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

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

Visualization of vibrational-resolution charge transfer enhanced resonance Raman scattering spectroscopy

In this paper, we report visualization of vibrational-resolution charge transfer enhanced resonance Raman scattering Spectroscopy. Based on the first-principles calculation method, we calculated and analyzed the electronic excitation characteristics of the molecules as well as the spontaneous Raman and resonance Raman spectra. Through the visualization of the electronic excitation characteristics, it is found that the Raman signal of the atomic group vibration mode occupied by the charge transfer excitons is significantly enhanced. Super-exchange charge transfer excitons enhance the polarizability by enhancing the dipole moment, ultimately enhancing the Raman optical signal.

Flexible PET/ITO/Ag SERS Platform for Label-Free Detection of Pesticides

We show a new type of elastic surface-enhanced Raman spectroscopy (SERS) platform made of poly(ethylene terephthalate) (PET) covered with a layer of indium tin oxide (ITO). This composite is subjected to dielectric barrier discharge (DBD) that develops the active surface of the PET/ITO foil. To enhance the Raman signal, a modified composite was covered with a thin layer of silver using the physical vapor deposition (PVD) technique. The SERS platform was used for measurements of para-mercaptobenzoic acid (p-MBA) and popular pesticides, i.e., Thiram and Carbaryl. The detection and identification of pesticides on the surface of fruits and vegetables is a crucial issue due to extensive use of those chemical substances for plant fungicide and insecticide protection. Therefore, the developed PET/ITO/Ag SERS platform was dedicated to quantitative analysis of selected pesticides, i.e., Thiram and Carbaryl from fruits. The presented SERS platform exhibits excellent enhancement and reproducibility of the Raman signal, which enables the trace analysis of these pesticides in the range up to their maximum residues limit. Based on the constructed calibration curves, the pesticide concentrations from the skin of apples was estimated as 2.5 µg/mL and 0.012 µg/mL for Thiram and Carbaryl, respectively. Additionally, the PET/ITO/Ag SERS platform satisfies other spectroscopic properties required for trace pesticide analysis e.g., ease, cost-effective method of preparation, and specially designed physical properties, especially flexibility and transparency, that broaden the sampling versatility to irregular surfaces.

Photovoltaic cells as a highly efficient system for biomedical and electrochemical surface-enhanced Raman spectroscopy analysis

Surface-enhanced Raman scattering (SERS) has been intensively used recently as a highly sensitive, non-destructive, chemical specific, and label-free technique for a variety of studies. Here, we present a novel SERS substrate for: (i) the standard ultra-trace analysis, (ii) detection of whole microorganisms, and (iii) spectroelectrochemical measurements. The integration of electrochemistry and SERS spectroscopy is a powerful approach for in situ investigation of the structural changes of adsorbed molecules, their redox properties, and for studying the intermediates of the reactions. We have developed a conductive SERS platform based on photovoltaic materials (PV) covered with a thin layer of silver, especially useful in electrochemical SERS analysis. These substrates named Ag/PV presented in this study combine crucial spectroscopic features such as high sensitivity, reproducibility, specificity, and chemical/physical stability. The designed substrates permit the label-free identification and differentiation of cancer cells (renal carcinoma) and pathogens (Escherichia coli and Bacillus subtilis). In addition, the developed SERS platform was adopted as the working electrode in an electrochemical SERS approach for p-aminothiophenol (p-ATP) studies. The capability to monitor in real-time the electrochemical changes spectro-electro-chemically has great potential for broadening the application of SERS.

We have developed a conductive SERS platform based on photovoltaic materials (PV) covered with a thin layer of silver, especially useful in electrochemical SERS analysis.

Environmentally sustainable route to SiO2@Au-Ag nanocomposites for biomedical and catalytic applications

A facile, sustainable, operationally simple and mild method for the synthesis of SiO2@Au-Ag nanocomposites (NCs) using Nephrolepis cordifolia tuber extract is described and its catalytic, antibacterial and cytotoxic properties were investigated. The fabricated SiO2@Au-Ag NCs were well characterized by UV-visible spectroscopy, transmission electron microscopy (TEM), energy-dispersive X-ray (EDX), Fourier transform infrared (FT-IR) spectroscopy, powder X-ray diffraction (XRD), thermogravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS) to determine the optical activity, size and morphology, elemental composition, functional groups present, crystallinity, thermal stability and chemical state respectively. The obtained SiO2@Au-Ag NCs exhibited spherical shape SiO2 decorated with Au and Ag nanoparticles. The diameter of the SiO2 nanoparticles ranges from 200-246 with average 3 nm diameter of Au and Ag NPs. Synthetic utility of this protocol has been demonstrated by exploring its effective catalytic activities for the solvent-free amidation of carboxylic acid with a primary amine with excellent yields. Moreover, the synthesized nanocomposite exhibited as noticeable antibacterial effect against Gram negative and Gram positive bacteria and better bio-compatibility against human keratinocytes. Thus, additive free SiO2@Au-Ag NCs display the potential for catalysis and biomedical applications.

Direct surface-enhanced Raman scattering (SERS) spectroscopy of nucleic acids: from fundamental studies to real-life applications

In this tutorial review, we summarize and discuss the most recent cutting-edge research in the field of direct surface-enhanced Raman scattering (SERS) analysis of nucleic acids.

Surface-enhanced resonance Raman scattering (SERRS) simulates PCR for sensitive DNA detection

This paper describes a novel double-stranded DNA detection method through resonance between SYBR Green I and DNA with the surface-enhanced resonance Raman scattering (SERRS) assay, which opens an avenue to the quantitative and reliable application of SERRS in DNA detection.

Cooperative hydrogen-bonding of the adenine–thymine pair as a strategy for lowering the limit of detection of thymine by surface-enhanced Raman spectroscopy

The formation of cooperative hydrogen bonds between the thymine–adenine pair was used to indirectly determine thymine by SERS, improving the limit of detection values up to two orders of magnitude.

Silver colloids as plasmonic substrates for direct label-free surface-enhanced Raman scattering analysis of DNA

Unraveling the role played by the surface chemistry of silver colloids in the direct SERS analysis of DNA.

Tuning plasmonic and chemical enhancement for SERS detection on graphene-based Au hybrids

Various graphene-based Au nanocomposites have been developed as surface-enhanced Raman scattering (SERS) substrates recently. However, efficient use of SERS has been impeded by the difficulty of tuning SERS enhancement effects induced from chemical and plasmonic enhancement by different preparation methods of graphene. Herein, we developed graphene-based Au hybrids through physical sputtering gold NPs on monolayer graphene prepared by chemical vapor deposition (CVD) as a CVD-G/Au hybrid, as well as graphene oxide-gold (GO/Au) and reduced-graphene oxide (rGO/Au) hybrids prepared using the chemical in situ crystallization growth method. Plasmonic and chemical enhancements were tuned effectively by simple methods in these as-prepared graphene-based Au systems. SERS performances of CVD-G/Au, rGO/Au and GO/Au showed a gradually monotonic increasing tendency of enhancement factors (EFs) for adsorbed Rhodamine 6G (R6G) molecules, which show clear dependence on chemical bonds between graphene and Au, indicating that the chemical enhancement can be steadily controlled by chemical groups in a graphene-based Au hybrid system. Most notably, we demonstrate that the optimized GO/Au was able to detect biomolecules of adenine, which displayed high sensitivity with a detection limit of 10(-7) M as well as good reproducibility and uniformity.

Atomic-layer-deposited silver and dielectric nanostructures for plasmonic enhancement of Raman scattering from nanoscale ultrathin films

Plasmonic silver nanostructures and a precise ZnO cover layer prepared by capacitively coupled plasma atomic layer deposition (ALD) were exploited to enhance the Raman scattering from nanoscale ultrathin films on a Si substrate. The plasmonic activity was supported by a nanostructured Ag (nano-Ag) layer, and a ZnO cover layer was introduced upon the nano-Ag layer to spectrally tailor the localized surface plasmon resonance to coincide with the laser excitation wavelength. Because of the optimized dielectric environment provided by the precise growth of ZnO cover layer using ALD, the intensity of Raman scattering from nanoscale ultrathin films was significantly enhanced by an additional order of magnitude, leading to the observation of the monoclinic and tetragonal phases in the nanoscale ZrO2 high-K gate dielectric as thin as ∼6 nm on Si substrate. The excellent agreement between the finite-difference time-domain simulation and experimental measurement further confirms the so-called [absolute value]E(->)[absolute value](4) dependence of the surface-enhanced Raman scattering. This technique of plasmonic enhancement of Raman spectroscopy, assisted by the nano-Ag layer and optimized dielectric environment prepared by ALD, can be applied to characterize the structures of ultrathin films in a variety of nanoscale materials and devices, even on a Si substrate with overwhelming Raman background.

A sensitive SERS substrate based on Au/TiO2/Au nanosheets

Sensitive SERS substrates based on Au/TiO2/Au nanosheet have been prepared by physically sputtering Au nanoparticles onto fabricated TiO2 nanosheets. The Au/TiO2/Au nanosheets show much stronger SERS signal as compared to normal Au/Ti substrates by increasing surface area and effectively inducing plasmonic coupling between adjoining Au nanoparticles. In addition, influence factors such as concentration of probe solution and deposition time of gold nanoparticles were discussed. This study provides an easy-prepared and label-free substrate for the detection of biomolecule.

Stealth surface modification of surface-enhanced Raman scattering substrates for sensitive and accurate detection in protein solutions

Reliable surface-enhanced Raman scattering (SERS) based biosensing in complex media is impeded by nonspecific protein adsorptions. Because of the near-field effect of SERS, it is challenging to modify SERS-active substrates using conventional nonfouling materials without introducing interference from their SERS signals. Herein, we report a stealth surface modification strategy for sensitive, specific and accurate detection of fructose in protein solutions using SERS by forming a mixed self-assembled monolayer (SAM). The SAM consists of a short zwitterionic thiol, N,N-dimethyl-cysteamine-carboxybetaine (CBT), and a fructose probe 4-mercaptophenylboronic acid (4-MPBA). The specifically designed and synthesized CBT not only resists protein fouling effectively, but also has very weak Raman activity compared to 4-MPBA. Thus, the CBT SAM provides a stealth surface modification to SERS-active substrates. The surface compositions of mixed SAMs were investigated using X-ray photoelectron spectroscopy (XPS) and SERS, and their nonfouling properties were studied with a surface plasmon resonance (SPR) biosensor. The mixed SAM with a surface composition of 94% CBT demonstrated a very low bovine serum albumin (BSA) adsorption (∼3 ng/cm(2)), and moreover, only the 4-MPBA signal appeared in the SERS spectrum. With the use of this surface-modified SERS-active substrate, quantification of fructose over clinically relevant concentrations (0.01-1 mM) was achieved. Partial least-squares regression (PLS) analysis showed that the detection sensitivity and accuracy were maintained for the measurements in 1 mg/mL BSA solutions. This stealth surface modification strategy provides a novel route to introduce nonfouling property to SERS-active substrates for SERS biosensing in complex media.

New insight of squaraine-based biocompatible surface-enhanced Raman scattering nanotag for cancer-cell imaging

Aim: Development of highly sensitive diagnostic nanoprobe for cancer imaging based on surface-enhanced Raman scattering (SERS) platform. Materials & methods: Synthesis of novel squaraine dyes as a Raman signature molecule denoted as lipoic-squaraine-lipoic (LSL), propyl-squaraine-lipoic (PSL) and propyl-squaraine-propyl (PSP). The SERS-nanotag constructed with a Raman signature molecule which is attached on gold nanoparticle and further encapsulated with heterofunctionalized PEG. Antibody conjugation with best SERS-nanotag for target specific recognition. Results: SERS nanotag Au-LSL-PEG showed significant signal intensity and remarkable stability. Anti-EGF receptor and Her2-conjugated Au-LSL-PEG-nanotag were successfully applied for selective recognition of cancer cells like A549, OSCC and MCF7. Conclusion: The newly developed SERS-nanotag Au-LSL-PEG serves as a valuable tool for diagnostic detection of cancer cells, and may find potential applications for cancer screening in real patient samples.

Using surface-enhanced Raman spectroscopy and electrochemically driven melting to discriminate Yersinia pestis from Y. pseudotuberculosis based on single nucleotide polymorphisms within unpurified polymerase chain reaction amplicons

The development of sensors for the detection of pathogen-specific DNA, including relevant species/strain level discrimination, is critical in molecular diagnostics with major impacts in areas such as bioterrorism and food safety. Herein, we use electrochemically driven denaturation assays monitored by surface-enhanced Raman spectroscopy (SERS) to target single nucleotide polymorphisms (SNPs) that distinguish DNA amplicons generated from Yersinia pestis, the causative agent of plague, from the closely related species Y. pseudotuberculosis. Two assays targeting SNPs within the groEL and metH genes of these two species have been successfully designed. Polymerase chain reaction (PCR) was used to produce Texas Red labeled single-stranded DNA (ssDNA) amplicons of 262 and 251 bases for the groEL and metH targets, respectively. These amplicons were used in an unpurified form to hybridize to immobilized probes then subjected to electrochemically driven melting. In all cases electrochemically driven melting was able to discriminate between fully homologous DNA and that containing SNPs. The metH assay was particularly challenging due to the presence of only a single base mismatch in the middle of the 251 base long PCR amplicon. However, manipulation of assay conditions (conducting the electrochemical experiments at 10 °C) resulted in greater discrimination between the complementary and mismatched DNA. Replicate data were collected and analyzed for each duplex on different days, using different batches of PCR product and different sphere segment void (SSV) substrates. Despite the variability introduced by these differences, the assays are shown to be reliable and robust providing a new platform for strain discrimination using unpurified PCR samples.

Detection of DNA sequences refractory to PCR amplification using a biophysical SERRS assay (Surface Enhanced Resonant Raman Spectroscopy)

The analysis of ancient or processed DNA samples is often a great challenge, because traditional Polymerase Chain Reaction – based amplification is impeded by DNA damage. Blocking lesions such as abasic sites are known to block the bypass of DNA polymerases, thus stopping primer elongation. In the present work, we applied the SERRS-hybridization assay, a fully non-enzymatic method, to the detection of DNA refractory to PCR amplification. This method combines specific hybridization with detection by Surface Enhanced Resonant Raman Scattering (SERRS). It allows the detection of a series of double-stranded DNA molecules containing a varying number of abasic sites on both strands, when PCR failed to detect the most degraded sequences. Our SERRS approach can quickly detect DNA molecules without any need for DNA repair. This assay could be applied as a pre-requisite analysis prior to enzymatic reparation or amplification. A whole new set of samples, both forensic and archaeological, could then deliver information that was not yet available due to a high degree of DNA damage.

Identification of intracellular gold nanoparticles using surface-enhanced Raman scattering

The identification of intracellular distributions of noble metal nanoparticles is of great utility for many biomedical applications. We present an effective method to distinguish intracellular from extracellular nanoparticles by selectively quenching the SERS signals from dye molecules adsorbed onto star-shaped gold nanoparticles that have not been internalized by cells.

Microfluidics and Raman microscopy: current applications and future challenges

Raman microscopy systems are becoming increasingly widespread and accessible for characterising chemical species. Microfluidic systems are also progressively finding their way into real world applications. Therefore, it is anticipated that the integration of Raman systems with microfluidics will become increasingly attractive and practical. This review aims to provide an overview of Raman microscopy-microfluidics integrated systems for researchers who are actively interested in utilising these tools. The fundamental principles and application strengths of Raman microscopy are discussed in the context of microfluidics. Various configurations of microfluidics that incorporate Raman microscopy methods are presented, with applications highlighted. Data analysis methods are discussed, with a focus on assisting the interpretation of Raman-microfluidics data from complex samples. Finally, possible future directions of Raman-microfluidic systems are presented.

Raman imaging at biological interfaces: applications in breast cancer diagnosis

BACKGROUND

One of the most important areas of Raman medical diagnostics is identification and characterization of cancerous and noncancerous tissues. The methods based on Raman scattering has shown significant potential for probing human breast tissue to provide valuable information for early diagnosis of breast cancer. A vibrational fingerprint from the biological tissue provides information which can be used to identify, characterize and discriminate structures in breast tissue, both in the normal and cancerous environment.

RESULTS

The paper reviews recent progress in understanding structure and interactions at biological interfaces of the human tissue by using confocal Raman imaging and IR spectroscopy. The important differences between the noncancerous and cancerous human breast tissues were found in regions characteristic for vibrations of carotenoids, fatty acids, proteins, and interfacial water. Particular attention was paid to the role played by unsaturated fatty acids and their derivatives as well as carotenoids and interfacial water.

CONCLUSIONS

We demonstrate that Raman imaging has reached a clinically relevant level in regard to breast cancer diagnosis applications. The results presented in the paper may have serious implications on understanding mechanisms of interactions in living cells under realistically crowded conditions of biological tissue.

Molecularly-mediated assemblies of plasmonic nanoparticles for Surface-Enhanced Raman Spectroscopy applications

In recent years, Surface-Enhanced Raman Spectroscopy (SERS) has experienced a tremendous increase of attention in the scientific community, expanding to a continuously wider range of diverse applications in nanoscience, which can mostly be attributed to significant improvements in nanofabrication techniques that paved the way for the controlled design of reliable and effective SERS nanostructures. In particular, the plasmon coupling properties of interacting nanoparticles are extremely intriguing due to the concentration of enormous electromagnetic enhancements at the interparticle gaps. Recently, great efforts have been devoted to develop new nanoparticle assembly strategies in suspension with improved control over hot-spot architecture and cluster structure, laying the foundation for the full exploitation of their exceptional potential as SERS materials in a wealth of chemical and biological sensing. In this review we summarize in an exhaustive and systematic way the state-of-art of plasmonic nanoparticle assembly in suspension specifically developed for SERS applications in the last 5 years, focusing in particular on those strategies which exploited molecular linkers to engineer interparticle gaps in a controlled manner. Importantly, the novel advances in this rather new field of nanoscience are organized into a coherent overview aimed to rationally describe the different strategies and improvements in the exploitation of colloidal nanoparticle assembly for SERS application to real problems.

Poly-L-lysine-coated silver nanoparticles as positively charged substrates for surface-enhanced Raman scattering

Positively charged nanoparticles to be used as substrates for surface-enhanced Raman scattering (SERS) were prepared by coating citrate-reduced silver nanoparticles with the cationic polymer poly-l-lysine. The average diameter of the coated nanoparticles is 75 nm, and their zeta potential is +62.3 ± 1.7 mV. UV-vis spectrophotometry and dynamic light scattering measurements show that no aggregation occurs during the coating process. As an example of their application, the so-obtained positively charged coated particles were employed to detect nanomolar concentrations of the anionic chromophore bilirubin using SERS. Because of their opposite charge, bilirubin molecules interact with the coated nanoparticles, allowing SERS detection. The SERS intensity increases linearly with concentration in a range from 10 to 200 nM, allowing quantitative analysis of bilirubin aqueous solutions.

Positively charged silver nanoparticles and their effect on surface-enhanced Raman scattering of dye-labelled oligonucleotides

Improved positively charged nanoparticles are described to provide a simplified SERS substrate for DNA detection. Complete flocculation of the nanoparticles is prevented due to the controlled analyte induced aggregation. This provides a stable aggregation state which significantly extends the analysis window simplifying DNA detection by SERS.

Using commercially available personal glucose meters for portable quantification of DNA

DNA detection is commonly used in molecular biology, pathogen analysis, genetic disorder diagnosis, and forensic tests. While traditional methods for DNA detection such as polymerase chain reaction (PCR) and DNA microarrays have been well developed, they require sophisticated equipment and operations, and thus it is still challenging to develop a portable and quantitative DNA detection method for the public use at home or in the field. Although many other techniques and devices have been reported to make the DNA detection simple and portable, very few of them are currently accessible to the public for quantitative DNA detection because of either the requirement of laboratory-based instrument or lack of quantitative detection. Herein we report application of personal glucose meters (PGMs), which are widely available, low cost, and simple to use, for quantitative detection of DNA, including a hepatitis B virus DNA fragment. The quantification is based on target-dependent binding of cDNA-invertase conjugate with the analyte DNA, thereby transforming the concentration of DNA in the sample into glucose through invertase-catalyzed hydrolysis of sucrose. Instead of amplifying DNA strands through PCR, which is vulnerable to contaminations commonly encountered for home and field usage, we demonstrate here signal amplifications based on enzymatic turnovers, making it possible to detect 40 pM DNA using PGM that can detect glucose only at the mM level. The method also shows excellent selectivity toward single nucleotide mismatches.

Free-standing one-dimensional plasmonic nanostructures

The field of plasmonics has become one of the most interesting and active research areas in nanotechnology, enabling numerous fundamental studies and applications. The ability to tailor the size, shape, and environment of metal nanostructures is the key component for controlling the plasmonic properties of individual or aggregated nanostructures. In this feature article, a category of chemically nanofabricated, unique free-standing one-dimensional (1D) plasmonic nanostructures has been summarized. The dispersible plasmonic nanostructures were obtained in high yield with control over gap size and feature size. This ability was exploited to tune the emerging plasmonic properties overcoming the difficulties of other methods to do so, leading to applications in analytical detection, biological sensing, and nanoelectronics.

Surface-enhanced Raman spectroscopy (SERS): progress and trends

Surface-enhanced Raman spectroscopy (SERS) combines molecular fingerprint specificity with potential single-molecule sensitivity. Therefore, the SERS technique is an attractive tool for sensing molecules in trace amounts within the field of chemical and biochemical analytics. Since SERS is an ongoing topic, which can be illustrated by the increased annual number of publications within the last few years, this review reflects the progress and trends in SERS research in approximately the last three years. The main reason why the SERS technique has not been established as a routine analytic technique, despite its high specificity and sensitivity, is due to the low reproducibility of the SERS signal. Thus, this review is dominated by the discussion of the various concepts for generating powerful, reproducible, SERS-active surfaces. Furthermore, the limit of sensitivity in SERS is introduced in the context of single-molecule spectroscopy and the calculation of the 'real' enhancement factor. In order to shed more light onto the underlying molecular processes of SERS, the theoretical description of SERS spectra is also a growing research field and will be summarized here. In addition, the recording of SERS spectra is affected by a number of parameters, such as laser power, integration time, and analyte concentration. To benefit from synergies, SERS is combined with other methods, such as scanning probe microscopy and microfluidics, which illustrates the broad applications of this powerful technique.

SERS detection of protein biochip fabricated by etching polystyrene template

In this study, a nanoscale protein chip is prepared by using an etched polystyrene (PS) template. This protein chip can be directly used for immunoassay, with the help of Surface Enhanced Raman Scattering (SERS) spectra. Some glass slides submerged in aldehyde is initially prepared, modified with antibodies, human immunoglobulin G (IgG). Then PS arrays are self-assembled on these slides with the Langmuir-Blodgett method. The PS template pattern is transferred to the human IgG substrate using an etching process-slides are exposed to O(2) plasma for 90s. The PS nanoparticles are then washed away using phosphate buffered saline solution. Next, the slides are dipped into bovine serum albumin solution to ensure that the anti IgG would bond only to the human IgG. At this moment, a patterned protein chip is obtained. When used for protein detection, the protein chip could be immersed into labeled specificity antigen solution. Here we chose fluorescein isothiocyanate anti-human IgG. After washing, only bonded antigens remain. Fluorescence microscopy and SERS is used to characterize the samples. The SERS spectra intensity shows liner correlation with the concentration of anti-human IgG. All the experiments are conducted in a phosphate buffered saline solution at 37°C for 2 h.