Zn-CD@Eu Ratiometric Fluorescent Probe for the Detection of Dipicolinic Acid, Uric Acid, and Ex Vivo Uric Acid Imaging

Development of reliable methods for the detection of potential biomarkers is of the utmost importance for an early diagnosis of critical diseases and disorders. In this study, a novel lanthanide-functionalized carbon dot-based fluorescent probe Zn-CD@Eu is reported for the ratiometric detection of dipicolinic acid (DPA) and uric acid (UA). The Zn-CD@Eu nanoprobe was obtained from a simple room-temperature reaction of zinc-doped carbon dots (Zn-CD) and the EDTA-Eu lanthanide complex. Under optimal conditions, a good linear response was obtained for DPA in two concentration ranges of 0-55 and 55-100 μM with a limit of detection of 0.53 and 2.2 μM respectively, which is significantly below the infectious dosage of anthrax (∼55 μM). Furthermore, the Zn-CD@Eu/DPA system was employed for the detection of UA with a detection limit of 0.36 μM in the linear range of 0-100 μM. The fluorescent probe was successfully implemented for determining DPA and UA in human blood serum, sweat, and natural water bodies with considerable recovery rates. In addition, the potential of the nanoprobe for ex vivo visualization of UA was demonstrated in fruit fly (Drosophila melanogaster) as a model organism.

A smartphone-intergrated dual-emission fluorescent nanoprobe for visual and ratiometric detection of anthrax biomarkers

A novel dual-emission fluorescent nanoprobe based on rare-earth nanosheets was fabricated to detect 2,6-pyridine dicarboxylic acid (DPA), which is the biomarker of Bacillus anthracis. 2-amino terephthalic acid (BDC-NH2) and surfactant sodium dodecyl sulfate (SDS) were co-intercalated into layered europium hydroxide (LEuH) to prepare the organic/inorganic composite, which was delaminated to obtain the rare-earth nanosheets. The ratio detection of DPA is possible due to the antenna effect between DPA and Eu3+. The nanoprobe shows high accuracy and sensitivity due to the large specific surface area of the rare-earth nanosheets. The limit of detection (LOD) is 4.4 nM for DPA in the range of 0-20 μM. In addition, a more convenient and faster smartphone-based visual detection platform was established based on the obvious color change. This work offers an effective way for developing visual sensing platforms, which opens a new path for designing fluorescent probes with superior sensing capabilities.

Combining surface-accessible Ag and Au colloidal nanomaterials with SERS for in situ analysis of molecule-metal interactions in complex solution environments

The interactions between molecules and noble metal nanosurfaces play a central role in many areas of nanotechnology. The surface chemistry of noble metal surfaces under ideal, clean conditions has been extensively studied; however, clean conditions are seldom met in real-world applications. We developed a sensitive and robust characterization technique for probing the surface chemistry of nanomaterials in the complex environments that are directly relevant to their applications. Surface-enhanced Raman spectroscopy (SERS) can be used to probe the interaction of plasmonic nanoparticles with light to enhance the Raman signals of molecules near the surface of nanoparticles. Here, we explain how to couple SERS with surface-accessible plasmonic-enhancing substrates, which are capped with weakly adsorbing capping ligands such as citrate and chloride ions, to allow molecule-metal interactions to be probed in situ and in real time, thus providing information on the surface orientation and the formation and breaking of chemical bonds. The procedure covers the synthesis and characterization of surface-accessible colloids, the preliminary SERS screening with agglomerated colloids, the synthesis and characterization of interfacial nanoparticle assemblies, termed metal liquid-like films, and the in situ biphasic SERS analysis with metal liquid-like films. The applications of the approach are illustrated using two examples: the probing of π-metal interactions and that of target/ligand-particle interactions on hollow bimetallic nanostars. This protocol, from the initial synthesis of the surface-accessible plasmonic nanoparticles to the final in situ biphasic SERS analysis, requires ~14 h and is ideally suited to users with basic knowledge in performing Raman spectroscopy and wet synthesis of metal nanoparticles.

Zirconium-Directed Supramolecular Self-Assembly of Coenzyme A@GNCs with Enhanced Phosphorescence for Developing Ultrasensitive Tracer Probe of Dipicolinic Acid, a Biomarker of Bacterial Spores

Luminescent gold nanoclusters (GNCs) are a class of attractive quantum-sized nanomaterials bridging the gap between organogold complexes and gold nanocrystals. They typically have a core-shell structure consisting of a Au(I)-organoligand shell-encapsulated few-atom Au(0) core. Their luminescent properties are greatly affected by their Au(I)-organoligand shell, which also supports the aggregation-induced emission (AIE) effect. However, so far, the luminescent Au nanoclusters encapsulated with the organoligands containing phosphoryl moiety have rarely been reported, not to mention their AIE. In this study, coenzyme A (CoA), an adenosine diphosphate (ADP) analogue that is composed of a bulky 5-phosphoribonucleotide adenosine moiety connected to a long branch of vitamin B5 (pantetheine) via a diphosphate ester linkage and ubiquitous in all living organisms, has been used to synthesize phosphorescent GNCs for the first time. Interestingly, the synthesized phosphorescent CoA@GNCs could be further induced to generate AIE via the PO32- and Zr4+ interactions, and the observed AIE was found to be highly specific to Zr4+ ions. In addition, the enhanced phosphorescent emission could be quickly turned down by dipicolinic acid (DPA), a universal and specific component and also a biomarker of bacterial spores. Therefore, a Zr4+-CoA@GNCs-based DPA biosensor for quick, facile, and highly sensitive detection of possible spore contamination has been developed, showing a linear concentration range from 0.5 to 20 μM with a limit of detection of 10 nM. This study has demonstrated a promising future for various organic molecules containing phosphoryl moiety for the preparation of AIE-active metal nanoclusters.

Recent Trends in SERS-Based Plasmonic Sensors for Disease Diagnostics, Biomolecules Detection, and Machine Learning Techniques

Surface-enhanced Raman spectroscopy/scattering (SERS) has evolved into a popular tool for applications in biology and medicine owing to its ease-of-use, non-destructive, and label-free approach. Advances in plasmonics and instrumentation have enabled the realization of SERS's full potential for the trace detection of biomolecules, disease diagnostics, and monitoring. We provide a brief review on the recent developments in the SERS technique for biosensing applications, with a particular focus on machine learning techniques used for the same. Initially, the article discusses the need for plasmonic sensors in biology and the advantage of SERS over existing techniques. In the later sections, the applications are organized as SERS-based biosensing for disease diagnosis focusing on cancer identification and respiratory diseases, including the recent SARS-CoV-2 detection. We then discuss progress in sensing microorganisms, such as bacteria, with a particular focus on plasmonic sensors for detecting biohazardous materials in view of homeland security. At the end of the article, we focus on machine learning techniques for the (a) identification, (b) classification, and (c) quantification in SERS for biology applications. The review covers the work from 2010 onwards, and the language is simplified to suit the needs of the interdisciplinary audience.

Assessment of a 50:50 mixture of two Bacillus subtilis strains as growth promoters for finishing pigs: productivity improvement and noxious gas reduction

In this study, we aimed to assess the potential of a 50:50 mixture of two Bacillus subtilis strains in improving the productivity and health of finishing pigs and reducing noxious gases in their feces. These strains were found to abundantly secrete surfactin which has been shown to alleviate the effects of lipopolysaccharides in vitro. For the 10-wk experiment, 200 finishing pigs ([Landrace × Yorkshire] × Duroc) with an average body weight of 54.15 ± 1.70 kg were divided into four groups. Each group was fed with a basal diet supplemented with an equal amount of spores from the two B. subtilis strains at different levels: control group, no addition; treatment group 1, 0.5 × 109; treatment group 2, 1.0 × 109; treatment group 3, 1.5 × 109 cfu·kg-1 addition. During the 10-wk feeding period, dietary supplementation of 0.5 × 109, 1.0 × 109, and 1.5 × 109 cfu·kg-1 of the spore cells from these two strains resulted in a 0.9%, 1.9%, and 2.5% increase in body weight, respectively (linear P < 0.095). During the final 5 wk, the average daily gain (ADG) in weight was increased by the strains at amounts of 0.5 × 109, 1.0 × 109, and 1.5 × 109 cfu·kg-1 with a clear dosage effect (linear P < 0.05). However, neither the gain-to-feed ratio, the average daily feed intake, nor nutrient digestibility was affected by the supplementation. In blood, the endotoxin lipopolysaccharides, and two liver toxicity indicator enzymes; aspartate aminotransferase and lactate dehydrogenase were decreased (P < 0.05) in the 1.0 × 109 cfu·kg-1 spores-feeding group. Furthermore, four noxious gases were reduced by 8 to 20% in feces excreted by pigs fed with 1.5 × 109 cfu·kg-1 spores with a linear dosage effect (linear P < 0.001 to 0.05) during the final 5 wk. Our findings suggest that the mixture of B. subtilis strains may enhance the productivity of finishing pigs by reducing the risk of mild endotoxemia, rather than increasing digestibility or daily feed intake. Therefore, these Bacillus strains have the potential to act as growth promoters for pigs, leading to improved animal health and productivity. These results have significant implications for pig farmers seeking to optimize the health and growth of their animals.

Integrated ratiometric fluorescence probe-based acoustofluidic platform for visual detection of anthrax biomarker

The sensitive detection of dipicolinic acid (DPA) as an excellent biomarker of Bacillus anthracis, especially through visual point-of-care testing, is significant for accurate and rapid diagnosis of anthrax to timely prevent anthrax disease or biological terrorist attack. Herein, an acoustofluidics-based colorimetric platform with the integrated ratiometric fluorescence probe (INT-probe) was fabricated, which improved the sensitivity of visual detection for DPA and overcame the poor reproducibility of the existing acoustofluidics-assisted colorimetric analysis. For the design of INT-probe, Eu³⁺-EDTA complex as sensing moiety was grafted onto the surface of blue organosilane-functionalized carbon dots (SiCDs)-doped SiO₂ nanoparticles (NPs). Upon exposure to DPA, Eu³⁺ was sensitized by DPA to emit red luminescence, while the SiCDs as reference inside the SiO₂ NPs still kept the blue fluorescence unchanged. Attributed to the acoustic radiation force-driven enrichment of the INT-probe, slight color changes caused by low concentration of DPA could be amplified and distinguished by naked-eyes/smartphone. With the increase of DPA concentration, obvious color variations of INT-probe/DPA aggregates from blue to pink could be observed, and the color information of the fluorescent aggregates was converted to red, green and blue values for quantitative analysis, whose lowest detectable concentration reached 100 nM that is about 2-3 orders of magnitude lower than the infectious dosage of Bacillus anthracis spores (60 μM). Importantly, benefiting from the great color signal enhancement by acoustofluidic sensing platform, the usage of Eu³⁺ reduced to as low as 0.273 μmol per gram of SiO₂ NPs, providing a meaningful way to utilize lanthanide resource efficiently.

A time-resolved ratiometric luminescent anthrax biomarker nanosensor based on Ir(III) complex-doped coordination polymer network

Herein, an Ir(III) complex-doped coordination polymer networks (Ir(III)@GMP-Eu3+) is firstly fabricated for the ratiometric luminescent detection of anthrax biomarker 2,6-dipicolinic acid (DPA) through time-resolved emission spectra (TRES) measurement. The detection...

Three novel metal-organic frameworks with different coordination modes for trace detection of anthrax biomarkers

Dipicolinic acid (DPA) is an anthrax biomarker. Its serious consequences make its detection a great need. In this paper, three novel metal-organic frameworks (MOFs) with different coordination modes were synthesized by a simple solvothermal method, which can be used as highly efficient fluorescence sensors for the highly selective and sensitive trace detection of DPA. MOFs 1-3 showed rapid responses to DPA (<30 s), and the limits of detection (LODs) were calculated to be 1.01 × 10^-6 M^-1 (MOF 1), 1.17 × 10^-6 M^-1 (MOF 2) and 2.07 × 10^-6 M^-1 (MOF 3). DPA detection based on MOFs 1-3 in fetal bovine serum is highly reliable based on the high recovery rates (90% to 115%). Hence, the three MOF-based sensors can be used in the real-time detection of DPA.

Learning from Nature: Bacterial Spores as a Target for Current Technologies in Medicine (Review)

The capability of some representatives of Clostridium spp. and Bacillus spp. genera to form spores in extreme external conditions long ago became a subject of medico-biological investigations. Bacterial spores represent dormant cellular forms of gram-positive bacteria possessing a high potential of stability and the capability to endure extreme conditions of their habitat. Owing to these properties, bacterial spores are recognized as the most stable systems on the planet, and spore-forming microorganisms became widely spread in various ecosystems.

Spore-forming bacteria have been attracted increased interest for years due to their epidemiological danger. Bacterial spores may be in the quiescent state for dozens or hundreds of years but after they appear in the favorable conditions of a human or animal organism, they turn into vegetative forms causing an infectious process. The greatest threat among the pathogenic spore-forming bacteria is posed by the causative agents of anthrax (B. anthracis), food toxicoinfection (B. cereus), pseudomembranous colitis (C. difficile), botulism (C. botulinum), gas gangrene (C. perfringens).

For the effective prevention of severe infectious diseases first of all it is necessary to study the molecular structure of bacterial spores and the biochemical mechanisms of sporulation and to develop innovative methods of detection and disinfection of dormant cells. There is another side of the problem: the necessity to investigate exo- and endospores from the standpoint of obtaining similar artificially synthesized models in order to use them in the latest medical technologies for the development of thermostable vaccines, delivery of biologically active substances to the tissues and intracellular structures. In recent years, bacterial spores have become an interesting object for the exploration from the point of view of a new paradigm of unicellular microbiology in order to study microbial heterogeneity by means of the modern analytical tools.

Advanced Raman Spectroscopy Detection of Oxidative Damage in Nucleic Acid Bases: Probing Chemical Changes and Intermolecular Interactions in Guanosine at Ultralow Concentration

DNA/RNA synthesis precursors are especially vulnerable to damage induced by reactive oxygen species occurring following oxidative stress. Guanosine triphosphates are the prevalent oxidized nucleotides, which can be misincorporated during replication, leading to mutations and cell death. Here, we present a novel method based on micro-Raman spectroscopy, combined with ab initio calculations, for the identification, detection, and quantification of oxidized nucleotides at low concentration. We also show that the Raman signature in the terahertz spectral range (<100 cm^-1) contains information on the intermolecular assembly of guanine in tetrads, which allows us to further boost the oxidative damage detection limit. Eventually, we provide evidence that similar analyses can be carried out on samples in very small volumes at very low concentrations by exploiting the high sensitivity of surface-enhanced Raman scattering combined with properly designed superhydrophobic substrates. These results pave the way for employing such advanced spectroscopic methods for quantitatively sensing the oxidative damage of nucleotides in the cell.

The Role of Raman Spectroscopy Within Quantitative Metabolomics

Ninety-four years have passed since the discovery of the Raman effect, and there are currently more than 25 different types of Raman-based techniques. The past two decades have witnessed the blossoming of Raman spectroscopy as a powerful physicochemical technique with broad applications within the life sciences. In this review, we critique the use of Raman spectroscopy as a tool for quantitative metabolomics. We overview recent developments of Raman spectroscopy for identification and quantification of disease biomarkers in liquid biopsies, with a focus on the recent advances within surface-enhanced Raman scattering-based methods. Ultimately, we discuss the applications of imaging modalities based on Raman scattering as label-free methods to study the abundance and distribution of biomolecules in cells and tissues, including mammalian, algal, and bacterial cells.

Ultra-sensitive reusable SERS sensor for multiple hazardous materials detection on single platform

We demonstrate the detection of dipicolinic acid, (DPA), a biomarker of bacterial spores for Bacillus anthracis, 2,4-Dinitrotoluene (DNT) and picric acid (PA) nitroaromatic hazardous chemicals on ultra-sensitive, reusable femtosecond laser textured Au nanostructures decorated with hierarchical AuNPs as a SERS substrate. The AuNPs were achieved by ablating an Au sheet using two different laser scan speeds (1 and 0.1 mm/s) in linear and crossed patterns. The morphological studies revealed dense hierarchical nanostructures decorated with spherical AuNPs possessing 30-40 nm in size in 0.1 mm/s laser scan. The limits of detection (LOD) of the sensor were determined from the detailed SERS measurements and were estimated to be 0.83 pg/L, 3.6 pg/L and 2.3 pg/L for DPA, DNT, and PA, respectively. To the best of our knowledge, the achieved sensitivity is nearly 2 orders improved for DPA when compared with the currently reported LODs using other techniques and 1 order in the case of SERS. Moreover, for DNT and PA the LODs were found to be either superior or comparable with recent reports. We have also demonstrated the competence of our SERS substrates by testing a few real samples (water spiked with these analytes) and again obtained very good sensitivity.

Rare-Earth Eu3+/Gold Nanocluster Ensemble-Based Fluorescent Photoinduced Electron Transfer Sensor for Biomarker Dipicolinic Acid Detection

The use of metal ions to bridge the fluorescent materials to target analytes has been demonstrated to be a promising way to sensor design. Herein, the effect of rare-earth ions on the fluorescence of l-methionine-stabilized gold nanoclusters (Met-AuNCs) was investigated. It was found that europium (Eu³⁺) can significantly suppress the emission of Met-AuNCs, while other rare-earth ions showed a negligible impact. The mechanism on the observed fluorescence quenching of Met-AuNCs triggered by Eu³⁺ was systematically explored, with results revealing the dominant role of photoinduced electron transfer (PET). Eu³⁺ can bind to the surface of Met-AuNCs by the coordination effect and accepts the electron from the excited Met-AuNCs, which results in Met-AuNC fluorescence suppression. After introducing dipicolinic acid (DPA), an excellent biomarker for spore-forming pathogens, Eu³⁺ was removed from the surface of Met-AuNCs owing to the higher binding affinity between Eu³⁺ and DPA. Consequently, an immediate fluorescence recovery occurred when DPA was present in the system. Based on the Met-AuNC/Eu³⁺ ensemble, we then established a simple and sensitive fluorescence strategy for turn-on determination of biomarker DPA, with a linear range of 0.2-4 μM and a low limit of detection of 110 nM. The feasibility of the proposed method was further validated by the quantitative detection of DPA in the soil samples. We believe that this study would significantly facilitate the construction of metal-ion-mediated PET sensors for the measurement of various interested analytes by applying fluorescent AuNCs as detection probes.

Cu(II)-assisted orange/green dual-emissive carbon dots for the detection and imaging of anthrax biomarker

The spores of Bacillus anthracis are highly deadly to human beings and animals, and are concurrently potential biological warfare agents. Hence, the rapid and sensitive monitoring Bacillus anthracis biomarker, dipicolinic acid (DPA), is very desirable. Herein, orange/green dual-emissive carbon dots (OG-CDs) were synthesized via the hydrothermal approach. The OG-CDs not only emitted dual fluorescence at 527 and 590 nm under the single 503 nm excitation, but also exhibited excellent water solubility, good photostability and great salt tolerance. The fluorescence of the OG-CDs at 527 nm can be completely quenched when chelated with Cu(II). However, because of the stronger chelation between DPA and Cu(II), the fluorescence restored rapidly on subsequent addition of DPA. As such, the CD-Cu(II) system can be used for determination of DPA based on the fluorescence "off-on" response. Under optimum conditions, the detection limit for DPA was 56 nM, with a linear range of 0.5-12.5 μM. The established CD-Cu(II) based spectrofluorometric method has been applied to the analysis of DPA in real water samples with recoveries of 93.6%-104.3%. More remarkably, the CD-Cu(II) probe also has been successfully applied for the imaging of DPA in Escherichia coli with excellent bio-compatibility.

Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing

This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.

Bacteria Detection: From Powerful SERS to Its Advanced Compatible Techniques

The rapid, highly sensitive, and accurate detection of bacteria is the focus of various fields, especially food safety and public health. Surface-enhanced Raman spectroscopy (SERS), with the advantages of being fast, sensitive, and nondestructive, can be used to directly obtain molecular fingerprint information, as well as for the on-line qualitative analysis of multicomponent samples. It has therefore become an effective technique for bacterial detection. Within this progress report, advances in the detection of bacteria using SERS and other compatible techniques are discussed in order to summarize its development in recent years. First, the enhancement principle and mechanism of SERS technology are briefly overviewed. The second part is devoted to a label-free strategy for the detection of bacterial cells and bacterial metabolites. In this section, important considerations that must be made to improve bacterial SERS signals are discussed. Then, the label-based SERS strategy involves the design strategy of SERS tags, the immunomagnetic separation of SERS tags, and the capture of bacteria from solution and dye-labeled SERS primers. In the third part, several novel SERS compatible technologies and applications in clinical and food safety are introduced. In the final part, the results achieved are summarized and future perspectives are proposed.

Novel Synthesis of Thiolated Gold Nanoclusters Induced by Lanthanides for Ultrasensitive and Luminescent Detection of the Potential Anthrax Spores' Biomarker

In this study, we reported a facile, one-pot, and "green" synthesis of glutathione-protected gold nanoclusters (GSH@AuNCs) initiated by samarium (Sm³⁺) lanthanides for the first time. Sm³⁺ lanthanides more efficiently induced the formation of GSH@AuNCs with significantly enhanced luminescence than other lanthanides or heavy metal ions (Cd²⁺, Pb²⁺) did. Using this strategy, a detection for Sm³⁺ was made with a linearity range of (10.0-100.0 μM) and a limit of detection (LOD) of 0.5 μM. The Sm³⁺-based GSH@AuNCs were characterized by eco-friendliness, photostability, and low-cost synthesis with low biological toxicity and had great potential in the application for biosensing and bioimaging. They were successfully employed in the detection of dipicolinic acid (DPA), a well-reported biomarker for sensing potential infection by strongly hazardous anthrax spores. A good linear response was obtained for DPA detection ranging from 1.0 to 120.0 μM with a low LOD of 0.1 μM, which was much lower (600 times) than the infectious dosage of anthrax spores (6 × 10^-5 M). The detection was due to the strong binding affinity and strong chelation capability of DPA to Sm³⁺ lanthanides, which caused the dissociation of the aggregates with an obvious decrease or even a turning-off effect of their luminescence.

Present and Future of Surface-Enhanced Raman Scattering

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article.

Placeholder Strategy with Upconversion Nanoparticles-Eriochrome Black T Conjugate for a Colorimetric Assay of an Anthrax Biomarker

The timely warning of the germination of bacterial spores and their prevention are highly important to minimize their potential detrimental effects and for disease control. Thus, a sensitive and selective assay of biomarkers is most desirable. In this work, a nanoprobe is constructed by conjugating lanthanide upconversion nanoparticles (UCNPs) with sodium tripolyphosphate (TPP) and eriochrome black T (EBT). The nanoprobe, UCNPs-TPP/EBT, serves as a platform for the detection of the anthrax biomarker, dipicolinic acid (DPA). In principle, DPA displaces EBT from the UCNPs-TPP/EBT nanoconjugate, resulting in a color change from magenta to blue because of the release of free EBT into the aqueous solution. The binding sites on UCNPs are partly preblocked with TPP as the placeholder molecule, leaving a desired number of binding sites for EBT conjugation. On the basis of this dye displacement reaction, a novel colorimetric assay protocol for DPA is developed, deriving a linear calibration range from 2 to 200 μM with a detection limit of 0.9 μM, which is well below the infectious dose of the spores (60 μM). The assay platform exhibits excellent anti-interference capability when treating a real biological sample matrix. The present method is validated by the analysis of DPA in human serum, and its practical application is further demonstrated by monitoring the DPA release upon spore germination.

Quantitative surface-enhanced Raman spectroscopy of single bases in oligodeoxynucleotides

To address the question of whether the SERS signals of ss-DNA are simply combinations of the signals from the individual bases that comprise the sequence, SERS spectra of unmodified ss-DNA sequences were obtained using a hydroxylamine-reduced Ag colloid aggregated with MgSO₄. Initially, synthetic oligodeoxynucleotides with systematic structural variations were used to investigate the effect of adding single nucleobases to the 3' terminus of 10-mer and 20-mer sequences. It was found that the resulting SERS difference spectra could be used to identify the added nucleobases since they closely matched reference spectra of the same nucleobase. Investigation of the variation in intensity of an adenine probe which was moved along a test sequence showed there was a small end effect where nucleobases near the 3' terminus gave slightly larger signals but the effect was minor (30%). More significantly, in a sample set comprising 25-mer sequences where A, T or G nucleobases were substituted either near the centres of the sequences or the 5' or 3' ends, the SERS difference spectra only matched the expected form in approximately half the cases tested. This variation appeared to be due to changes in secondary structure induced by altering the sequences since uncoiling the sequences in a thermal pre-treatment step gave difference spectra which in all cases matched the expected form. Multivariate analysis of the set of substitution data showed that 99% of the variance could be accounted for in a model with just three factors whose loadings matched the spectra of the A, T, and G nucleobases and which contained no positional information. This suggests that aside from the differences in secondary structure which can be eliminated by thermal pre-treatment, the SERS spectra of the 25-mers studied here are simply the sum of their component parts. Although this means that SERS provides very little information on the primary sequence it should be excellent for the detection of post-transcription modifications to DNA which can occur at multiple positions along a given sequence.

Confining analyte droplets on visible Si pillars for improving reproducibility and sensitivity of SALDI-TOF MS

We present a universal method to efficiently improve reproducibility and sensitivity of surface-assisted laser desorption/ionization time of flight mass spectrometry (SALDI-TOF MS). In this method, the Si pillar array with unique surface wettability is used as substrate for ionizing analyte. The Si pillar is fabricated based on the combination of photolithography and metal-assisted chemical etching, which is of hydrophilic top and hydrophobic bottom and side wall. Based on the surface wettability of the Si pillar, a droplet of an aqueous analyte solution can be confined on the top of the Si pillar. After evaporation of solvent, an analyte deposition spot is formed on the top of Si pillar. The visible size of the Si pillar allows the sample spot to be easily found. Meanwhile, the diameter of the Si pillar is smaller than that of the laser, allowing the observation of all analyte molecules under one laser shot. Therefore, the reproducibility and sensitivity are highly improved with this method, which allows for the quantitative analysis. Furthermore, this method is applicable for different analytes dissolved in water, including amino acids, dye molecules, polypeptides, and polymers. The application of this substrate is demonstrated by analyzing real samples at low concentration. It should be a promising method for sensitive and reproducible detection for SALDI-TOF MS. Graphical abstract ᅟ.

Applications of SERS in the Detection of Stress-Related Substances

A wide variety of biotic and abiotic stresses continually attack plants and animals, which adversely affect their growth, development, reproduction, and yield realization. To survive under stress conditions, highly sophisticated and efficient tolerance mechanisms have been evolved to adapt to stresses, which consist of the variation of effector molecules playing vital roles in physiological regulation. The development of a sensitive, facile, and rapid analytical methods for stress factors and effector molecules detection is significant for gaining deeper insight into the tolerance mechanisms. As a nondestructive analysis technique, surface-enhanced Raman spectroscopy (SERS) has unique advantages regarding its biosensing applications. It not only provides specific fingerprint spectra of the target molecules, conformation, and structure, but also has universal capacity for simultaneous detection and imaging of targets owing to the narrow width of the Raman vibrational bands. Herein, recent progress on biotic and abiotic stresses, tolerance mechanisms and effector molecules is summarized. Moreover, the development and promising future trends of SERS detection for stress-related substances combined with nanomaterials as substrates and SERS tags are discussed. This comprehensive and critical review might shed light on a new perspective for SERS applications.

Hydroxyapatite nanoparticle based fluorometric turn-on determination of dipicolinic acid, a biomarker of bacterial spores

Hydroxyapatite nanoparticles (HAP-NPs) were rendered fluorescence by doping with Eu(III) ion. The resulting fluorescent NPs are shown to be viable probes for sensitive and selective determination of dipicolinic acid (DPA), a major constituent of bacterial spores as used in bioterrorism. It is found that the addition of DPA to solutions of such HAP-NPs result in an enhancement of fluorescence due to the coordination of DPA with the Eu(III) dopant. The assay allows DPA to be detected in the 0.1 to 40 μM concentration range and with a 77 nM detection limit. The assay was applied to the detection of spores of Bacillus subtilis. The attractive properties of the probe make it a promising candidate for used in rapid detection of pathogenic bacterial spores. Graphical abstract Fluorescent hydroxyapatite nanoparticles (HAP-NPs) are shown to be a viable probe for detection of dipicolinic acid, a major constituent of bacterial spores. The red asterisks represent the fluorescence intensity of the HAP-NPs.

Facing Challenges in Real-Life Application of Surface-Enhanced Raman Scattering: Design and Nanofabrication of Surface-Enhanced Raman Scattering Substrates for Rapid Field Test of Food Contaminants

Surface-enhanced Raman scattering (SERS) is capable of detecting a single molecule with high specificity and has become a promising technique for rapid chemical analysis of agricultural products and foods. With a deeper understanding of the SERS effect and advances in nanofabrication technology, SERS is now on the edge of going out of the laboratory and becoming a sophisticated analytical tool to fulfill various real-world tasks. This review focuses on the challenges that SERS has met in this progress, such as how to obtain a reliable SERS signal, improve the sensitivity and specificity in a complex sample matrix, develop simple and user-friendly practical sensing approach, reduce the running cost, etc. This review highlights the new thoughts on design and nanofabrication of SERS-active substrates for solving these challenges and introduces the recent advances of SERS applications in this area. We hope that our discussion will encourage more researches to address these challenges and eventually help to bring SERS technology out of the laboratory.

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.

Bioanalytical applications of surface-enhanced Raman spectroscopy: de novo molecular identification

Surface enhanced Raman scattering (SERS) has become a powerful technique for trace analysis of biomolecules. The use of SERS-tags has evolved into clinical diagnostics, the enhancement of the intrinsic signal of biomolecules on SERS active materials shows tremendous promise for the analysis of biomolecules and potential biomedical assays. The detection of the de novo signal from a wide range of biomolecules has been reported to date. In this review, we examine different classes of biomolecules for the signals observed and experimental details that enable their detection. In particular, we survey nucleic acids, amino acids, peptides, proteins, metabolites, and pathogens. The signals observed show that the interaction of the biomolecule with the enhancing nanostructure has a significant influence on the observed spectrum. Additional experiments demonstrate that internal standards can correct for intensity fluctuations and provide quantitative analysis. Experimental methods that control the interaction at the surface are providing for reproducible SERS signals. Results suggest that combining advances in methodology with the development of libraries for SERS spectra may enable the characterization of biomolecules complementary to other existing methods.

Quantitative detection of codeine in human plasma using surface-enhanced Raman scattering via adaptation of the isotopic labelling principle

In this study surface-enhanced Raman scattering (SERS) combined with the isotopic labelling (IL) principle has been used for the quantification of codeine spiked into both water and human plasma.