Combining functionalised nanoparticles and SERS for the detection of DNA relating to disease

Surface-enhanced Raman scattering used to study the structure of layers formed on metal surfaces from single-stranded DNA and 6-mercaptohexan-1-ol: influence of hybridization with the complementary DNA and influence of the metal substrate

Capture single-stranded DNA with an attached alkanethiol linking moiety (capture HS-ssDNA) and 6-mercaptohexan-1-ol were chemisorbed on nanostructured GaN covered with sputtered layers of plasmonic metals (like silver and gold). The structure of the formed layer was determined by surface-enhanced Raman scattering (SERS) measurements. Hybridization with the target ssDNA, complementary to the chains of immobilized capture HS-ssDNA, induced changes in the conformation of the chains of chemisorbed ω-substituted alkanetiols (6-mercaptohexan-1-ol and the alkanethiol linking moiety of HS-ssDNA). Such changes are significantly larger in the case of experiments on silver than on gold and gold/silver SERS substrates. This means that silver substrates are significantly more promising for the SERS observation of such hybridization-induced rearrangements than the gold substrates previously used. Although the sputtered metal films have a nanograin structure, the nanostructuring of the GaN substrates plays an important role in the SERS-activity of this nanomaterial.

Smart Nanodevices for Point-of-Care Applications

Background::

While significant strides have been made to avoid mortality during the treatment of chronic diseases, it is still one of the biggest health-care challenges that have a profound effect on humanity. The development of specific, sensitive, accurate, quick, low-cost, and easy-to-use diagnostic tools is therefore still in urgent demand. Nanodiagnostics is defined as the application of nanotechnology to medical diagnostics that can offer many unique opportunities for more successful and efficient diagnosis and treatment for infectious diseases.

Methods::

In this review we provide an overview of infectious disease using nanodiagnostics platforms based on nanoparticles, nanodevices for point-of-care (POC) applications.

Results::

Current state-of-the-art and most promising nanodiagnostics POC technologies, including miniaturized diagnostic tools, nanorobotics and drug delivery systems have been fully examined for the diagnosis of diseases. It also addresses the drawbacks, problems and potential developments of nanodiagnostics in POC applications for chronic diseases.

Conclusions::

While progress is gaining momentum in this field and many researchers have dedicated their time in developing new smart nanodevices for POC applications for various chronic diseases, the ultimate aim of achieving longterm, reliable and continuous patient monitoring has not yet been achieved. Moreover, the applicability of the manufactured nanodevices to rural patients for on-site diagnosis, cost, and usability are the crucial aspects that require more research, improvements, and potential testing stations. Therefore, more research is needed to develop the demonstrated smart nanodevices and upgrade their applicability to hospitals away from the laboratories.

Detection and quantification of warfarin in pharmaceutical dosage form and in spiked human plasma using surface enhanced Raman scattering

Analytical approaches for the quantitation of warfarin in plasma are high in demand. In this study, a novel surface enhanced Raman scattering (SERS) technique for the quantification of the widely used anticoagulant warfarin sodium in pharmaceutical dosage form and in spiked human plasma was developed. The colloidal-based SERS measurements were carefully optimized considering the laser wavelength, the type of metal nanoparticles, their surface functionalization and concentration as well as the time required for warfarin to associate with the metal surface. Poly(diallyldimethylammonium chloride) coated silver nanoparticles (PDDA-AgNPs) were established as a substrate which greatly enhanced the weak warfarin Raman signal with high reproducibility. The limit of detection was calculated in both water and human plasma to be 0.56 nM (0.17 ngmL^-1) and 0.25 nM (0.08 ngmL^-1) respectively, with a high degree of accuracy and reproducibility. The proposed method is simple, economical, and easily applied for routine application requiring only small plasma samples and also could be potentially useful for pharmacokinetic research on warfarin.

SERS Studies of Adsorption on Gold Surfaces of Mononucleotides with Attached Hexanethiol Moiety: Comparison with Selected Single-Stranded Thiolated DNA Fragments

The attachment of DNA strands to gold surfaces is performed in many devices, such as various DNA sensors. One of the standard methods used to immobilize DNA on gold surfaces involves two steps: the attachment of a thiol linker group (usually in the form of alkanethiol moiety) to the DNA strand, and the chemical reaction between the thiol-terminated DNA and the gold surface. Since thiols react chemically with the surface of gold substrates, forming very stable Au-S bonds, it is often assumed that the chemisorption on the gold surface of nucleotides with an attached thiol linker group leads to the formation of an order layer with the linking moieties relatively densely packed on the gold surface. In this contribution we show that chemisorption of thiolated mononucleotides does not occur according to this model. For example, the thiolated mononucleotide containing adenine strongly interacts with the gold surface via the adenine moiety. Moreover, bonding of the mononucleotide containing adenine to the gold surface is relatively similar to the bonding of adenine, and the main difference is that the adenine interacts with the gold surface mainly through the pyrimidine ring, while for adenine mononucleotide interaction via the imidazole ring also significantly contributes to the total bonding. A similar effect was observed for the mononucleotide containing cytosine, and the main difference between the interaction with the gold surface of cytosine and cytosine mononucleotide is that mononucleotide containing cytosine interacts with the gold surface to a significantly larger extend via the carboxylic group of the base. We also show that the structure of the layer formed on the gold surface by the thiolated mononucleotides may be significantly different than the structure of the layer formed by thiolated single-stranded DNA containing even as few as two bases.

Enhancement of Single Molecule Raman Scattering using Sprouted Potato Shaped Bimetallic Nanoparticles

Herein, for the first time, we report the single molecule surface enhanced resonance Raman scattering (SERRS) and surface enhanced Raman scattering (SERS) spectra with high signal to noise ratio (S/N) using plasmon-active substrates fabricated by sprouted potato shaped Au-Ag bimetallic nanoparticles, prepared using a new one-step synthesis method. This particular shape of the nanoparticles has been obtained by fixing the amount of Au and carefully adjusting the amount of Ag. These nanoparticles have been characterized using scanning electron microscopy, extinction spectroscopy, and glancing angle X-ray diffraction. The single molecule sensitivity of SERS substrates has been tested with two different molecular Raman probes. The origin of the electromagnetic enhancement of single molecule Raman scattering in the presence of sprouted shape nanoparticles has been explained using quasi-static theory as well as finite element method (FEM) simulations. Moreover, the role of (i) methods for binding Raman probe molecules to the substrate, (ii) concentration of molecules, and (iii) Au-Ag ratio on the spectra of molecules has been studied in detail.

Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting

Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the most suitable for the analysis of mixed cultures in future studies. Furthermore, our results suggest that while each of these spectroscopic approaches may favour different organisms (sample types), when combined, they would provide complementary and more in-depth knowledge (structural and/or metabolic state) of biological systems. To the best of our knowledge, this is the first time that such a comparative and combined spectroscopic study (using FT-IR, Raman and SERS) has been carried out on microbial samples.

Introducing 12 new dyes for use with oligonucleotide functionalised silver nanoparticles for DNA detection with SERS

Oligonucleotide functionalised metallic nanoparticles (MNPs) have been shown to be an effective tool in the detection of disease-specific DNA and have been employed in a number of diagnostic assays. The MNPs are also capable of facilitating surface enhanced Raman scattering (SERS) enabling detection to become highly sensitive. Herein we demonstrate the expansion of the range of specific SERS-active oligonucleotide MNPs through the use of 12 new Raman-active monomethine and trimethine chalcogenopyrylium and benzochalcogenopyrylium derivatives. This has resulted in an increased ability to carry out multiplexed analysis beyond the current small pool of resonant and non-resonant Raman active molecules, that have been used with oligonucleotide functionalised nanoparticles. Each dye examined here contains a variation of sulphur and selenium atoms in the heterocyclic core, together with phenyl, 2-thienyl, or 2-selenophenyl substituents on the 2,2′,6, and 6′ positions of the chalcogenopyrylium dyes and 2 and 2′ positions of the benzochalcogenopyrylium dyes. The intensity of SERS obtained from each dye upon conjugate hybridisation with a complementary single stranded piece of DNA was explored. Differing concentrations of each dye (1000, 3000, 5000 and 7000 equivalents per NP-DNA conjugate) were used to understand the effects of Raman reporter coating on the overall Raman intensity. It was discovered that dye concentration did not affect the target/control ratio, which remained relatively constant throughout and that a lower concentration of Raman reporter was favourable in order to avoid NP instability. A relationship between the dye structure and SERS intensity was discovered, leaving scope for future development of specific dyes containing substituents favourable for discrimination in a multiplex by SERS. Methine dyes containing S and Se in the backbone and at least 2 phenyls as substituents give the highest SERS signal following DNA-induced aggregation. Principal component analysis (PCA) was performed on the data to show differentiation between the dye classes and highlight possible future multiplexing capabilities of the 12 investigated dyes.

12 new Raman active dyes are reported to increase the SERS intensity upon hybridisation of a targeted DNA to oligonucleotide-NP conjugates and can be potentially used together in a multiplex.

Multiplex in vitro detection using SERS

This review focuses on the recent advances in SERS and its potential to detect multiple biomolecules in clinical samples.

Isolation and identification of bacteria by means of Raman spectroscopy

Bacterial detection is a highly topical research area, because various fields of application will benefit from the progress being made. Consequently, new and innovative strategies which enable the investigation of complex samples, like body fluids or food stuff, and improvements regarding the limit of detection are of general interest. Within this review the prospects of Raman spectroscopy as a reliable tool for identifying bacteria in complex samples are discussed. The main emphasis of this work is on important aspects of applying Raman spectroscopy for the detection of bacteria like sample preparation and the identification process. Several approaches for a Raman compatible isolation of bacterial cells have been developed and applied to different matrices. Here, an overview of the limitations and possibilities of these methods is provided. Furthermore, the utilization of Raman spectroscopy for diagnostic purposes, food safety and environmental issues is discussed under a critical view.

Selective TERS detection and imaging through controlled plasmonics

Enhanced Raman spectroscopy offers capabilities to detect molecules in the complex molecular environments and image chemical heterogeneity in a wide range of samples. It has been shown that plasmonic interactions between a TERS tip and a metal surface produce significant enhancements. In this report we show how SERS spectra from purified molecules can be used to selectively image proteins on surfaces and in cell membranes. The SERS response from the purified protein can be used to create a multivariate regression model that can be applied to nanoparticles that bind to protein receptors. Filtering the observed TERS spectra with the regression model can then selectively image the protein receptor. Experiments with mutant proteins suggest that key amino acids provide significant contributions to the observed TERS signal, which enables the differentiation of protein receptors. These results demonstrate the selectivity that can be obtained in TERS images through a controlled plasmonic interaction. This approach has further implications for identifying membrane receptors that bind specific molecules relevant to drug targeting and chemical signaling.

Illuminating disease and enlightening biomedicine: Raman spectroscopy as a diagnostic tool

The discovery of the Raman effect in 1928 not only aided fundamental understanding about the quantum nature of light and matter but also opened up a completely novel area of optics and spectroscopic research that is accelerating at a greater rate during the last decade than at any time since its inception. This introductory overview focuses on some of the most recent developments within this exciting field and how this has enabled and enhanced disease diagnosis and biomedical applications. We highlight a small number of stimulating high-impact studies in imaging, endoscopy, stem cell research, and other recent developments such as spatially offset Raman scattering amongst others. We hope this stimulates further interest in this already exciting field, by 'illuminating' some of the current research being undertaken by the latest in a very long line of dedicated experimentalists interested in the properties and potential beneficial applications of light.

Biomarker discovery and applications for foods and beverages: proteomics to nanoproteomics

Foods and beverages have been at the heart of our society for centuries, sustaining humankind - health, life, and the pleasures that go with it. The more we grow and develop as a civilization, the more we feel the need to know about the food we eat and beverages we drink. Moreover, with an ever increasing demand for food due to the growing human population food security remains a major concern. Food safety is another growing concern as the consumers prefer varied foods and beverages that are not only traded nationally but also globally. The 21st century science and technology is at a new high, especially in the field of biological sciences. The availability of genome sequences and associated high-throughput sensitive technologies means that foods are being analyzed at various levels. For example and in particular, high-throughput omics approaches are being applied to develop suitable biomarkers for foods and beverages and their applications in addressing quality, technology, authenticity, and safety issues. Proteomics are one of those technologies that are increasingly being utilized to profile expressed proteins in different foods and beverages. Acquired knowledge and protein information have now been translated to address safety of foods and beverages. Very recently, the power of proteomic technology has been integrated with another highly sensitive and miniaturized technology called nanotechnology, yielding a new term nanoproteomics. Nanoproteomics offer a real-time multiplexed analysis performed in a miniaturized assay, with low-sample consumption and high sensitivity. To name a few, nanomaterials - quantum dots, gold nanoparticles, carbon nanotubes, and nanowires - have demonstrated potential to overcome the challenges of sensitivity faced by proteomics for biomarker detection, discovery, and application. In this review, we will discuss the importance of biomarker discovery and applications for foods and beverages, the contribution of proteomic technology in this process, and a shift towards nanoproteomics to suitably address associated issues. This article is part of a Special Issue entitled: Translational plant proteomics.

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.

Label-free in situ detection of individual macromolecular assemblies by surface enhanced Raman scattering

We demonstrate label-free detection of lipid vesicles and polystyrene beads freely diffusing in aqueous solution using surface enhanced Raman scattering (SERS). The signals observed enable real-time identification and monitoring of individual particles interacting with the SERS substrate. SERS is demonstrated as a label-free method capable of monitoring transient species in solution on the millisecond time scale.

Tip-enhanced Raman detection of antibody conjugated nanoparticles on cellular membranes

Tip enhanced Raman scattering (TERS) microscopy is used to image antibody conjugated nanoparticles on intact cellular membranes. The combination of plasmonic coupling and the resultant electric field obtained from intermediate focusing of a radially polarized source gives rise to Raman images with spatial resolution below 50 nm. Finite element method calculations are used to explain the origins of the observed image resolution and spectroscopic signals. The observed Raman scattering provides information about the biomolecules present near the nanoparticle probes. The results show that aggregates of nanoparticles produce spectroscopic results similar to those reported from other surface enhanced Raman spectroscopies, e.g., shell isolated nanoparticle enhanced Raman spectroscopy (SHINERS) and aggregated nanoparticles; however, TERS enables the detection of isolated nanoparticles on cell membranes where the observed spectra provide information about the interaction of the specific biomolecule conjugated to the nanoparticle probe. These measurements present a new technique for exploring biomolecular interactions on the surface of cells and tissue.

Clinical SERS: are we there yet?

Surface Enhanced Raman Spectroscopy or SERS has witnessed many successes over the past 3 decades, owing particularly to its simplicity of use as well as its highly-multiplexing capability. This article provides an overview of SERS and its applicability in the field of bio-medicine. We will preview recent developments in SERS substrate designs, and the various sensing technologies that are based on the SERS phenomenon. An overview of the clinical applications of SERS is also included. Finally, we provide an opinion on the future trends of this unique spectroscopic technique.

Stable dye-labelled oligonucleotide-nanoparticle conjugates for nucleic acid detection

Metallic nanoparticles functionalized with oligonucleotides are used for a number of nucleic acid detection strategies. However, oligonucleotide-nanoparticle conjugates suffer from a lack of stability when exposed to certain conditions associated with DNA detection assays. In this study, we report the synthesis of thiol and thioctic acid-modified oligonucleotide gold nanoparticle (OGNs) conjugates functionalized with a dye label and varying spacer groups. The thioctic acid-modified conjugates exhibit increased stability when treated with dithiothreitol (DTT) compared to the more commonly used thiol modification. When the dye labelled oligonucleotide nanoparticle conjugates are exposed to the same conditions there is a pronounced increase in the stability for both thioctic acid and thiol modified sequences. These results open up the possibility of simply using a dye label to enhance the stability of oligonucleotide-nanoparticle conjugates in DNA detection assays where the enhanced stability of the conjugate system can be advantageous in more complex biological environments.