Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection

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.

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.

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.

Alkyne-tethered oligodeoxynucleotides that allow simultaneous detection of multiple DNA/RNA targets using Raman spectroscopy

Detection of multiple DNA/RNA targets is essential for understanding cellular function. Herein, we propose a general method for the simultaneous detection of plural nucleic acids based on surface-enhanced Raman scattering (SERS) using gold nanoparticles bearing functional oligodeoxynucleotides (ODNs) on their surface. Modified ODNs bearing an acetylene tag hybridized with their complementary ODNs on the surface of the gold nanoparticles, inducing a strong SERS signal of the acetylene tag. The addition of the target nucleic acid to the system resulted in a spontaneous displacement of the strand on the particle and dissociation of the alkyne-tagged ODN from the particle, resulting in a dramatic decrease in signal intensity. By using an alkyne tag for each of the multiple target nucleic acids, each target could be detected simultaneously. In addition, we successfully detected cellular microRNA. Different targets showed changes with different wavenumbers in the Raman spectra, allowing for the detection of multiple nucleic acids.

Heteropolyacids: An Ultrasensitive Ionic Volume-Enhanced Raman Scattering Platform

Surface-enhanced Raman scattering (SERS) is regarded as the most direct and powerful tool to identify chemical fingerprints. However, current SERS substrate materials still face some critical challenges, including low molecular utilization efficiency and low selectivity. Herein, a novel oxygen vacancy heteropolyacid─H₁₀Fe₃Mo₂₁O₅₁ (HFMO)─is developed as a high-performance volume-enhanced Raman scattering (VERS)-active platform. Due to its merit of water solubility, HFMO forms a special coordination bond with the probe molecule at the molecular level, which allows its enhancing ability to be comparable to that of noble metals. An enhancement factor of 1.26 × 10⁹ and a very low detection limit of 10^-13 M for rhodamine 6G were obtained. A robust O-N coordination bond was formed between the anion of HFMO and the probe molecule, resulting in a special electron transfer path (Mo-O-N) with high selectivity, which is verified using X-ray photoelectron spectroscopy analysis and density functional theory calculations. That is to say, the proposed HFMO platform has excellent VERS enhancing effect, specifically for the molecules containing the imino group (e.g., methyl blue, detection limit: 10^-11 M), offering the merits of high reproducibility and uniformity, high-temperature resistance, long-time laser irradiation, and strong acid resistance. Such an initial effort on the ionic type VERS platform may enable the further development of highly sensitive, highly selective, and water-soluble VERS technology.

Conformal Conductive Features on Curvilinear Surfaces with Self-Assembled Silver Nanoplate Thin Films

In this study, a water transfer method was developed to fabricate conducive thin-film patterns on 3D curvilinear surfaces. Crystalline silver nanoplates (AgNPLs) with a dimension of 700 nm and a thickness of 35 nm were suspended in ethanol with an anionic surfactant, sodium dodecyl sulfate, to improve the suspension stability. The prepared AgNPL suspension was then spread over the water surface via the Langmuir-Blodgett approach to generate a self-assembled thin film. By dipping an accepting object with a robotic arm, the floating AgNPL thin film with nanometer thickness can be effectively transferred to the object surfaces and exhibited a superior conductivity up to 15% of bulk silver without thermal sintering. Besides good conductivity, the AgNPL conductive thin films can also be transferred efficiently on any curvilinear (concave and convex) surface. Moreover, with the help of masks, conductive patterns can be produced on water surfaces and transferred to curvilinear surfaces for electronic applications. As a proof of concept, several examples were demonstrated to display the capability of this approach for radiofrequency identification and other printed circuit applications.

Wafer-Level Highly Dense Metallic Nanopillar-Enabled High-Performance SERS Substrates for Molecular Detection

Seeking sensitive, large-scale, and low-cost substrates is highly important for practical applications of surface-enhanced Raman scattering (SERS) technology. Noble metallic plasmonic nanostructures with dense hot spots are considered an effective construction to enable sensitive, uniform, and stable SERS performance and thus have attracted wide attention in recent years. In this work, we reported a simple fabrication method to achieve wafer-scale ultradense tilted and staggered plasmonic metallic nanopillars filled with numerous nanogaps (hot spots). By adjusting the etching time of the PMMA (polymethyl methacrylate) layer, the optimal SERS substrate with the densest metallic nanopillars was obtained, which possessed a detection limit down to 10^-13 M by using crystal violet as the detected molecules and exhibited excellent reproducibility and long-term stability. Furthermore, the proposed fabrication approach was further used to prepare flexible substrates; for example, a SERS flexible substrate was proven to be an ideal platform for analyzing low-concentration pesticide residues on curved fruit surfaces with significantly enhanced sensitivity. This type of SERS substrate possesses potential in real-life applications as low-cost and high-performance sensors.

Utilization of a lateral flow colloidal gold immunoassay strip based on surface-enhanced Raman spectroscopy for rapid detection of glycinin

Glycinin is an important storage protein in soybean, but it can also lead to allergic reactions in humans. In this study, based on a low-cost, simple, rapid and portable lateral flow immunoassay test strip, combined with high sensitivity surface enhanced Raman spectroscopy (SERS) technology, a sandwich lateral flow immunochromatographic test strip for rapid detection of soybean allergen glycinin is established. In the experiment, colloidal gold was covalently conjugated with rabbit-derived polyclonal antibodies of glycinin and Raman probe molecule 4-aminothiophenol(4-PATP) to prepare the immunoprobe. The respective optimal PATP and optimal antibody labeling amounts of colloidal gold solution were 1.05 × 10^-2mol/L and 4.6 × 10^-8mol/L. The detection limit of the test strip for glycinin was 4.87 ng/mL. The recovery rate ranged from 91 to 107 % and the CV was between 3 and 10 %. The test strip underwent no cross-reaction with β-conglycinin, sesame protein, peanut protein, wheat protein or whey protein. The results of the experiment showed that this method exhibits high sensitivity and specificity.

A ratiometric SERS aptasensor array for human DNA glycosylaseat single-cell sensitivity/resolution

Human 8-oxoguanine DNA glycosylase (hOGG1) is involved in the cellular genomic 8-oxoguanine (8-oxoG) excision repair to maintain genome stability. Accurate detection of hOGG1 activity is essential for clinical diagnosis and treatment of various human pathology. Yet, the quantitative detection of hOGG1 remains challenging for existing methods due to poor reproducibility and portability. Herein, we propose a ratiometric array-based SERS point-of-care testing method for hOGG1 activity. A kind of reproducible, uniform and stable plasmonic multi-microarray reaction cells was constructed by assembling AuNPs on the substrate modified by aminosilane and segmented by silica gel gasket, which greatly improved the sensitivity, portability and repeatability of SERS measurement. Based on this, the ratiometric method is further used to effectively overcome the instability of single SERS signal intensity, which allows signal rationing and provides built-in correction for environment effects. In specific, we designed two different Raman-labeled probes for the detection of hOGG1, a thiol- and Cy3-labeled aptamer as an internal standard and a Rox-labeled 8-oxoG-modified complementary aptamer as a signal probe. The ratio value between Cy3 and Rox SERS intensity is well linear with the hOGG1 activity on logarithmic scales in the range from 5 × 10^-5 to 5 × 10^-3 U/mL, and the limit of detection reaches 3.3 × 10^-5 U/mL. Moreover, this strategy can be applied for the screening of inhibitors and the monitoring of cellular hOGG1 activity fluctuation at single-cell levels, providing a flexible and adaptive tool for clinical diagnosis, biochemical processes and drug discovery.

Confined Target-Triggered Hot Spots for In Situ SERS Analysis of Intranuclear Genotoxic Markers

The γH2AX is a type of confined target in nuclei which is highly expressed around the damaged DNA during genotoxicity and has therefore been identified as a marker of genotoxicity. Convenient and intuitive in situ real-time detection of γH2AX is crucial for an accurate assessment of genotoxicity. Selective and nondestructive surface-enhanced Raman spectroscopy (SERS) is suitable to achieve this goal. However, the detection of substances in the nucleus by SERS is still limited due to the contradiction of probes between the nuclei entry efficiency and signal enhancement. This study utilized the characteristics of γH2AX as a confined target and constructed a γH2AX immunosensor based on gold nanoprobes with a small size (15 nm), which was modified with the TAT nuclear targeting peptide to ensure high nuclei entry efficiency. Once DNA damage was induced, the local overexpression of γH2AX further recruited the probe through immune recognition, so that hot spots could be assembled in situ to generate strong Raman signals, which were applied to evaluate the genotoxicity of drug impurities. This study proposed a novel SERS detection strategy, characterized by confined target-induced size conversion and hot spot formation, for in situ real-time analysis of intranuclear targets at the single-living-cell level, which intelligently simplified the structure of SERS probes and the operation process.

Active Enrichment of Nanoparticles for Ultra-Trace Point-of-Care COVID-19 Detection

Active enrichment can detect nucleic acid at ultra-low concentrations without relatively time-consuming polymerase chain reaction (PCR), which is an important development direction for future rapid nucleic acid detection. Here, we reported an integrated active enrichment platform for direct hand-held detection of nucleic acid of COVID-19 in nanoliter samples without PCR. The platform consists of a capillary-assisted liquid-carrying system for sampling, integrated circuit system for ultrasound output, and cell-phone-based surface-enhanced Raman scattering (SERS) system. Considering the acoustic responsiveness and SERS-enhanced performance, gold nanorods were selected for biomedical applications. Functionalized gold nanorods can effectively capture and enrich biomarkers under ultrasonic aggregation. Such approaches can actively assemble gold nanorods in 1-2 s and achieved highly sensitive (6.15 × 10-13 M) SERS detection of COVID-19 biomarkers in nanoliter (10-7 L) samples within 5 min. We further demonstrated the high stability, repeatability, and selectivity of the platform, and validated its potential for the detection of throat swab samples. This simple, portable, and ultra-trace integrated active enrichment detection platform is a promising diagnostic tool for the direct and rapid detection of COVID-19.

Recent advances in plasmon-enhanced luminescence for biosensing and bioimaging

Plasmon-enhanced luminescence (PEL) is a unique photophysical phenomenon in which the interaction between luminescent moieties and metal nanostructures results in a marked luminescence enhancement. PEL offers several advantages and has been extensively used to design robust biosensing platforms for luminescence-based detection and diagnostics applications, as well as for the development of many efficient bioimaging platforms, enabling high-contrast non-invasive real-time optical imaging of biological tissues, cells, and organelles with high spatial and temporal resolution. This review summarizes recent progress in the development of various PEL-based biosensors and bioimaging platforms for diverse biological and biomedical applications. Specifically, we comprehensively assessed rationally designed PEL-based biosensors that can efficiently detect biomarkers (proteins and nucleic acids) in point-of-care tests, highlighting significant improvements in the sensing performance upon the integration of PEL. In addition to discussing the merits and demerits of recently developed PEL-based biosensors on substrates or in solutions, we include a brief discussion on integrating PEL-based biosensing platforms into microfluidic devices as a promising multi-responsive detection method. The review also presents comprehensive details about the recent advances in the development of various PEL-based multi-functional (passive targeting, active targeting, and stimuli-responsive) bioimaging probes, highlighting the scope of future improvements in devising robust PEL-based nanosystems to achieve more effective diagnostic and therapeutic insights by enabling imaging-guided therapy.

Nanomedicine: New Frontiers in Fighting Microbial Infections

Microbes have dominated life on Earth for the past two billion years, despite facing a variety of obstacles. In the 20th century, antibiotics and immunizations brought about these changes. Since then, microorganisms have acquired resistance, and various infectious diseases have been able to avoid being treated with traditionally developed vaccines. Antibiotic resistance and pathogenicity have surpassed antibiotic discovery in terms of importance over the course of the past few decades. These shifts have resulted in tremendous economic and health repercussions across the board for all socioeconomic levels; thus, we require ground-breaking innovations to effectively manage microbial infections and to provide long-term solutions. The pharmaceutical and biotechnology sectors have been radically altered as a result of nanomedicine, and this trend is now spreading to the antibacterial research community. Here, we examine the role that nanomedicine plays in the prevention of microbial infections, including topics such as diagnosis, antimicrobial therapy, pharmaceutical administration, and immunizations, as well as the opportunities and challenges that lie ahead.

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.

Preparation of SERS active filter paper for filtration and detection of pesticides residue from complex sample

The selectivity is needed mostly in SERS sensing because analytes of interest are commonly present in a complex mixture containing particles and impurities, which hinder the interactions between the laser and analyte being detected. In this manuscript, we describe our efforts developing a simple and instant. method to prepare a filter paper SERS sensor. Colloidal Ag nanoparticles were immobilized on one side of filter paper via an in-situ growth method. The fabrication process of the sensor could be finished in several minutes, and no special facility needed. The filter paper SERS sensor demonstrated a spectra uniformity with a 7.0 % point-by-point signal deviation. And the filter function of the sensor could effectively filter out interferences from samples in 1 min, that allowing the direct detection of thiram in ketchup by SERS with detection limit of 93 ppb. Furthermore, we used a Quick Easy Cheap Effective Rugged and Safe (QuEChERS) sample preparation method to detect malachite green (MG) in soil with a sensitivity as low as 0.01 ppm without any sample pre-treatment or purification. A SERS filter paper may open a new avenue for rapid testing of food quality during manufacturing as well as fast detection of potential contaminants in a myriad of substrates.

A simple and efficient strategy for trace detection of ferroptosis-related miRNAs based on novel hydrophobic paper-based plasmonic substrate and "inverse molecular sentinel (iMS)" nanoprobes

Monitoring ferroptosis-related miRNAs is crucial for the treatment and prognosis of patients with intracerebral hemorrhage. In this work, a novel hydrophobic paper (h-paper)-based plasmonic substrate was produced by dropping DS Au nanorods with a narrow range of sizes and morphologies onto h-paper. Raman reporter molecules were adsorbed to the array surface, and surface-enhanced Raman scattering spectra at randomly selected points reveal uniform and significant SERS enhancement. Hairpin DNAs labelled with Raman reporters and hybridized with placeholder DNAs were decorated on SERS substrate to fabricate SERS biosensor. Target miRNAs initiated the "inverse Molecular Sentinel" process. During the process, PHs were removed and the conformation of HPs changed toward the hairpin structure, thus eliciting the proximity of Raman reporter to substrate and a stronger SERS signal. The proposed SERS biosensor performs well in terms of stability, reproducibility, and selectivity. The limits of detection of miR-122-5p and miR-140-5p in serum were 4.17 aM and 4.49 aM, respectively. Finally, the fabricated SERS biosensor was applied to detect miR-122-5p and miR-140-5p in ICH patients and healthy subjects, and the results obtained by SERS were consistent with the results from quantitative real-time polymerase chain reaction, revealing the accuracy of the method. This simple, rapid approach offers great potential for the simultaneous detection of miRNAs in practical clinical applications.

Raman Signal Enhancement by DABCYL-Substitution on DNA Aptamer for Identification of Cellular ATP

Raman probes have attracted widespread attention for the visualization and identification of biomolecules, because they can be applied to identify detailed chemical structures, detect multiple molecules simultaneously, and visualize cellular functional molecules. However, the biological application of Raman probes is still limited because of their weak signal intensity. Herein, we present a molecular system that shows an enhanced Raman signal using a nonfluorescent dye. We introduced a DABCYL molecule bearing an acetylene unit into thymidine at the 5-position. The resulting modified nucleobase, d^DAU, showed a robust signal around 2200 cm^-1, which was attributed to the acetylene unit, due to resonance Raman induced by the DABCYL group. We further prepared a DNA aptamer modified with d^DAU, and characterized the change of the Raman spectra. Combination with gold nanoparticles, which enhanced the Raman signal by surface-enhanced Raman scattering (SERS), allowed sensitive detection of cellular adenosine derivatives including ATP. Thus, the present system is a promising tool for the detection of biological materials by Raman spectroscopy.

SERS combined with PCR as a potent tool for detecting mutations: a case study of tomato plants

Conventional methods of detecting economically essential mutations have several disadvantages. Even though fluorescence-based methods are still the best option, Surface-Enhanced Raman Spectroscopy (SERS) may soon emerge as an alternative to the current techniques for detecting these mutations, because of its ability to detect molecular vibrational signatures. We were able to identify and develop a PCR-based SERS assay that can relentlessly differentiate between different types of indels, and SNPs as demonstrated in the case of tomato genome related to tomato yellow leaf curl virus and root-knot nematodes, diseases that are economically significant to the global agriculture industry and where the selection of resistant crops is the best solution. This tri-primer assay utilizes mutation-specific forward primers and SERS probes tagged with FAM and Cy3 dyes, specific for each allele of a particular gene (Ty-3 and Mi-1). The unique Raman spectral features of these dyes enabled to perform of multiplexing, which made it possible to detect not only the indel type but also the zygosity in a single experiment. Moreover, this technique successfully differentiated between two different SNP-based alleles. Therefore, due to its efficient multiplexing capability and lack of the need for quenchers, it has the potential to become a powerful onsite and offsite screening tool in the not-too-distant future.

Fluorescent copper conjugated curcumin cysteine nanoprobe for selective determination of Fe3+ and G-quadruplex DNA

The synthesis of fluorescent copper-curcumin-cysteine (Cu-CC) as a sensing platform is reported. The synthesized probe has been confirmed by UV-visible spectroscopy, FT-IR, XRD, SEM, and TEM characterization techniques, respectively. The mechanistic aspects of selective sensing of Fe³⁺ and detection of different G-quadruplex DNA have been illustrated based on the "turn-off-on" concept of a regeneratable fluorescence sensing probe at λ_ex 450 nm. Interestingly, we have noticed a high selectivity to Fe³⁺ ion by the developed Cu-CC sensing probe in comparison with other metal ions. Furthermore, the restoration of fluorescence of the sensing probe in the presence of different DNA sequences is illustrating a cost-effective, convenient, and reliable detection methodology of DNA detection. It is highly sensitive for the determination of Pu27, promoter c-MYC quadruplex DNA in a wide linear range of 100-700 nM having a detection limit of 13.1 nM (RSD: 0.15%) and sensitivity of 37.2 cps/nM. Whereas, the Pu18 and H-telo telomeric DNA sequences are showing a narrow linear range, i.e., 10 nM-200 nM and 10 nM-180 nM, respectively. The real-world sample analysis performance of the regeneratable sensing probe for Pu27 DNA detection in fresh human blood serum samples is showing a satisfactory result.

Biomimetic Transparent Nanoplasmonic Meshes by Reverse-Nanoimprinting for Bio-Interfaced Spatiotemporal Multimodal SERS Bioanalysis

Multicellular systems, such as microbial biofilms and cancerous tumors, feature complex biological activities coordinated by cellular interactions mediated via different signaling and regulatory pathways, which are intrinsically heterogeneous, dynamic, and adaptive. However, due to their invasiveness or their inability to interface with native cellular networks, standard bioanalysis methods do not allow in situ spatiotemporal biochemical monitoring of multicellular systems to capture holistic spatiotemporal pictures of systems-level biology. Here, a high-throughput reverse nanoimprint lithography approach is reported to create biomimetic transparent nanoplasmonic microporous mesh (BTNMM) devices with ultrathin flexible microporous structures for spatiotemporal multimodal surface-enhanced Raman spectroscopy (SERS) measurements at the bio-interface. It is demonstrated that BTNMMs, supporting uniform and ultrasensitive SERS hotspots, can simultaneously enable spatiotemporal multimodal SERS measurements for targeted pH sensing and non-targeted molecular detection to resolve the diffusion dynamics for pH, adenine, and Rhodamine 6G molecules in agarose gel. Moreover, it is demonstrated that BTNMMs can act as multifunctional bio-interfaced SERS sensors to conduct in situ spatiotemporal pH mapping and molecular profiling of Escherichia coli biofilms. It is envisioned that the ultrasensitive multimodal SERS capability, transport permeability, and biomechanical compatibility of the BTNMMs can open exciting avenues for bio-interfaced multifunctional sensing applications both in vitro and in vivo.

Potential of fluorescent nanoprobe in diagnosis and treatment of Alzheimer's disease

Alzheimer's disease (AD) is well known for its insidious nature, slow progression and high incidence as a neurodegenerative disease. In the past, diagnosis of AD mainly depended on analysis of a patient's cognitive ability and behavior. Without a unified standard for analysis methods, this is prone to produce incorrect diagnoses. Currently, definitive diagnosis mainly relies on histopathological examination. Because of the advantages of precision, noninvasiveness, low toxicity and high spatiotemporal resolution, fluorescent nanoprobes are suitable for the early diagnosis of AD. This review summarizes the research progress of different kinds of fluorescent nanoprobes for AD diagnosis and therapy in recent years and provides an outlook on the development prospects of fluorescent nanoprobes.

Identifying and Differentiating Topological G-Quadruplex Structures with DNA-Encoded Plasmonic Gold Nanoparticles

DNA G-quadruplexes (G4s) have been identified as critical elements in modulating genomic functions and many other biological processes. Their functions are highly dependent on the primary nucleotides and secondary folding structures. Therefore, to understand their functions, methods to identify and differentiate structures of G4 with speed and accuracy are required but limited. In this report, we have applied a synthetic G4 DNA-encoded nanoparticle approach to identify and differentiate G4 DNA molecules with different topologies and nucleotide residues. We found that the resulting plasmonic properties of the gold nanoparticles, monitored by UV/Vis spectroscopy, are quite sensitive to different G4 structures, including stacking layers, loop sequences, capping bases on G4s, and topological structures. Through these systematic investigations, we demonstrate that this G4-encoded gold nanoparticle approach can be used to profile the G4 structures and distinguish G4s from human telomeres. Such a method may have wide applications in G4 research.