DNA detection by surface enhanced resonance Raman scattering (SERRS)

Demonstration of a Superior Deep-UV Surface-Enhanced Resonance Raman Scattering (SERRS) Substrate and Single-Base Mutation Detection in Oligonucleotides

In life science, rapid mutation detection in oligonucleotides is in a great demand for genomic and medical screening. To satisfy this demand, surface-enhanced resonance Raman spectroscopy (SERRS) in the deep-UV (DUV) regime offers a promising solution due to its merits of label-free nature, strong electromagnetic confinement, and charge transfer effect. Here, we demonstrate an epitaxial aluminum (Al) DUV-SERRS substrate that resonates effectively with the incident Raman laser and the ss-DNA at 266 nm, yielding significant SERRS signals of the detected analytes. For the first time, to the best of our knowledge, we obtaine SERRS spectra for all bases of oligonucleotides, not only revealing maximum characteristic Raman peaks but also recording the highest enhancement factor of up to 10⁶ for a 1 nm thick adenine monomer. Moreover, our epitaxial Al DUV-SERRS substrate is able to enhance the Raman signal of all four bases of 12-mer ss-DNA and to further linearly quantify the single-base mutation in the 12-mer ss-DNA.

Magnetically Enhanced Liquid SERS for Ultrasensitive Analysis of Bacterial and SARS-CoV-2 Biomarkers

In this work, it is shown that surface-enhanced Raman scattering (SERS) measurements can be performed using liquid platforms to perform bioanalysis at sub-pM concentrations. Using magnetic enrichment with gold-coated magnetic nanoparticles, the high sensitivity was verified with nucleic acid and protein targets. The former was performed with a DNA fragment associated with the bacteria Staphylococcus aureus, and the latter using IgG antibody, a biomarker for COVID-19 screening. It is anticipated that this work will inspire studies on ultrasensitive SERS analyzers suitable for large-scale applications, which is particularly important for in vitro diagnostics and environmental studies.

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS

The incidence of opportunistic yeast infections in humans has been increasing over recent years. These infections are difficult to treat and diagnose, in part due to the large number and broad diversity of species that can underlie the infection. In addition, resistance to one or several antifungal drugs in infecting strains is increasingly being reported, severely limiting therapeutic options and showcasing the need for rapid detection of the infecting agent and its drug susceptibility profile. Current methods for species and resistance identification lack satisfactory sensitivity and specificity, and often require prior culturing of the infecting agent, which delays diagnosis. Recently developed high-throughput technologies such as next generation sequencing or proteomics are opening completely new avenues for more sensitive, accurate and fast diagnosis of yeast pathogens. These approaches are the focus of intensive research, but translation into the clinics requires overcoming important challenges. In this review, we provide an overview of existing and recently emerged approaches that can be used in the identification of yeast pathogens and their drug resistance profiles. Throughout the text we highlight the advantages and disadvantages of each methodology and discuss the most promising developments in their path from bench to bedside.

Synthesis of gold-palladium nanowaxberries/dodecylamine-functionalized graphene quantum dots-graphene micro-aerogel for voltammetric determination of peanut allergen Ara h 1

The paper reports synthesis of gold-palladium nanowaxberries(AuPd NWs)/dodecylamine-functionalized graphene quantum dots(D-GQDs)-graphene micro-aerogel(GMA). D-GQDs was used as a solid particle surfactant for stabilizing Pickering emulsion of toluene-in-graphene oxide aqueous dispersion. Graphene oxide sheets in the aqueous phase are reduced by hydrazine hydrate, diffused into the toluene droplet and self-assembled into graphene oxide micro-gels. Followed by freeze-drying, thermal annealing and hybridized with AuPd NWs. The as-prepared AuPd NWs/D-GQDs-GMA shows an unique three-dimensional structure with the size of microns. The small size and strong polarity make it can be directly dispersed in ethanol to form stable dispersion for sensor preparation. The hybrid of GMA, D-GQDs and AuPd NWs greatly improves the electron transfer, electroactive surface area and ion diffusion. The architecture of conductor/semiconductor/conductor achieves to a significant amplification of detection signal. The DNA biosensor based on the AuPd NWs/D-GQDs-GMA exhibits ultrasensitive differential pulse voltammetric (DPV) response towards peanut allergen Ara h 1. The DPV signal linearly increases with increasing DNA concentration in the range of 1.0 × 10^-22-1.0 × 10^-17 M with the detection limit of 4.7 × 10^-23 M (S/N = 3). The analytical method was successfully applied to voltammetric determination of peanut allergen Ara h 1 in peanut milk beverage.

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.

Prospects for point-of-care pathogen diagnostics using surface-enhanced Raman scattering (SERS)

This review highlights recent advances in the application of surface-enhanced Raman scattering (SERS) in pathogen detection and discusses many of the challenges in moving this technology to the point-of-care (POC) arena.

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.

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.

Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

Molecular and nonmolecular diagnostic methods for invasive fungal infections

Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use.

Label-free detection of Phytophthora ramorum using surface-enhanced Raman spectroscopy

Label-free and species-specific detection of the plant pathogen Phytophthora ramorum from real samples employing SERS as an analytical tool.

Probing the effect of charge transfer enhancement in off resonance mode SERS via conjugation of the probe dye between silver nanoparticles and metal substrates

The charge transfer-mediated surface enhanced Raman scattering (SERS) of crystal violet (CV) molecules that were chemically conjugated between partially polarized silver nanoparticles and optically smooth gold and silver substrates has been studied under off-resonant conditions. Tyrosine molecules were used as a reducing agent to convert silver ions into silver nanoparticles where oxidised tyrosine caps the silver nanoparticle surface with its semiquinone group. This binding through the quinone group facilitates charge transfer and results in partially oxidised silver. This establishes a chemical link between the silver nanoparticles and the CV molecules, where the positively charged central carbon of CV molecules can bind to the terminal carboxylate anion of the oxidised tyrosine molecules. After drop casting Ag nanoparticles bound with CV molecules it was found that the free terminal amine groups tend to bind with the underlying substrates. Significantly, only those CV molecules that were chemically conjugated between the partially polarised silver nanoparticles and the underlying gold or silver substrates were found to show SERS under off-resonant conditions. The importance of partial charge transfer at the nanoparticle/capping agent interface and the resultant conjugation of CV molecules to off resonant SERS effects was confirmed by using gold nanoparticles prepared in a similar manner. In this case the capping agent binds to the nanoparticle through the amine group which does not facilitate charge transfer from the gold nanoparticle and under these conditions SERS enhancement in the sandwich configuration was not observed.

Recent developments and future directions in SERS for bioanalysis

The ability to develop new and sensitive methods of biomolecule detection is crucial to the advancement of pre-clinical disease diagnosis and effective patient specific treatment. Surface enhanced Raman scattering (SERS) is an optical spectroscopy amenable to this goal, as it is capable of extremely sensitive biomolecule detection and multiplexed analysis. This perspective highlights where SERS has been successfully used to detect target biomolecules, specifically DNA and proteins, and where in vivo analysis has been successfully utilised. The future of SERS development is discussed and emphasis is placed on the steps required to transport this novel technique from the research laboratory to a clinical setting for medical diagnostics.

Tuning and maximizing the single-molecule surface-enhanced Raman scattering from DNA-tethered nanodumbbells

We extensively study the relationships between single-molecule surface-enhanced Raman scattering (SMSERS) intensity, enhancement factor (EF) distribution over many particles, interparticle distance, particle size/shape/composition and excitation laser wavelength using the single-particle AFM-correlated Raman measurement method and theoretical calculations. Two different single-DNA-tethered Au-Ag core-shell nanodumbbell (GSND) designs with an engineerable nanogap were used in this study: the GSND-I with various interparticle nanogaps from ∼4.8 nm to <1 nm or with no gap and the GSND-II with the fixed interparticle gap size and varying particle size from a 23-30 nm pair to a 50-60 nm pair. From the GSND-I, we learned that synthesizing a <1 nm gap is a key to obtain strong SMSERS signals with a narrow EF value distribution. Importantly, in the case of the GSND-I with <1 nm interparticle gap, an EF value of as high as 5.9 × 10(13) (average value = 1.8 × 10(13)) was obtained and the EF values of analyzed particles were narrowly distributed between 1.9 × 10(12) and 5.9 × 10(13). In the case of the GSND-II probes, a combination of >50 nm Au cores and 514.5 nm laser wavelength that matches well with Ag shell generated stronger SMSERS signals with a more narrow EF distribution than <50 nm Au cores with 514.5 nm laser or the GSND-II structures with 632.8 nm laser. Our results show the usefulness and flexibility of these GSND structures in studying and obtaining SMSERS structures with a narrow distribution of high EF values and that the GSNDs with < 1 nm are promising SERS probes with highly sensitive and quantitative detection capability when optimally designed.

Plasmon-tuned silver colloids for SERRS analysis of methemoglobin with preserved nativity

Optically tuned silver nanoparticles (AgNP's) functionalized with ω-mercaptoalkanoic acids are synthesized and used as a signal amplifier for the surface-enhanced resonance Raman scattering (SERRS) study of heme cofactor in methemoglobin (metHb). Even though both mercaptopropionic acid (MPA)- and mercaptononanoic acid (MNA)-functionalized AgNP's exemplify vastly enhanced SERRS signal of metHb, MNA-AgNP's amplify the SERRS signal amid preservation of the nativity of the heme pocket, unlike MPA-AgNP's. The electrostatic interaction between MNA-AgNP's and metHb leads to instant signal enhancement with a Raman enhancement factor (EF(SERS)) of 4.2 × 10(3). Additionally, a Langmuir adsorption isotherm has been employed for the adsorption of metHb on the MNA-AgNP surface, which provides the real surface coverage and equilibrium constant (K) of metHb as 139 nM and 3.6 × 10(8) M(-1), respectively. The lowest detection limit of 10 nM for metHb has been demonstrated using MNA-AgNP's besides retaining the nativity of the heme pocket.

Detection of SERS active labelled DNA based on surface affinity to silver nanoparticles

Developments in specific DNA detection assays have been shown to be increasingly beneficial for molecular diagnostics and biological research. Many approaches use optical spectroscopy as an assay detection method and, owing to the sensitivity and molecular specificity offered, surface enhanced Raman scattering (SERS) spectroscopy has become a competitively exploited technique. This study utilises SERS to demonstrate differences in affinity of dye labelled DNA through differences in electrostatic interactions with silver nanoparticles. Results show clear differences in the SERS intensity obtained from single stranded DNA, double stranded DNA and a free dye label and demonstrate surface attraction is driven through electrostatic charges on the nucleotides and not the SERS dye. It has been further demonstrated that, through optimisation of experimental conditions and careful consideration of sequence composition, a DNA detection method with increased sample discrimination at lower DNA concentrations can be achieved.

Silica encapsulated SERS nanoprobe conjugated to the bacteriophage tailspike protein for targeted detection of Salmonella

Silica-encapsulated Raman-reporter embedded SERS nanoprobes, named nanoaggregate embedded beads (NAEBs), were conjugated to the Salmonella specific tailspike protein (TSP) isolated from the P22 bacteriophage to enable a highly specific and ultrasensitive optical transduction platform. We demonstrate three successful surface conjugation strategies and highlight the detection of a single bacterium using SERS.

Surface-enhanced Raman study of the interactions between tripodal cationic polyamines and polynucleotides

Raman and surface-enhanced Raman spectra of new DNA/RNA-binding compounds consisting of three imidazole (Im) and three pyridine (Py) rings connected by tripodal polyaminomethylene linkages were obtained by the near-infrared excitation at 1064 nm. Study of interactions of Im and Py polyamines with single-stranded RNA polynucleotides (poly A, poly G, poly C, poly U), double-stranded DNA polynucleotides (poly dAdT-poly dAdT, poly dGdC-poly dGdC) and calf thymus DNA (ct-DNA) by surface-enhanced Raman spectroscopy (SERS) reveals unambiguous enhancement of the Raman scattering from the small molecules as well as appearance of new bands in spectra associated mainly with nucleobases. The SERS experiments point toward comparable interactions of Im and Py polyamines with single-stranded purine and pyrimidine polynucleotides. Furthermore, SERS experiments with double stranded polynucleotides reveal the base-pair dependent selectivity of Im and Py, whereby interactions within both, major and minor groove are indicated for poly dAdT-poly dAdT, at variance to preferred binding of Im and Py to only major groove of poly dGdC-poly dGdC. SERS spectra of Im and Py with ct-DNA imply that protonated amino groups of these compounds preferentially interact with N7 atoms (adenine, guanine) while nitrogen in aromatic rings of polyamines might be attracted to C6-NH(2) (adenine), all sites being located at the major groove of the DNA helix. Wavenumber downshift of the imidazole (Im) and pyridine (Py) ring vibrations supports aromatic stacking interactions of imidazole and pyridine aromatic moieties with DNA base-pairs.

Bio-imaging, detection and analysis by using nanostructures as SERS substrates

Surface-enhanced Raman scattering (SERS) is a phenomenon that occurs on nanoscale-roughed metallic surface. The magnitude of the Raman scattering signal can be greatly enhanced when the scatterer is placed in the very close vicinity of the surface, which enables this phenomenon to be a highly sensitive analytical technique. SERS inherits the general strongpoint of conventional Raman spectroscopy and overcomes the inherently small cross section problem of a Raman scattering. It is a sensitive and nondestructive spectroscopic method for biological samples, and can be exploited either for the delivery of molecular structural information or for the detection of trace levels of analytes. Therefore, SERS has long been regarded as a powerful tool in biomedical research. Metallic nanostructure plays a key role in all the biomedical applications of SERS because the enhanced Raman signal can only be obtained on the surface of a finely divided substrate. This review focuses on progress made in the use of SERS as an analytical technique in bio-imaging, analysis and detection. Recent progress in the fabrication of SERS active nanostructures is also highlighted.

Solution-based direct readout surface enhanced Raman spectroscopic (SERS) detection of ultra-low levels of thiram with dogbone shaped gold nanoparticles

We report the use of two different sizes of dogbone shaped gold nanoparticles as colloidal substrates for surface enhanced Raman spectroscopy (SERS) based detection of ultra-low levels of thiram, a dithiocarbamate fungicide. We demonstrate the ability to use a solution based, direct readout SERS method as a quantitative tool for the detection of ultra-low levels of thiram. The two different sizes of dogbone shaped gold nanoparticles are synthesized by using the seed-mediated growth method and characterized by using UV-visible spectroscopy and transmission electron microscopy (TEM). The smaller dogbone shaped nanoparticles have an average size of 43 ± 13 nm. The larger dogbone shaped gold nanoparticles have an average size of 65 ± 15 nm. The nanoparticle concentration is 1.25 × 10(11) nanoparticles per mL for the smaller dogbone shaped gold nanoparticles and is 1.13 × 10(11) nanoparticles per mL for the larger dogbone shaped gold nanoparticles. Different concentrations of thiram are allowed to bind to the two different sizes of dogbone shaped gold nanoparticles and the SERS spectra are obtained. From the calibration curve, the limit of detection for thiram is 43.9 ± 6.2 nM when the smaller dogbone shaped gold nanoparticles are used as colloidal SERS substrates In the case of the larger dogbone shaped gold nanoparticles, the limit of detection for thiram is 11.8 ± 3.2 nM. The lower limit of detection obtained by using the larger dogbone shaped gold nanoparticles as colloidal substrates is due to the lightning rod effect, higher contributions from the electromagnetic enhancement effect, and larger number of surface sites for thiram to bind.

Recent advancements in optical DNA biosensors: exploiting the plasmonic effects of metal nanoparticles

The emerging field of plasmonics, the study of electromagnetic responses of metal nanostructures, has revealed many novel signal enhancing phenomena. As applied to the development of label-free optical DNA biosensors, it is now well established that plasmon-based surface enhanced spectroscopies on nanostructured metal surfaces or metal nanoparticles can markedly improve the sensitivity of optical biosensors, with some showing great promise for single molecule detection. In this review, we first summarize the basic concepts of plasmonics in metal nanostructures, as well as the characteristic optical phenomena to which plasmons give rise. We will then describe recent advances in optical DNA biosensing systems enabled by metal nanoparticle-derived plasmonic effects, including the use of surface enhanced Raman scattering (SERS), colorimetric methods, "scanometric" processes, and metal-enhanced fluorescence (MEF).

PCR-free quantification of multiple splice variants in a cancer gene by surface-enhanced Raman spectroscopy

We demonstrate a surface-enhanced Raman spectroscopy (SERS) based array platform to monitor gene expression in cancer cells in a multiplex and quantitative format without amplification steps. A strategy comprising DNA/RNA hybridization, S1 nuclease digestion, and alkaline hydrolysis was adopted to obtain DNA targets specific to two splice junction variants, Delta(9,10) and Delta(5), of the breast cancer susceptibility gene 1 from MCF-7 and MDA-MB-231 breast cancer cell lines. These two targets were identified simultaneously, and their absolute quantities were estimated by a SERS strategy utilizing the inherent plasmon-phonon Raman mode of gold nanoparticle probes as a self-referencing standard to correct for the variability in surface enhancement. The results were then validated by reverse-transcription polymerase chain reaction. Our proposed methodology could be expanded to a higher level of multiplexing for quantitative gene expression analysis of any gene without any amplification steps.

Plasmonic nanoprobes for SERS biosensing and bioimaging

This article provides an overview of the development and application of plasmonic nanoprobes developed in our laboratory for biosensing and bioimaging. We describe the use of plasmonics surface-enhanced Raman scattering (SERS) gene probes for the detection of diseases using DNA hybridization to target biospecies (HIV gene, breast cancer genes etc.). For molecular imaging, we describe a hyperspectral surface-enhanced Raman imaging (HSERI) system that combines imaging capabilities with SERS detection to identify cellular components using Raman dye-labeled silver nanoparticles in cellular systems The detection of specific target DNA sequences associated with breast cancer using "molecular sentinel" nanoprobes and the use of a plasmonic nanosensor to monitor pH in single cells are presented and discussed.

Quantitative surface-enhanced Raman for gene expression estimation

We demonstrate for the first time, to our knowledge, a unique gene expression assay by surface-enhanced Raman scattering (SERS) using nonfluorescent Raman labels to quantify gene expression at the resolution of alternative splicing using RNA extracted from cancer cells without any amplification steps. Our approach capitalizes on the inherent plasmon-phonon mode of SERS substrates as a self-referencing standard for the detection and quantification of genetic materials. A strategy integrating S1 nuclease digestion with SERS detection was developed to quantify the expression levels of splice junction Delta(9,10), a segment of the breast cancer susceptibility gene 1 (BRCA1) from MCF-7 and MDA-MB-231 cells. Quantification results were cross-validated using two Raman tags and qualitatively confirmed by RT-PCR. Our methodology based on SERS technology provides reliable gene expression data with high sensitivity, bypassing the intricacies involved in fabricating a consistent SERS substrate.

Accurate concentration measurements using surface-enhanced Raman and deuterium exchanged dye pairs

Quantitative applications of surface-enhanced resonance Raman scattering (SERRS) are often limited by the reproducibility of SERRS intensities, given the difficulty of controlling analyte-substrate interactions and the associated local field enhancement. As demonstrated here, SERRS from dye molecules even within the same structural class that compete with similar substrates display distinct spectral intensities that are not proportional to analyte concentrations, which limits their use as internal standardization probes and/or for multiplex analysis. Recently, we demonstrated that isotopic variants of rhodamine 6G (R6G), namely R6G-d0 and R6G-d4, can be used for internal standards in SERRS experiments with a linear optical response from picomolar to micromolar concentrations (of total analytes). Here we extend these results by describing a straightforward method for obtaining isotopomeric pairs of other Raman active dyes by hydrogen-deuterium exchange conditions for substitution at electron rich aromatic heterocycles. Most of the known SERRS active probes can be converted into the corresponding isotopomeric molecule by this exchange method, which significantly expands the scope of the isotopic edited internal standard (IEIS) approach. The relative quantification using IEIS enables accurate, reproducible (residual standard deviation+/-2.2%) concentration measurements over a range of 200 pM to 2 microM. These studies enable easy access to a variety of isotopically substituted Raman active dyes and establish the generality of the methodology for quantitative SERRS measurements. For the first time, three rhodamine 6G isotopomers have been created and show distinct Raman spectra, demonstrating the principle of the approach for application as a multiplex technique in biomolecular detection/quantification.

Cetyltrimethylammonium bromide-modified spherical and cube-like gold nanoparticles as extrinsic Raman labels in surface-enhanced Raman spectroscopy based heterogeneous immunoassays

This paper reports on the characterization and preliminary comparison of gold nanoparticles of differing surface modification and shape when used as extrinsic Raman labels (ERLs) in high-sensitivity heterogeneous immunoassays based on surface enhanced Raman scattering (SERS). ERLs are gold nanoparticles coated with an adlayer of an intrinsically strong Raman scatterer, followed by a coating of a molecular recognition element (e.g., antibody). Three types of ERLs, all with a nominal size of approximately 30 nm, were fabricated by using spherical citrate-capped gold nanoparticles (sp-cit-Au NPs), spherical CTAB-capped gold nanoparticles (sp-CTAB-Au NPs), or cube-like CTAB-capped gold nanoparticles (cu-CTAB-Au NPs) as cores. The performance of these particles was assessed via a sandwich immunoassay for human IgG in phosphate buffered saline. The ERLs fabricated with sp-CTAB-Au NPs as cores proved to be more than 50 times more sensitive than those with sp-cit-Au NPs as cores; the same comparison showed that the ERLs with cu-CTAB-Au NPs as cores were close to 200 times more sensitive. Coupled with small differences in levels of nonspecific adsorption, these sensitivities translated to a limit of detection (LOD) of 94, 2.3, and 0.28 ng/mL, respectively, for the detection of human IgG in the case of sp-cit-Au NPs, sp-CTAB-Au NPs, and cu-CTAB-Au NPs. The LOD of the cu-CTAB-Au NPs is therefore approximately 340 times below that for the sp-cit-Au NPs. Potential applications of these labels to bioassays are briefly discussed.

Impact of protein shedding on detection of Mycobacterium avium subsp. paratuberculosis by a whole-cell immunoassay incorporating surface-enhanced Raman scattering

The etiological agent of Johne's disease is Mycobacterium avium subsp. paratuberculosis. Controlling the spread of this disease is hindered by the lack of sensitive, selective, and rapid detection methods for M. avium subsp. paratuberculosis. By using a recently optimized sandwich immunoassay (B. J. Yakes, R. J. Lipert, J. P. Bannantine, and M. D. Porter, Clin. Vaccine Immunol. 15:227-234, 2008), which incorporates a new monoclonal antibody for the selective capture and labeling of M. avium subsp. paratuberculosis and surface-enhanced Raman scattering for sensitive readout, detection limits of approximately 630 and approximately 740 M. avium subsp. paratuberculosis cells/ml are achieved in phosphate-buffered saline and whole milk samples, respectively, after spiking with heat-treated M. avium subsp. paratuberculosis. Surprisingly, these detection limits are 3 orders of magnitude lower than expected based on theoretical predictions. Experiments designed to determine the origin of the improvement revealed that the major membrane protein targeted by the monoclonal antibody was present in the sample suspensions as shed protein. This finding indicates that the capture and labeling of shed protein function as a facile amplification strategy for lowering the limit of detection for M. avium subsp. paratuberculosis that may also be applicable to the design of a wide range of highly sensitive assays for other cells and viruses.

Detection of Mycobacterium avium subsp. paratuberculosis by a sonicate immunoassay based on surface-enhanced Raman scattering

A sandwich immunoassay for the rapid, low-level detection of Mycobacterium avium subsp. paratuberculosis has been developed. M. avium subsp. paratuberculosis is the causative agent of Johne's disease in cattle, and one of the major obstacles in controlling the spread of this disease is the inability to rapidly detect small amounts of bacteria or other diagnostic markers shed during the subclinical stage of infection. This paper details the development and performance of an assay for sonicated M. avium subsp. paratuberculosis lysate that is based on surface-enhanced Raman scattering (SERS). There are two key components of the assay: (i) an immobilized layer of monoclonal antibodies that target a surface protein on the microorganism; and (ii) extrinsic Raman labels (ERLs) that are designed to selectively bind to captured proteins and produce large SERS signals. By correlating the number of M. avium subsp. paratuberculosis bacilli present prior to sonication to the amount of total protein in the resulting sonicate, the detection limit determined for total protein can be translated to the microorganism concentration. These findings yield detection limits of 100 and 200 ng/ml (estimated to be 500 and 1,000 M. avium subsp. paratuberculosis bacilli/ml) for sonicate spiked in phosphate buffer and sonicate spiked in whole milk, respectively. Moreover, the time required to complete the assay, which includes sample preparation, antigen extraction, ERL incubation, and readout, is less than 24 h. The potential for incorporation of this novel assay into diagnostic laboratories is also briefly discussed.

Preparation of gold-tellurium hybrid nanomaterials for surface-enhanced Raman spectroscopy

We report a simple method for preparing three different SERS-active substrates. Concentrated hydrazine solution as the reducing agent and tellurium dioxide as the precursor were used to prepare Te nanowires (NWs). The as-prepared Te NWs have an average length of 547.7 +/- 111.6 nm and an average width of 15.1 +/- 2.7 nm. Through the reaction of Te NWs with sodium tetrachloroaurate in the presence of hexadecyltrimethylammonium bromide (CTAB) over reaction times of 10, 20, and 60 min, gold-tellurium nanodumbbells, gold-tellurium nanopeapods, and gold pearl-necklace nanomaterials (Au PNNs) were obtained, respectively. By controlling the reaction time, the distance between adjacent gold nanoparticles (Au NPs) in each Te nanowire was tunable, allowing us to investigate its effect on the SERS signals. Having shorter distances among Au NPs (greater electromagnetic fields), the Au PNNs provided a reproducible enhancement factor of 5.6 x 10(9).

Quantitative enhanced Raman scattering of labeled DNA from gold and silver nanoparticles

Surface-enhanced resonance Raman scattering (SERRS) from silver nanoparticles using 514.5-nm excitation has been shown to offer huge potential for applications in highly sensitive multiplexed DNA assays. If the technique is to be applied to real biological samples and integrated with other methods, then the use of gold nanoparticles and longer wavelengths of excitation are desirable. The data presented here demonstrate that dye-labeled oligonucleotide sequences can be directly detected by SERRS using gold nanoparticles in a quantitative manner for the first time. The performance of gold and silver nanoparticles as SERRS substrates was assessed using 514.5-, 632.8-, and 785-nm excitation and a range of 13 commercially available dye-labeled oligonucleotides. The quantitative response allowed the limit of detection to be determined for each case and demonstrates that the technique is highly effective, sensitive, and versatile. The possibility of excitation at multiple wavelengths further enhances the multiplexing potential of the technique. The importance of effectively combining the optical properties of the nanoparticle and the dye label is demonstrated. For example, at 632.8-nm excitation, the dye BODIPY TR-X and gold nanoparticles make a strong SERRS combination with very little background fluorescence. This study allows the choice of nanoparticle and dye label for particular experimental setups, and significantly expands the applicability of enhanced Raman scattering for use in many disciplines.

Highly sensitive detection of dye-labelled DNA using nanostructured gold surfaces

Careful control of surface chemistry results in strong surface enhanced resonance Raman scattering from dye-labelled oligonucleotides assembled on nanostructured gold surfaces, releasing their potential as reliable enhancing surfaces.

Raman spectroscopy: the gateway into tomorrow's virology

In the molecular world, researchers act as detectives working hard to unravel the mysteries surrounding cells. One of the researchers' greatest tools in this endeavor has been Raman spectroscopy. Raman spectroscopy is a spectroscopic technique that measures the unique Raman spectra for every type of biological molecule. As such, Raman spectroscopy has the potential to provide scientists with a library of spectra that can be used to unravel the makeup of an unknown molecule. However, this technique is limited in that it is not able to manipulate particular structures without disturbing their unique environment. Recently, a novel technology that combines Raman spectroscopy with optical tweezers, termed Raman tweezers, evades this problem due to its ability to manipulate a sample without physical contact. As such, Raman tweezers has the potential to become an incredibly effective diagnostic tool for differentially distinguishing tissue, and therefore holds great promise in the field of virology for distinguishing between various virally infected cells. This review provides an introduction for a virologist into the world of spectroscopy and explores many of the potential applications of Raman tweezers in virology.