SERS detection of indirect viral DNA capture using colloidal gold and methylene blue as a Raman label

Trends and challenges in electroanalytical biosensing methodologies for infectious viral diseases

Viral pandemic diseases have disruptive global consequences leading to millions of deaths and a severe impact on the global economy. Inadequate preventative protocols have led to an overwhelming demand for intensive care leading to uncontrollable burdens and even breakdown of healthcare sectors across many countries. The rapid detection of viral disease helps in the understanding of the relevant intricacies, helping to tackle infection with improved guidelines. Portable biosensor devices offer promising solutions by facilitating on-site detection of viral pathogens. This review summarizes the latest innovative strategies reported using electroanalytical methods for the screening of viral antigens. The structural components of viruses and their categories are presented followed by the various recognition elements and transduction techniques involved in biosensors. Core sections focus on biosensors reported for viral genomic detection(DNA and RNA) and antigenic capsid protein. Strategies for addressing the challenges of electroanalytical biosensing of viral components are also presented. The advantages, and disadvantages of biorecognition elements and nanozymes for the detection of viral disease are highlighted. Such technical insights will help researchers working in chemistry, and biochemistry as well as clinicians working in medical diagnostics.

Facile Microwave Assisted Synthesis of Silver Nanostars for Ultrasensitive Detection of Biological Analytes by SERS

We report a very simple, rapid and reproducible method for the fabrication of anisotropic silver nanostars (AgNS) that can be successfully used as highly efficient SERS substrates for different bioanalytes, even in the case of a near-infra-red (NIR) excitation laser. The nanostars have been synthesized using the chemical reduction of Ag+ ions by trisodium citrate. This is the first research reporting the synthesis of AgNS using only trisodium citrate as a reducing and stabilizing agent. The key elements of this original synthesis procedure are rapid hydrothermal synthesis of silver nanostars followed by a cooling down procedure by immersion in a water bath. The synthesis was performed in a sealed bottom flask homogenously heated and brought to a boil in a microwave oven. After 60 s, the colloidal solution was cooled down to room temperature by immersion in a water bath at 35 °C. The as-synthesized AgNS were washed by centrifugation and used for SERS analysis of test molecules (methylene blue) as well as biological analytes: pharmaceutical compounds with various Raman cross sections (doxorubicin, atenolol & metoprolol), cell lysates and amino acids (methionine & cysteine). UV-Vis absorption spectroscopy, (Scanning) Transmission Electron Microscopy ((S)TEM) and Atomic Force Microscopy (AFM) have been employed for investigating nanostars' physical properties.

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.

Analysis of Biomolecules Based on the Surface Enhanced Raman Spectroscopy

Analyzing biomolecules is essential for disease diagnostics, food safety inspection, environmental monitoring and pharmaceutical development. Surface-enhanced Raman spectroscopy (SERS) is a powerful tool for detecting biomolecules due to its high sensitivity, rapidness and specificity in identifying molecular structures. This review focuses on the SERS analysis of biomolecules originated from humans, animals, plants and microorganisms, combined with nanomaterials as SERS substrates and nanotags. Recent advances in SERS detection of target molecules were summarized with different detection strategies including label-free and label-mediated types. This comprehensive and critical summary of SERS analysis of biomolecules might help researchers from different scientific backgrounds spark new ideas and proposals.

Aluminum Nanocrystals: A Sustainable Substrate for Quantitative SERS-Based DNA Detection

Since its discovery in the 1970s, surface-enhanced Raman scattering (SERS) has been primarily associated with substrates composed of nanostructured noble metals. Here we investigate chemically synthesized nanocrystal aggregates of aluminum, an inexpensive, highly abundant, and sustainable metal, as SERS substrates. Al nanocrystal aggregates are capable of substantial near-infrared SERS enhancements, similar to Au nanoparticles. The intrinsic nanoscale surface oxide of Al nanocrystals supports molecule-substrate interactions that differ dramatically from noble metal substrates. The preferential affinity of the single-stranded DNA (ssDNA) phosphate backbone for the Al oxide surface preserves both the spectral features and nucleic acid cross sections relative to conventional Raman spectroscopy, enabling quantitative ssDNA detection and analysis.

Exploiting the Anti-Aggregation of Gold Nanostars for Rapid Detection of Hand, Foot, and Mouth Disease Causing Enterovirus 71 Using Surface-Enhanced Raman Spectroscopy

Enterovirus 71 (EV71) is a major public health threat that requires rapid point-of-care detection. Here, we developed a surface-enhanced Raman spectroscopy (SERS)-based scheme that utilized protein-induced aggregation of colloidal gold nanostars (AuNS) to rapidly detect EV71 without the need for fabricating a solid substrate, Raman labels or complicated sample handling. We used AuNS (hydrodynamic diameter, DH of 105.12 ± 1.13 nm) conjugated to recombinant scavenger receptor class B, member 2 (SCARB2) protein with known affinity to EV71. In the absence of EV71, AuNS-SCARB2 aggregated in biological media and produced four enhanced Raman peaks at 390, 510, 670, and 910 cm-1. In the presence of EV71, the three peaks at 510, 670, and 910 cm-1 disappeared, while the peak at 390 cm-1 diminished in intensity as the virus bound to AuNS-SCARB2 and prevented them from aggregation. These three peaks (510, 670, and 910 cm-1) were potential markers for specific detection of EV71 as their disappearance was not observable with a different dengue virus (DENV) as our control. Furthermore, the Raman measurements from colloidal SERS were more sensitive in probing the aggregation of AuNS-SCARB2 for detecting the presence of EV71 in protein-rich samples compared to UV-vis spectrum measurements. With this facile "anti-aggregation" approach, we were able to detect EV71 in protein-rich biological medium within 15 min with reasonable sensitivity of 107 pfu/mL and minimal sample preparation, making this translatable for point-of-care applications.

SERS detection of microRNA biomarkers for cancer diagnosis using gold-coated paramagnetic nanoparticles to capture SERS-active gold nanoparticles

A highly sensitive magnetic-capture SERS assay for detecting cancer-related microRNAs was developed by enhancing the formation of SERS “hot spots”.

Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization

Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.

Immunoassay for tumor markers in human serum based on Si nanoparticles and SiC@Ag SERS-active substrate

An immunoassay protocol is described to detect tumor markers in human serum based on a sandwich structure consisting of nano-Si immune probes and SiC@Ag SERS-active immune substrate.

Self-assembled plasmonic templates produced by microwave annealing: applications to surface-enhanced Raman scattering

Perhaps the simplest method for creating metal nanoparticles on a substrate is by driving their self-assembly with the thermal annealing of a thin metal film. By properly tuning the annealing parameters one hopes to discover a recipe that allows the pre-determined design of the NP arrangement. However, thermal treatment is known for detrimental effects and is not really the manufacturer's route of choice when it comes to large-scale applications. An alternative method is the use of microwave annealing, a method that has never been applied for metal processing, due to the high reflectance of microwave radiation at the surface of a metal. However, in this work we challenge the widely used nanostructuring methods by proving the microwave's annealing ability to produce plasmonic templates, out of extremely thin metal films, by simply using a domestic microwave oven apparatus. We show that this process is generic and independent of the deposition method used for the metal and we further quantify the suitability of these plasmonic templates for use in surface-enhanced Raman scattering applications.

SERS-based direct and sandwich assay methods for mir-21 detection

In this study, two different assay methods were developed using a surface enhanced Raman scattering (SERS) label for sensitive miR-21 detection. In the first method (direct assay), the miR-21 probe was attached to SERS-labelled, rod-shaped gold nanoparticles and hybridised with the target miR-21, which was previously immobilised onto the gold slide. In the second method (sandwich assay), the target miR-21 was captured by an miR-21 probe immobilised onto the gold slide and hybridised with a second miR-21 probe immobilised on the SERS-labeled, rod-shaped gold nanoparticles. SERS signals of developed assays were obtained via a SERS spectrum of 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) on the rod-shaped nanoparticles. The calibration curves were plotted to measure the different concentrations of miR-21. The detection limits of the direct and sandwich assays, which last less than 40 min, were found to be 0.36 and 0.85 nM, respectively. The developed SERS-based methods offer rapid, selective, sensitive and easy detection of miR-21, especially compared to conventional PCR-based methods.

Identification of virulence determinants in influenza viruses

To date there is no rapid method to screen for highly pathogenic avian influenza strains that may be indicators of future pandemics. We report here the first development of an oligonucleotide-based spectroscopic assay to rapidly and sensitively detect a N66S mutation in the gene coding for the PB1-F2 protein associated with increased virulence in highly pathogenic pandemic influenza viruses. 5'-Thiolated ssDNA oligonucleotides were employed as probes to capture RNA isolated from six influenza viruses, three having N66S mutations, two without the N66S mutation, and one deletion mutant not encoding the PB1-F2 protein. Hybridization was detected without amplification or labeling using the intrinsic surfaced-enhanced Raman spectrum of the DNA-RNA complex. Multivariate analysis identified target RNA binding from noncomplementary sequences with 100% sensitivity, 100% selectivity, and 100% correct classification in the test data set. These results establish that optical-based diagnostic methods are able to directly identify diagnostic indicators of virulence linked to highly pathogenic pandemic influenza viruses without amplification or labeling.

Nanocrystalline Ag microflowers as a versatile SERS platform

In this paper, the synthesis of Ag microflowers for use as manipulable and reusable substrates in surface enhanced Raman spectroscopy (SERS) is demonstrated, working with ultra-low volumes of the analyte. Flower-like AgBr crystallites with a growth direction of 〈110〉 were first obtained by thermolysing a complex obtained by the stabilization of (AgCl2)(-) anions with tetraoctylammonium bromide. NaBH4 reduction leads to the formation of porous Ag microflowers (50-100 μm) with interconnected nanoparticles. The coupling of the nanoparticles in the microflower results in broadband extinction from visible to IR wavelengths, facilitating SERS using both red and green wavelengths. Using thiophenol as test analyte, uniform SERS enhancement factors in the range of 10(6)-10(8) have been achieved from different parts of the microflower. The microflowers have been used for labeled and non-labeled detection of both single- and double-stranded DNA and using simple manipulation techniques, SERS data have been collected from ultra-low volumes of the analyte solution (∼0.34 nL). The reusability of the substrate for SERS over multiple cycles involving a rapid and efficient wet chemical cleaning procedure is also demonstrated. Finally, by placing the microflower in a microfluidic device, chemical reactions have been examined in situ.

Performance-enhancing methods for Au film over nanosphere surface-enhanced Raman scattering substrate and melamine detection application

A new high-performance surface-enhanced Raman scattering (SERS) substrate with extremely high SERS activity was produced. This SERS substrate combines the advantages of Au film over nanosphere (AuFON) substrate and Ag nanoparticles (AgNPs). A three order enhancement of SERS was observed when Rhodamine 6G (R6G) was used as a probe molecule to compare the SERS effects of the new substrate and commonly used AuFON substrate. These new SERS substrates can detect R6G down to 1 nM. The new substrate was also utilized to detect melamine, and the limit of detection (LOD) is 1 ppb. A linear relationship was also observed between the SERS intensity at Raman peak 682 cm⁻¹ and the logarithm of melamine concentrations ranging from 10 ppm to 1 ppb. This ultrasensitive SERS substrate is a promising tool for detecting trace chemical molecules because of its simple and effective fabrication procedure, high sensitivity and high reproducibility of the SERS effect.

Hybrids of carbon nanotube forests and gold nanoparticles for improved surface plasmon manipulation

We report the fabrication and characterization of hybrids of vertically-aligned carbon nanotube forests and gold nanoparticles for improved manipulation of their plasmonic properties. Raman spectroscopy of nanotube forests performed at the separation area of nanotube-nanoparticles shows a scattering enhancement factor of the order of 1 × 10(6). The enhancement is related to the plasmonic coupling of the nanoparticles and is potentially applicable in high-resolution scanning near-field optical microscopy, plasmonics, and photovoltaics.

Applications of surface-enhanced Raman scattering in advanced bio-medical technologies and diagnostics

In this review of the literature on surface-enhanced Raman scattering (SERS), we describe recent developments of this technique in the medical field. SERS has developed rapidly in the last few years as a result of the fascinating advancements in instrumentation and the ability to interpret complex Raman data using high-processional, computer-aided programs. This technique, has many advantages over ordinary spectroscopic analytical techniques - such as extremely high sensitivity, molecular selectivity, intense signal and great precision - that can be leveraged to address complex medical diagnostics problems. This review focuses on the SERS-active substrate, as well as major advances in cancer and bacteria detection and imaging. Finally, we present a perspective on anticipated future advancements in SERS techniques to address some of the most critical challenges in the areas of diagnostics, detection, and sensing.

Fast fabrication of homogeneous Ag nanostructures on dual-acid doped polyaniline for SERS applications

We demonstrate a dual-acid doping technique for PANI membranes, which enables fast fabrication of homogeneous Ag nanostructures as SERS-active platforms for chemical detection.

The development of surface-enhanced Raman scattering as a detection modality for portable in vitro diagnostics: progress and challenges

This perspective provides an overview of the diverse surface-enhanced Raman scattering (SERS)-based sensor platforms that have been developed for in vitro diagnostic applications. To provide focus, protein and nucleic acid detection assays based on the principle of extrinsic SERS sensing are emphasized, as well as their potential for translation to fully integrated point-of-care (POC) test platforms. The development of intrinsic SERS sensors, which are predicated on the direct detection of analytes by laser excitation, entails unique opportunities and challenges deserving of their own attention. As the robust sensing of disease pathogens and cancers in both clinical facilities and limited resource settings is the targeted objective of many next-generation biosensors, the majority of the research progress summarized here centers on SERS sensors developed for the rapid, sensitive and selective detection of disease-causing pathogens and biomarkers. In our effort to communicate a realistic assessment of the progress that has been made and the challenges that lie ahead, we avoid an overtly optimistic appraisal of the current status of SERS diagnostics that does not tacitly acknowledge the difficulties inherent in aligning SERS-based technologies alongside ELISA and PCR technologies as a complementary method for bioanalyte detection possessing unique advantages.

Limitations of surface enhanced Raman scattering in sensing DNA hybridization demonstrated by label-free DNA oligos as molecular rulers of distance-dependent enhancement

This article presents a critical evaluation of silver nanorod arrays as substrates for assaying nucleic acid hybridization by surface enhanced Raman scattering (SERS). SERS spectra acquired on complementary oligos, alone or in combination, contain the known spectral signatures of the nucleotides that comprise the oligo; however, no signature bands characteristic of the hybrid were observed. Spectra acquired on an oligo with a 5'- or 3'-thiol were distinctly different from that acquired on the identical oligo without a thiol pendant group suggesting a degree of control over the orientation of the oligo on the nanorod surface. A set of oligos consisting of adenine tracts in a polycytosine chain served as molecular rulers to probe the distance dependence of the SERS enhancement. Using these, we have identified the point at which the characteristic bands for the nucleotides that comprise the oligo disappear from the spectrum. These findings suggest that the applicability of SERS for label-free detection of nucleic acid hybridization is limited to short oligos of less than nine nucleotides.

Surface-enhanced Raman scattering detection of DNAs derived from virus genomes using Au-coated paramagnetic nanoparticles

A magnetic capture-based, surface-enhanced Raman scattering (SERS) assay for DNA detection has been developed which utilizes Au-coated paramagnetic nanoparticles (Au@PMPs) as both a SERS substrate and effective bioseparation reagent for the selective removal of target DNAs from solution. Hybridization reactions contained two target DNAs, sequence complementary reporter probes conjugated with spectrally distinct Raman dyes distinct for each target, and Au@PMPs conjugated with sequence complementary capture probes. In this case, target DNAs were derived from the RNA genomes of the Rift Valley Fever virus (RVFV) or West Nile virus (WNV). The hybridization reactions were incubated for a short period and then concentrated within the focus beam of an interrogating laser by magnetic pull-down. The attendant SERS response of each individually captured DNA provided a limit of detection sensitivity in the range 20-100 nM. X-ray diffraction and UV-vis analysis validated both the desired surface plasmon resonance properties and bimetallic composition of synthesized Au@PMPs, and UV-vis spectroscopy confirmed conjugation of the Raman dye compounds malachite green (MG) and erythrosin B (EB) with the RVFV and WNV reporter probes, respectively. Finally, hybridization reactions assembled for multiplexed detection of both targets yielded mixed MG/EB spectra and clearly differentiated peaks which facilitate the quantitative detection of each DNA target. On the basis of the simple design of a single-particle DNA detection assay, the opportunity is provided to develop magnetic capture-based SERS assays that are easily assembled and adapted for high-level multiplex detection using low-cost Raman instrumentation.

Noble metal nanoparticles for biosensing applications

In the last decade the use of nanomaterials has been having a great impact in biosensing. In particular, the unique properties of noble metal nanoparticles have allowed for the development of new biosensing platforms with enhanced capabilities in the specific detection of bioanalytes. Noble metal nanoparticles show unique physicochemical properties (such as ease of functionalization via simple chemistry and high surface-to-volume ratios) that allied with their unique spectral and optical properties have prompted the development of a plethora of biosensing platforms. Additionally, they also provide an additional or enhanced layer of application for commonly used techniques, such as fluorescence, infrared and Raman spectroscopy. Herein we review the use of noble metal nanoparticles for biosensing strategies—from synthesis and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics laboratory.

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.

Surface-enhanced Raman scattering detection of DNA derived from the west nile virus genome using magnetic capture of Raman-active gold nanoparticles

A model paramagnetic nanoparticle (MNP) assay is demonstrated for surface-enhanced Raman scattering (SERS) detection of DNA oligonucleotides derived from the West Nile virus (WNV) genome. Detection is based on the capture of WNV target sequences by hybridization with complementary oligonucleotide probes covalently linked to fabricated MNPs and Raman reporter tag-conjugated gold nanoparticles (GNPs) and the subsequent removal of GNP-WNV target sequence-MNP hybridization complexes from solution by an externally applied magnetic source. Laser excitation of the pelleted material provided a signature SERS spectrum which is diagnostic for the reporter, 5,5'-dithiobis(succinimidy-2-nitrobenzoate) (DSNB), and restricted to hybridization reactions containing WNV target sequences. Hybridizations containing dilutions of the target oligonucleotide were characterized by a reduction in the intensification of the spectral peaks accorded to the SERS signaling of DSNB, and the limit of detection for target sequence in buffer was 10 pM. Due to the short hybridization times required to conduct the assay and ease with which reproducible Raman spectra can be acquired, the assay is amenable to adaptation within a portable, user-friendly Raman detection platform for nucleic acids.

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).

Qualitative analysis and the answer box: a perspective on portable Raman spectroscopy

Miniaturization of Raman instruments has created a new genre of devices for qualitative analysis of materials. These new devices are introducing Raman spectroscopy to a diverse range of applications.