique approach for observing and controlling the enhanced chemical responses with dynamic tunability.

Designing Superselectivity in Linker-Mediated Multivalent Nanoparticle Adsorption

Using a statistical mechanical model and numerical simulations, we provide the design principle for the bridging strength (ξ) and linker density (ρ) dependent superselectivity in linker-mediated multivalent nanoparticle adsorption. When the bridges are insufficient, the formation of multiple bridges leads to both ξ- and ρ-dependent superselectivity. When the bridges are excessive, the system becomes insensitive to bridging strength due to entropy-induced self-saturation and shows a superselective desorption with respect to the linker density. Counterintuitively, lower linker density or stronger bridging strength enhances the superselectivity. These findings help the understanding of relevant biological processes and open up opportunities for applications in biosensing, drug delivery, and programmable self-assembly.

Confined growth of Ag nanogap shells emitting stable Raman label signals for SERS liquid biopsy of pancreatic cancer

To develop a reliable surface-enhanced Raman scattering (SERS) immunoassay as a new liquid biopsy modality, SERS nanoprobes emitting strong and stable signals are necessary. However, Ag nanoparticles used as SERS nanoprobes are prone to rapid fading of SERS signals by oxidation. This has driven the development of a new strategy for Ag-based SERS nanoprobes emitting stable and strong SERS signals over time. Herein, Ag nanogap shells entrapping Raman labels are created in the confined pores of mesoporous silica nanoparticles (AgNSM) through a rapid single-step reaction for SERS liquid biopsy. Each AgNSM nanoprobe possesses multiple nanogaps of 1.58 nm to entrap Raman labels, allowing superior long-term SERS signal stability and large enhancement of 1.5 × 106. AgNSM nanoprobes conjugated with an antibody specific for carbohydrate antigen (CA)19-9 are employed in the SERS sandwich immunoassay including antibody-conjugated magnetic nanoparticles for CA19-9 detection, showing a two orders of magnitude lower limit of detection (0.025 U mL-1) than an enzyme-linked immunosorbent assay (0.3 U mL-1). The AgNSM nanoprobe immunoassay accurately quantifies CA19-9 levels from clinical serum samples of early and advanced pancreatic cancer. AgNSM nanoprobes with stable SERS signals provide a new route to SERS liquid biopsy for effective detection of blood biomarkers.

Convergence of Surface-Enhanced Raman Scattering with Molecular Diagnostics: A Perspective on Future Directions

Molecular diagnostics (MD) is widely employed in multiple scientific disciplines, such as oncology, pathogen detection, forensic investigations, and the pharmaceutical industry. Techniques such as polymerase chain reaction (PCR) revolutionized the rapid and accurate identification of nucleic acids (DNA, RNA). More recently, CRISPR and its CRISPR-associated protein (Cas) have been a ground-breaking discovery that is the latest revolution in molecular biology, including MD. Surface-enhanced Raman scattering (SERS) is a very attractive alternative to fluorescence as the currently most widely used optical readout in MD. In this Perspective, milestones in the development of MD, SERS-PCR, and next-generation approaches to MD, such as Specific High-Sensitivity Enzymatic Reporter UnLOCKing (SHERLOCK) and DNA Endonuclease-Targeted CRISPR Trans Reporter (DETECTR), are briefly summarized. Our perspective on the future convergence of SERS with MD is focused on SERS-based CRISPR/Cas (SERS-CRISPR) since we anticipate many promising applications in this rapidly emerging field. We predict that major future developments will exploit the advantages of real-time monitoring with the superior brightness, photostability, and spectral multiplexing potential of SERS nanotags in an automated workflow for rapid assays under isothermal, amplification-free conditions.

Porous rod-shaped Fe2O3/Ag/BP: a novel substrate for highly sensitive SERS detection of persistent organic pollutants

A surface enhanced Raman scattering (SERS) substrate of porous rod-shaped ferric oxide (Fe2O3) combined with silver nanoparticles (Ag NPs) and black phosphorus (Fe2O3/Ag/BP) was fabricated to detect the persistent organic pollutants (POPs) at low concentration. The organic pollutant Rhodamine 6G (R6G) was used as the probe molecule to study the performances of Fe2O3/Ag/BP, and 4-chlorobiphenyl (PCB-3) was the target of detection. The limit of detection (LOD) of R6G based on this novel SERS substrate Fe2O3/Ag/BP was as low as 1.0 × 10-15M, which was five orders of magnitude lower than that of Fe2O3/Ag (10-10M). The enhancement factor (EF) of Fe2O3/Ag/BP was 6.44 × 108, which was 3.1 times higher than that of porous rod-shaped Fe2O3/Ag (2.08 × 108). The Raman signal of R6G based on Fe2O3/Ag/BP had a good homogeneity, and the relative standard deviation (RSD) of Raman signal intensities of R6G at 1643 cm-1was only 5.97%. Furthermore, the Fe2O3/Ag/BP substrate exhibited a recyclability through the photocatalytic degradation of R6G. The LOD of PCB-3 based on Fe2O3/Ag/BP was 10-9M. Besides, Fe2O3/Ag/BP had a high SERS activity even it was kept in a centrifuge tube without requiring complicated treatment. These results highlight the potential application of Fe2O3/Ag/BP for ultra-trace detection of POPs in the environment.

Novel SERS Signal Amplification Strategy for Ultrasensitive and Specific Detection of Spinal Cord Injury-Related miRNA

The expression of microRNA (miRNA) changes in many diseases plays an important role in the diagnosis, treatment, and prognosis of diseases. Spinal cord injury (SCI) is a serious disease of the central nervous system, accompanied by inflammation, cell apoptosis, neuronal necrosis, axonal rupture, demyelination, and other pathological processes, resulting in impaired sensory and motor functions of patients. Studies have shown that miRNA expression has changed after SCI, and miRNAs participate in the pathophysiological process and treatment of SCI. Therefore, quantitative analysis and monitoring of the expression of miRNA were of great significance for the diagnosis and treatment of SCI. Through the SCI-related miRNA chord plot, we screened out miRNA-21-5p and miRNA-let-7a with a higher correlation. However, for traditional detection strategies, it is still a great challenge to achieve a fast, accurate, and sensitive detection of miRNA in complex biological environments. The most frequently used method for detecting miRNAs is polymerase chain reaction (PCR), but it has disadvantages such as being time-consuming and cumbersome. In this paper, a novel SERS sensor for the quantitative detection of miRNA-21-5p and miRNA-let-7a in serum and cerebrospinal fluid (CSF) was developed. The SERS probe eventually formed a sandwich-like structure of Fe3O4@hpDNA@miRNA@hpDNA@GNCs with target miRNAs, which had high specificity and stability. This SERS sensor achieved a wide range of detection from 1 fM to 1 nM and had a good linear relationship. The limits of detection (LOD) for miRNA-21-5p and miRNA-let-7a were 0.015 and 0.011 fM, respectively. This new strategy realized quantitative detection and long-term monitoring of miRNA-21-5p and miRNA-let-7a in vivo. It is expected to become a powerful biomolecule analysis tool and will provide ideas for the diagnosis and treatment of many diseases.

Nanomaterials in Medicine: Understanding Cellular Uptake, Localization, and Retention for Enhanced Disease Diagnosis and Therapy

Nanomaterials (NMs) have emerged as promising tools for disease diagnosis and therapy due to their unique physicochemical properties. To maximize the effectiveness and design of NMs-based medical applications, it is essential to comprehend the complex mechanisms of cellular uptake, subcellular localization, and cellular retention. This review illuminates the various pathways that NMs take to get from the extracellular environment to certain intracellular compartments by investigating the various mechanisms that underlie their interaction with cells. The cellular uptake of NMs involves complex interactions with cell membranes, encompassing endocytosis, phagocytosis, and other active transport mechanisms. Unique uptake patterns across cell types highlight the necessity for customized NMs designs. After internalization, NMs move through a variety of intracellular routes that affect where they are located subcellularly. Understanding these pathways is pivotal for enhancing the targeted delivery of therapeutic agents and imaging probes. Furthermore, the cellular retention of NMs plays a critical role in sustained therapeutic efficacy and long-term imaging capabilities. Factors influencing cellular retention include nanoparticle size, surface chemistry, and the cellular microenvironment. Strategies for prolonging cellular retention are discussed, including surface modifications and encapsulation techniques. In conclusion, a comprehensive understanding of the mechanisms governing cellular uptake, subcellular localization, and cellular retention of NMs is essential for advancing their application in disease diagnosis and therapy. This review provides insights into the intricate interplay between NMs and biological systems, offering a foundation for the rational design of next-generation nanomedicines.

Direct Detection of Tobacco Mosaic Virus in Infected Plants with SERS-Sensing Hydrogels

The impact of plant pathogens on global crop yields is a major societal concern. The current agricultural diagnostic paradigm involves either visual inspection (inaccurate) or laboratory molecular tests (burdensome). While field-ready diagnostic methods have advanced in recent years, issues remain with detection of presymptomatic infections, multiplexed analysis, and requirement for in-field sample processing. To overcome these issues, we developed surface-enhanced Raman scattering (SERS)-sensing hydrogels that detect pathogens through simple contact with a leaf. In this work, we developed a novel reagentless SERS sensor for the detection of tobacco mosaic virus (TMV) and embedded it in an optimized hydrogel material to produce sensing hydrogels. To test the diagnostic application of our sensing hydrogels, we demonstrate their use to detect TMV infection in tobacco plants. This technology has the potential to shift the current agricultural diagnostic paradigm by offering a field-deployable tool for presymptomatic and multiplexed molecular identification of pathogens.

Molecular-scale Insights into Cooperativity Switching of xTAB Adsorption on Gold Nanoparticles

Quantifying adsorption behaviors is crucial for various applications such as catalysis, separation, and sensing, yet it is generally challenging to access in solution. Here, we report a combined experimental and computational study of the adsorption behaviors of alkyl-trimethylammonium bromides (xTAB), a class of ligands important for colloidal nanoparticle stabilization and shape control, with various alkyl chain lengths x on Au nanoparticles. We use density functional theory (DFT) to calculate xTAB binding energies on Au{111} and Au{110} surfaces with standing-up and lying-down configurations, which provides insights into the adsorption affinity and cooperativity differences of xTAB on these two facets. We demonstrate the key role of van der Waals interactions in determining the xTAB adsorption behavior. These computational results predict and explain the experimental discovery of xTAB's adsorption behavior switch from stronger affinity, negative cooperativity to weaker affinity, positive cooperativity when the concentration of xTAB increases in solution. We also show that in the standing-up configuration, bilayer adsorption may occur on both facets, which can lead to different differential binding energies and consequently adsorption crossover between the two facets when the ligand concentration increases. Our combined experimental and computational approaches demonstrate a paradigm for gaining molecular-scale insights into adsorbate-surface interactions.

Fabrication of silver nanostructure array patterns (SNAPs) on silicon wafer for highly sensitive and reliable SERS substrates

Metal nanostructure arrays with large amounts of nano-gaps are important for surface enhanced Raman scattering applications, though the fabrications of such nanostructures are difficult due to the complex and multiple synthetic steps. In this research, we report silver nanostructure array patterns (SNAPs) on silicon wafer, which is fabricated with semiconductor manufacturing technology, Cu2O electrochemistry deposition, and Ag In-situ oxidation-reduction growth. Benefiting from the dense and uniform distribution of Ag nanowires, the fabricated SNAPs demonstrate a very strong and uniform surface-enhanced Raman scattering (SERS) effect. The efficiency of SNAPs was investigated by using rhodamine 6G (R6G) dye as an analyte molecule. The results show that the minimum detectable concentration of R6G can reach as low as 10-11 M, and the Raman signals in the random region show good signal homogeneity with a low relative standard deviation (RSD) of 4.77 %. These results indicate that the SNAPs perform a great sensitivity and uniformity as a SERS substrate. Furthermore, we used the SNAPs substrate to detect antibiotic sulfadiazine. The main peaks in sulfadiazine Raman and vibration modes assignments were obtained and the quantitative analysis model was established by principal component analysis (PCA). The detection and application results of sulfadiazine indicate that the SNAPs substrate can be applied for trace detection of antibiotics. In addition, we have cited the application of the SNAPs substrate in anti-counterfeiting labels. These practical applications demonstrate that the fabricated SNAPs can potentially provide a way to develop low-cost SERS platforms for environmental detections, biomedicine analysis, and commodities anti-counterfeiting.

Target-induced hot spot construction for sensitive and selective surface-enhanced Raman scattering detection of matrix metalloproteinase MMP-9

Studies have found that matrix metalloproteinase-9 (MMP-9) plays a significant role in cancer cell invasion, metastasis, and tumor growth. But it is a challenge to go for highly sensitive and selective detection and targeting of MMP-9 due to the similar structure and function of the MMP proteins family. Herein, a novel surface-enhanced Raman scattering (SERS) sensing strategy was developed based on the aptamer-induced SERS "hot spot" formation for the extremely sensitive and selective determination of MMP-9. To develop the nanosensor, one group of gold nanospheres was modified with MMP-9 aptamer and its complementary strand DNA1, while DNA2 (complementary to DNA1) and the probe molecule 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB) were grafted on the surface of the other group of gold nanospheres. In the absence of MMP-9, DTNB located on the 13-nm gold nanospheres has only generated a very weak SERS signal. However, when MMP-9 is present, the aptamer preferentially binds to the MMP-9 to construct MMP-9-aptamer complex. The bare DNA1 can recognize and bind to DNA2, which causes them to move in close proximity and create a SERS hot spot effect. Due to this action, the SERS signal of DTNB located at the nanoparticle gap is greatly enhanced, achieving highly sensitive detection of MMP-9. Since the hot spot effect is caused by the aptamer that specifically recognizes MMP-9, the approach exhibits excellent selectivity for MMP-9 detection. Based on the benefits of both high sensitivity and excellent selectivity, this method was used to distinguish the difference in MMP-9 levels between normal and cancer cells as well as the expression of MMP-9 from cancer cells with different degrees of metastasis. In addition, this strategy can accurately reflect the dynamic changes in intracellular MMP-9 levels, stimulated by the MMP-9 activator and inhibitor. This strategy is expected to be transformed into a new technique for diagnosis of specific cancers related to MMP-9 and assessing the extent of cancer occurrence, development and metastasis.

Highly sensitive and selective SERS detection of caspase-3 during cell apoptosis based on the target-induced hotspot effect

Caspase-3 is an important biomarker for the process of apoptosis, which is a key target for cancer treatment. Due to its low concentration in single cells and the structural similarity of caspase family proteins, it is exceedingly challenging to accurately determine the intracellular caspase-3 during apoptosis in situ. Herein, a biosensing strategy based on the target-induced SERS "hot spot" formation has been developed for the simultaneous highly sensitive and selective detection of intracellular caspase-3 level. The nanosensor is composed of gold nanoparticles modified with the probe molecule 4-mercaptophenylboronic acid (4-MPBA) and a peptide chain. The well-designed peptide chain contains two distinct functional domains, one with a sulfhydryl group for bonding to the gold nanoparticles and the other a fragment specifically recognized by caspase-3. When caspase-3 is present, the negatively charged segment (NH2-Asp-Asp-Asp-Glu-Val-Asp-OH) of the peptide chain is specifically hydrolyzed, leaving a positively charged fragment coated on the surface of the gold nanoparticles. At this time, the golden nanoparticles undergo significant coupling aggregation due to the electrostatic interaction, resulting in a large number of SERS "hot spot" formation. The SERS signal of the 4-MPBA located at the nano-gap is significantly boosted because of the local plasma enhancement effect. The highly sensitive determination of caspase-3 can be achieved according to the altered SERS signal intensity of 4-MPBA. The turn-on of the SERS signal-induced target contributes to the excellent selectivity and the formation of the SERS "hot spot" effect that further improves the sensitivity of caspase-3 detection. The advantages of this biosensing technique allow for the precise in situ monitoring of the dynamic changes in caspase-3 levels during apoptosis. In addition, the differences in caspase-3 levels during the apoptosis of various cell types were compared. Monitoring the caspase-3 levels can be used to track the cellular apoptosis process, evaluate the effect of drugs on cancer cells in real time, and provide guidance for the selection of the appropriate drug dosage.

Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment

The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1-2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.

Enhancing the Reliability of SERS Detection in Ampicillin Using Oriented Tetrahedral Framework Nucleic Acid Probes and a Long-Range SERS Substrate

Indirect surface-enhanced Raman scattering (SERS)-based methods are highly efficient in detecting and quantitatively analyzing trace antibiotics in complex samples. However, the poor reproducibility of indirect SERS assays caused by the diffusion and orientation changes of the probing molecules on SERS substrates still presents a significant challenge. To address this issue, this study reports the construction of a novel SERS sensing platform using tetrahedral framework nucleic acid (tFNA) as SERS probes in conjunction with a long-range SERS (LR-SERS) substrate. The tFNA was modified with sulfhydryl groups at three vertices and appended with a probing DNA at the remaining vertex, anchored on the substrate surface with a well-ordered orientation and stable coverage density, resulting in highly reproducible SERS signals. Owing to the weak SERS signal of tFNA inherited from its size being larger than the effective range of the enhancing electric field (E-field) of conventional SERS substrates, we utilized an LR-SERS substrate to enhance the signal of tFNA probes by capitalizing on its extended E-field. Correspondingly, the LR-SERS substrate demonstrated a 54-fold increase in the intensity of tFNA probes compared to the conventional substrate. Using this novel platform, we achieved a highly reliable detection of the antibiotic ampicillin with a wide linear range (10 fM to 1 nM), low detection limit (3.1 fM), small relative standard deviation (3.12%), and yielded quantitative recoveries of 97-102% for ampicillin in water, milk, and human serum samples. These findings, therefore, effectively demonstrate the achievement of highly reliable SERS detection of antibiotics using framework nucleic acids and an LR-SERS substrate.

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.

Thin layer chromatography coupled with surface enhanced Raman scattering for rapid separation and on-site detection of multi-components

The separation and detection of multi-component mixtures has always been a challenging task. Traditional detection methods often suffer from complex operation, high cost, and low sensitivity. Surface enhanced Raman scattering (SERS) technique is a high sensitivity, powerful and rapid detection tool, which can realize the specific detection of single substance components, but it must solve the problem that multi-component mixtures cannot be accurately determined. Thin layer chromatography (TLC) technology, as a high-throughput separation technology, uses chromatographic plate as the stationary phase, and could select different developing phases for separation experiments. The advantages of TLC technology in short distance and rapid separation are widely used in protein, dye and biomedical fields. However, TLC technology has limitations in detection ability and difficulty in obtaining ideal signal intensity. The combination of TLC technology and SERS technology made the operation procedure simple and the sample size small, which can achieve rapid on-site separation and quantitative detection of mixtures. Due to the rapid development of TLC-SERS technology, it has been widely used in the investigation of various complex systems. This paper reviews the application of TLC-SERS technology in food science, environmental pollution and biomedicine.

Inspired Beyond Nature: Three Decades of Spherical Nucleic Acids and Colloidal Crystal Engineering with DNA

The conception, synthesis, and invention of a nanostructure, now known as the spherical nucleic acid, or SNA, in 1996 marked the advent of a new field of chemistry. Over the past three decades, the SNA and its analogous anisotropic equivalents have provided an avenue for us to think about some of the most fundamental concepts in chemistry in new ways and led to technologies that are significantly impacting fields from medicine to materials science. A prime example is colloidal crystal engineering with DNA, the framework for using SNAs and related structures to synthesize programmable matter. Herein, we document the evolution of this framework, which was initially inspired by nature, and describe how it now allows researchers to chart paths to move beyond it, as programmable matter with real-world significance is envisioned and created.

Optical Biosensors for the Diagnosis of COVID-19 and Other Viruses-A Review

The sudden outbreak of the COVID-19 pandemic led to a huge concern globally because of the astounding increase in mortality rates worldwide. The medical imaging computed tomography technique, whole-genome sequencing, and electron microscopy are the methods generally used for the screening and identification of the SARS-CoV-2 virus. The main aim of this review is to emphasize the capabilities of various optical techniques to facilitate not only the timely and effective diagnosis of the virus but also to apply its potential toward therapy in the field of virology. This review paper categorizes the potential optical biosensors into the three main categories, spectroscopic-, nanomaterial-, and interferometry-based approaches, used for detecting various types of viruses, including SARS-CoV-2. Various classifications of spectroscopic techniques such as Raman spectroscopy, near-infrared spectroscopy, and fluorescence spectroscopy are discussed in the first part. The second aspect highlights advances related to nanomaterial-based optical biosensors, while the third part describes various optical interferometric biosensors used for the detection of viruses. The tremendous progress made by lab-on-a-chip technology in conjunction with smartphones for improving the point-of-care and portability features of the optical biosensors is also discussed. Finally, the review discusses the emergence of artificial intelligence and its applications in the field of bio-photonics and medical imaging for the diagnosis of COVID-19. The review concludes by providing insights into the future perspectives of optical techniques in the effective diagnosis of viruses.

Dual Signal Amplification by Urease Catalysis and Silver Nanoparticles for Ultrasensitive Colorimetric Detection of Nucleic Acids

Signal amplification techniques are highly desirable for the analysis of low-level targets that are closely related with diseases and the monitoring of important biological processes. However, it is still challenging to achieve this goal in a facile and economical way. Herein, we developed a novel dual signal amplification strategy by combining urease catalysis with the release of Ag⁺ from silver nanoparticles (AgNPs). This strategy was used for quantifying a DNA sequence (HIV-1) related with human immunodeficiency virus (HIV). DNA target HIV-1 hybridizes with the capture DNA probe on magnetic beads and the reporter DNA probe on AgNPs, forming a sandwich complex. The captured AgNPs are then transformed into numerous Ag⁺ ions that inactivate numerous ureases. Without catalytic production of ammonia from urea, the substrate solution shows a low pH 5.8 that will increase otherwise. The pH change is monitored by a pH indicator (phenol red), which allows for colorimetric detection. The proposed approach is sensitive, easy to use, economic, and universal, exhibiting a low detection limit of 9.7 fM (i.e., 1.94 attomoles) and a dynamic linear range of 4 orders for HIV-1 sequence detection.