Fabrication of large-scale gold nanoplate films as highly active SERS substrates for label-free DNA detection

Surface-Enhanced Raman Spectroscopy (SERS)-Based Sensors for Deoxyribonucleic Acid (DNA) Detection

Surface-enhanced Raman spectroscopy (SERS) has emerged as a powerful technique for the detection and analysis of biomolecules due to its high sensitivity and selectivity. In recent years, SERS-based sensors have received significant attention for the detection of deoxyribonucleic acid (DNA) molecules, offering promising applications in fields such as medical diagnostics, forensic analysis, and environmental monitoring. This paper provides a concise overview of the principles, advancements, and potential of SERS-based sensors for DNA detection. First, the fundamental principles of SERS are introduced, highlighting its ability to enhance the Raman scattering signal by several orders of magnitude through the interaction between target molecules with metallic nanostructures. Then, the fabrication technologies of SERS substrates tailored for DNA detection are reviewed. The performances of SERS substrates previously reported for DNA detection are compared and analyzed in terms of the limit of detection (LOD) and enhancement factor (EF) in detail, with respect to the technical parameters of Raman spectroscopy (e.g., laser wavelength and power). Additionally, strategies for functionalizing the sensor surfaces with DNA-specific capture probes or aptamers are outlined. The collected data can be of help in selecting and optimizing the most suitable fabrication technology considering nucleotide sensing applications with Raman spectroscopy.

Raman spectroscopy and its plasmon-enhanced counterparts: A toolbox to probe protein dynamics and aggregation

Protein unfolding and aggregation are often correlated with numerous diseases such as Alzheimer's, Parkinson's, Huntington's, and other debilitating neurological disorders. Such adverse events consist of a plethora of competing mechanisms, particularly interactions that control the stability and cooperativity of the process. However, it remains challenging to probe the molecular mechanism of protein dynamics such as aggregation, and monitor them in real-time under physiological conditions. Recently, Raman spectroscopy and its plasmon-enhanced counterparts, such as surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS), have emerged as sensitive analytical tools that have the potential to perform molecular studies of functional groups and are showing significant promise in probing events related to protein aggregation. We summarize the fundamental working principles of Raman, SERS, and TERS as nondestructive, easy-to-perform, and fast tools for probing protein dynamics and aggregation. Finally, we highlight the utility of these techniques for the analysis of vibrational spectra of aggregation of proteins from various sources such as tissues, pathogens, food, biopharmaceuticals, and lastly, biological fouling to retrieve precise chemical information, which can be potentially translated to practical applications and point-of-care (PoC) devices. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Diagnostic Tools > Diagnostic Nanodevices Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

Self-assembly of Au@AgNR along M13 framework: A SERS nanocarrier for bacterial detection and killing

Self-assembled functional nanomaterials with electromagnetic hot spots are crucial and highly desirable in surface-enhanced Raman scattering (SERS). Due to its versatile biological scaffold, the M13 phage has been employed to produce novel nano-building blocks and devices. In this study, we propose a novel M13 phage-based SERS nanocarrier, that utilizes the pVIII capsid in M13 to conjugate Au@Ag core-shell nanorod (Au@AgNR) with linker carboxy-PEG-thiol (M13-Au@AgNR) and the pIII capsid to specifically target Escherichia coli (E. coli). The M13-Au@AgNR@DTTC (3,3'- diethylthiocarbocyanine iodide) SERS probe was used to detect E. coli in a concentration range of 6 to 6 × 105 cfu/mL, achieving a limit of detection (LOD) of 0.5 cfu/mL. The proposed SERS platform was also tested in real samples, showing good recoveries (92%-114.3%) and a relative standard deviation (RSD) of 1.2%-4.7%. Furthermore, the system demonstrated high antibacterial efficiency against E. coli, approximately 90%, as measured by the standard plate-count method. The investigation provides an effective strategy for in vitro bacteria detection and inactivation.

Substrate-Free Fabrication of Single-Crystal Two-Dimensional Gold Nanoplates for Catalytic Application

Two-dimensional (2D) gold nanoplates (AuNPLs) have shown potential in catalysis, photonics, electronics, sensing, and biomedicine fields due to their high aspect ratio, fascinating surface chemistry, and quantum-size effect. Therefore, the synthesis of substrate-free, size-controlled single-crystal gold (Au) nanoplates is highly desirable for the development of catalysis and optical near-field enhancement applications. EDTA and hydroxide anions were used in this study to stimulate the formation of microscale single-crystal gold nanoplates under hydrothermal conditions. The reaction temperature, amount of EDTA, and hydroxyl anions all have a significant effect on the morphologies and size distributions of the gold nanoplates. The gold nanoplates had an average side length of between 3 and 11 μm. The application of the microscale single-crystal gold nanoplates as a nanocatalyst proved their excellent catalytic activity and recyclability for the catalysis of 4-nitrophenol to 4-aminophenol, implying that the large-size gold nanoplates were promising in heterogeneous catalysis applications.

Recent Advances in Engineered Noble Metal Nanomaterials as a Surface-Enhanced Raman Scattering Active Platform for Cancer Diagnostics

Recently, noble metal nanomaterials have been extensively studied in the fields of biosensing, environmental catalysis, and cancer diagnosis and treatment, due to their excellent electrical conductivity, high surface area, and individual physical and optical properties. Early research on the surface-enhanced Raman scattering (SERS) effect was focused on the cognition of the SERS phenomenon and enhancing its sensitivity for single-molecule detection. With the development of nanomaterials and nanotechnology, the advances and applications based on SERS substrates have been accelerated. Among them, noble metal nanomaterials are mainly used as SERS-active substrates to enhance SERS signals owing to their compelling surface plasmon resonance (SPR) properties. This review provides recent advances, perspectives, and challenges in SERS assays based on engineered noble metal nanomaterials for early cancer diagnosis.

Facial Fabrication of Large-Scale SERS-Active Substrate Based on Self-Assembled Monolayer of Silver Nanoparticles on CTAB-Modified Silicon for Analytical Applications

Surface-enhanced Raman spectroscopy (SERS) has been proven to be a promising analytical technique with sensitivity at the single-molecule level. However, one of the key problems preventing its real-world application lies in the great challenges that are encountered in the preparation of large-scale, reproducible, and highly sensitive SERS-active substrates. In this work, a new strategy is developed to fabricate an Ag collide SERS substrate by using cetyltrimethylammonium bromide (CTAB) as a connection agent. The developed SERS substrate can be developed on a large scale and is highly efficient, and it has high-density “hot spots” that enhance the yield enormously. We employed 4-methylbenzenethiol(4-MBT) as the SERS probe due to the strong Ag–S linkage. The SERS enhancement factor (EF) was calculated to be ~2.6 × 10⁶. The efficacy of the proposed substrate is demonstrated for the detection of malachite green (MG) as an example. The limit of detection (LOD) for the MG assay is brought down to 1.0 × 10⁻¹¹ M, and the relative standard deviation (RSD) for the intensity of the main Raman vibration modes (1620, 1038 cm⁻¹) is less than 20%.

Film wrap nanoparticle system with the graphene nano-spacer for SERS detection

Film wrap nanoparticle system (FWPS) is proposed and fabricated to perform SERS effect, where the Ag nanoparticle was completely wrapped by Au film and the double-layered graphene was selected as the sub-nano spacer. In this system, the designed nanostructure can be fully rather than partly used to generate hotspots and absorb probe molecules, compared to the nanoparticle to nanoparticle system (PTPS) or nanoparticle to film system (PTFS). The optimal fabricating condition and performance of this system were studied by the COMSOL Multiphysics. The simulation results show that the strongly large-scale localized electromagnetic field appears in the whole space between the Ag nanoparticle and Au film. The experimental results show that the FWPS presents excellent sensitivity (crystal violet (CV): 10^-11 M), uniformity, stability and high enhancement factor (EF: 2.23×10⁸). Malachite green (MG; 10^-10 M) on the surface of fish and DNA strands with different base sequence (A, T, C) were successfully detected. These advanced results indicate that FWPS is highly promising to be applied for the detection of environmental pollution and biomolecules.

Ritz Method in Vibration Analysis for Embedded Single-Layered Graphene Sheets Subjected to In-Plane Magnetic Field

Vibrations of single-layered graphene sheets subjected to a longitudinal magnetic field are considered. The Winkler-type and Pasternak-type foundation models are employed to reproduce the surrounding elastic medium. The governing equation is based on the modified couple stress theory and Kirchhoff–Love hypotheses. The effect of the magnetic field is taken into account due to the Lorentz force deriving from Maxwell’s equations. The developed approach is based on applying the Ritz method. The proposed method is tested by a comparison with results from the existing literature. The numerical calculations are performed for different boundary conditions, including the mixed ones. The influence of the material length scale parameter, the elastic foundation parameters, the magnetic parameter and the boundary conditions on vibration frequencies is studied. It is observed that an increase of the magnetic parameter, as well as the elastic foundation parameters, brings results closer to the classical plate theory results. Furthermore, the current study can be applied to the design of microplates and nanoplates and their optimal usage.

Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We?

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

Highly Sensitive and Reproducible SERS Sensor for Biological pH Detection Based on a Uniform Gold Nanorod Array Platform

Conventional research on surface-enhanced Raman scattering (SERS)-based pH sensors often depends on nanoparticle aggregation, whereas the variability in nanoparticle aggregation gives rise to poor repeatability in the SERS signal. Herein, we fabricated a gold nanorod array platform via an efficient evaporative self-assembly method. The platform exhibits great SERS sensitivity with an enhancement factor of 5.6 × 10⁷ and maintains excellent recyclability and reproducibility with relative standard deviation (RSD) values of less than 8%. On the basis of the platform, we developed a highly sensitive bovine serum albumin (BSA)-coated 4-mercaptopyridine (4-MPy)-linked (BMP) SERS-based pH sensor to report pH ranging from pH 3.0 to pH 8.0. The intensity ratio variation of 1004 and 1096 cm^-1 in 4-MPy showed excellent pH sensitivity, which decreased as the surrounding pH increased. Furthermore, this BMP SERS-based pH sensor was employed to measure the pH value in C57BL/6 mouse blood. We have demonstrated that the pH sensor has great advantages such as good stability, reliability, and accuracy, which could be extended for the design of point-of-care devices.

Tunable porous silver nanostructures for efficient surface-enhanced Raman scattering detection of trace pesticide residues

Silver porous nanostructures with tunable porosity were fabricated as an excellent enhancing substrate for SERS detection of trace pesticide residues.

A silica-based SERS chip for rapid and ultrasensitive detection of fluoride ions triggered by a cyclic boronate ester cleavage reaction

Chemical sensing for the convenient detection of trace aqueous fluoride ions (F^-) has been widely explored with the use of various sensing materials and techniques. It still remains a challenge to achieve ultrasensitive but simple, rapid, and inexpensive detection of F^- for environmental monitoring and protection. Here we reported a novel surface-enhanced Raman scattering (SERS) nanosensor, fluorescein phenylboronic acid covalently linked to 1,4-dimercapto-2,3-butanediol modified Au@Ag NPs by a cyclic boronate ester (Flu-PBA-Diol-Au@Ag NPs), for the rapid and ultrasensitive detection of F^-. Once the Flu-PBA approached the surface of Au@Ag NPs, the Raman signals of Flu-PBA were remarkably enhanced due to the strong SERS effect. However, the presence of F^- will induce the cleavage reaction of the cyclic boronate ester into the trifluoroborate anion (3F-Flu-PBA) and diol. The 3F-Flu-PBA molecules exfoliated from the surface of Au@Ag NPs, and the SERS signals of the nanosensor were quenched. Following the sensing mechanism, a silica-based SERS chip has been fabricated by the assembly of Flu-PBA-Diol-Au@Ag NPs on a piece of silicon wafer. The silica-based SERS chips showed high sensitivity for aqueous F^-, and the limit of detection (LOD) could reach as low as 0.1 nM. Each test using the SERS chip only needs a droplet of 20 μL sample and is accomplished within ∼10 min. The silica-based SERS chip has also been applied to the quantification of F^- in tap water and lake water.

SERS-active metal-dielectric nanostructures integrated in microfluidic devices for label-free quantitative detection of miRNA

In this work, SERS-based microfluidic PDMS chips integrating silver-coated porous silicon membranes were used for the detection and quantitation of microRNAs (miRNAs), which consist of short regulatory non-coding RNA sequences typically over- or under-expressed in connection with several diseases such as oncogenesis. In detail, metal–dielectric nanostructures which provide noticeable Raman enhancements were functionalized according to a biological protocol, adapted and optimized from an enzyme-linked immunosorbent assay (ELISA), for the detection of miR-222. Two sets of experiments based on different approaches were designed and performed, yielding a critical comparison. In the first one, the labelled target miRNA is revealed through hybridization to a complementary thiolated DNA probe, immobilized on the silver nanoparticles. In the second one, the probe is halved into shorter strands (half1 and half2) that interact with the complementary miRNA in two steps of hybridization. Such an approach, taking advantage of the Raman labelling of half2, provides a label-free analysis of the target. After suitable optimisation of the procedures, two calibration curves allowing quantitative measurements were obtained and compared on the basis of the SERS maps acquired on the samples loaded with several miRNA concentrations. The selectivity of the two-step assay was confirmed by the detection of target miR-222 mixed with different synthetic oligos, simulating the hybridization interference coming from similar sequences in real biological samples. Finally, that protocol was applied to the analysis of miR-222 in cellular extracts using an optofluidic multichamber biosensor, confirming the potentialities of SERS-based microfluidics for early-cancer diagnosis.

Dispersing hydrophilic nanoparticles in nonaqueous solvents with superior long-term stability

We report a general and robust polymerization–dissolution strategy for phase transfer of hydrophilic nanoparticles into nonaqueous solvents with a 100% transfer efficiency.

Sensitive determination of chlorogenic acid in pharmaceutical products based on the decoration of 3D macroporous carbon with Au nanoparticles via polyoxometalates

A simple and sensitive electrochemical sensor is constructed for the detection of chlorogenic acid (CGA).

Core-Shell Nanorod Columnar Array Combined with Gold Nanoplate-Nanosphere Assemblies Enable Powerful In Situ SERS Detection of Bacteria

Development of a label-free ultrasensitive nanosensor for detection of bacteria is presented. Sensitive assay for Gram-positive bacteria was achieved via electrostatic attraction-guided plasmonic bifacial superstructure/bacteria/columnar array assembled in one step. Dynamic optical hotspots were formed in the hybridized nanoassembly under wet-dry critical state amplifying efficiently the weak vibrational modes of three representative food-borne Gram-positive bacteria, that is, Staphylococcus xylosus, Listeria monocytogenes, and Enterococcus faecium. These three bacteria with highly analogous Raman spectra can be effectively differentiated through droplet wet-dry critical SERS approach combined with 3D PCA statistical analysis so that highly sensitive discrimination of bacterial species and samples containing mixtures of bacteria can be achieved.

A Nanostructured SERS Switch Based on Molecular Beacon-Controlled Assembly of Gold Nanoparticles

In this paper, highly purified and stable gold nanoparticle (AuNP) dimers connected at the two ends of DNA linkage were prepared by a versatile method. A nanostructured, surface-enhanced Raman scattering (SERS) switching sensor system was fabricated based on the controlled organization of gold nanoparticles (AuNPs) by a DNA nanomachine through the controlled formation/deformation of SERS “hotspots”. This strategy not only opens opportunities in the precise engineering of gap distances in gold-gold nanostructures in a highly controllable and reproducible fashion, but also provides a unique ability to research the origin of SERS and sequence-specific DNA detection.

Gold nanosheets synthesized with red marine alga Actinotrichia fragilis as efficient electrocatalysts toward formic acid oxidation

In this study, gold nanosheets were synthesized with red marine alga (Actinotrichia fragilis) collected from Persian Gulf and used as an electrocatalyst for oxidation of formic acid.

Hybridized enhancement of the SERS detection of chemical and bio-marker molecules through Au nanosphere ornamentation of hybrid amorphous/crystalline Si nanoweb nanostructure biochip devices

We report the fabrication of hybrid Si SERS nanobiosensor biochip devices.

Enzymatic Polymerization on DNA Modified Gold Nanowire for Label-Free Detection of Pathogen DNA

This paper presents a label-free biosensor for the detection of single-stranded pathogen DNA through the target-enhanced gelation between gold nanowires (AuNW) and the primer DNAs branched on AuNW. The target DNA enables circularization of the linear DNA template, and the primer DNA is elongated continuously via rolling circle amplification. As a result, in the presence of the target DNA, a macroscopic hydrogel was fabricated by the entanglement of the elongated DNA with AuNWs as a scaffold fiber for effective gelation. In contrast, very small separate particles were generated in the absence of the target DNA. This label-free biosensor might be a promising tool for the detection of pathogen DNAs without any devices for further analysis. Moreover, the biosensor based on the weaving of AuNW and DNAs suggests a novel direction for the applications of AuNWs in biological engineering.

3D silver nanoparticles decorated zinc oxide/silicon heterostructured nanomace arrays as high-performance surface-enhanced Raman scattering substrates

Three-dimensional (3D) hierarchical nanostructures have been considered as one of the most promising surface-enhanced Raman spectroscopy (SERS) substrates because of the ordered arrangement of high-density hotspots along the third dimension direction. Herein, we reported a unique 3D nanostructure for SERS detection based on silver nanoparticles (AgNPs) decorated zinc oxide/silicon (ZnO/Si) heterostructured nanomace arrays. They were prepared by two steps: (1) Si nanoneedles were grafted onto ZnO nanorod arrays via a catalyst-assisted vapor-liquid-solid (VLS) growth mechanism. (2) AgNPs were rapidly immobilized on the surface of nanomaces by a facile galvanic displacement reaction. The fabricated substrates were employed to detect rhodamine 6G (R6G) with a detection limit down to 10(-16) M, and exhibited a high-enhanced performance (enhancement factor (EF) as high as 8.7 × 10(7)). To illustrate the potential value of the prepared substrates, the different concentrations of melamine aqueous solution (from 10(-4) to 10(-10) M) were detected, and a quantitative relationship between the SERS spectrum intensity and the melamine concentration had been established. In addition, the measure of melamine residual in pure milk was carried out successfully, and the results indicated that the prepared 3D nanomace substrates had great potential in food inspection, environment protection, and a few other technologically important fields.

A label-free hemin/G-quadruplex DNAzyme biosensor developed on electrochemically modified electrodes for detection of a HBV DNA segment

A label-free biosensor based on Au/G–CMWCNTs-GCE was proposed for the detection of a HBV DNA segment with a low LOD.