Sensitive and Direct DNA Mutation Detection by Surface-Enhanced Raman Spectroscopy Using Rational Designed and Tunable Plasmonic Nanostructures

Direct detection of melamine in milk via surface-enhanced Raman scattering using gold-silver anisotropic nanostructures

As the degree of anisotropy in nanoparticle morphology increases, the resulting electromagnetic enhancement can be significantly intensified. Herein, we have attempted to develop anisotropic gold-silver (a-AuAg) nanoparticles deposited on a titanium sheet (a-AuAg@Ti) as a highly efficient Surface-enhanced Raman Spectroscopy (SERS) sensor for rapid detection of health-hazardous milk adulterants like melamine. Hierarchical a-AuAg nanoparticles have been synthesized via a facile seed and growth-mediated method, followed by immobilization on a titanium sheet using a drop-casting technique. The structural, morphological, chemical, and optical properties of a-AuAg@Ti sensors have been systematically investigated and correlated with their respective SERS performance. Morphological analysis revealed the occurrence of triangular, hexagonal, and pentagonal-shaped nanoparticles with an average particle size of ∼ 23 to 26 nm. Preliminary SERS analysis using Rhodamine 6G (R6G) probe molecule revealed significantly higher SERS activity for a-AuAg nanoparticles compared to their spherical counterparts. This could be attributed to the lightning rod effect associated with the synthesized anisotropic nanostructures. An enhancement factor of 1.7 x 108 has been estimated for a-AuAg@Ti sensor with excellent signal reproducibility. Further, the efficacy of melamine detection has been investigated by spiking it into water and milk samples. The estimated lower detection limit (LDL) near picomolar and nanomolar concentrations have been obtained for melamine-spiked samples in water and milk, respectively. High-performance liquid chromatography analysis for melamine revealed an LDL of only 0.1 µM, indicating the higher sensitivity of a-AuAg@Ti SERS sensor. Moreover, we have also analyzed commercial milk products to verify the melamine contents, but none of them showed melamine-specific fingerprint bands. Our findings highlight the superior sensitivity of a-AuAg@Ti substrates for real-time melamine detection, making them excellent optical sensing tools for food safety analysis.

Nanogap-Assisted SERS/PCR Biosensor Coupled Machine Learning for the Direct Sensing of Staphylococcus aureus in Food

Staphylococcus aureus (S. aureus) is the primary risk factor in food safety. Herein, a nanogap-assisted surface-enhanced Raman scattering/polymerase chain reaction (SERS/PCR) biosensor coupled with a machine-learning tool was developed for the direct and specific sensing of S. aureus in milk. The specific nuc gene (nuc T) from S. aureus was initially amplified through PCR and subsequently captured via the nanogap effect of I- and Mg2+-mediated bimetallic gold and silver nanoflowers (Au/Ag FL@I--Mg2+). These nanogaps generate hotspots for the direct signal amplification of enclosed nuc T. Subsequently, machine-learning tools were used to comparatively analyze the collected SERS signals. The bootstrapping soft shrinkage-partial least-squares method exhibited superior performance (root mean-square error of prediction: 0.437, prediction set correlation coefficient: 0.967). This study demonstrated a novel label-free strategy for specifically detecting S. aureus. The strategy could be advanced to serve as a platform for application to other types of foodborne pathogenic bacteria by engineering a suitable specific primer.

A novel platform for mutation detection in colorectal cancer using a PNA-LNA molecular switch

Detection of KRAS mutation in colorectal cancer (CRC) is important in the prediction of response to target therapy. The study aims to develop a novel mutation detection platform called the "PNA-LNA molecular switch" for the detection of KRAS mutation in CRC. We employed the enhanced binding specificity of peptide nucleic acid (PNA) and locked nucleic acid (LNA) in conjunction with a loop-mediated isothermal amplification (LAMP) approach to identify the mutation status of KRAS oncogene codon 12 (c.35G>T/G12V and c.35G>A/G12D) using synthetic oligonucleotides and colon cancer cell lines (Caco-2 and SW480). This method specifically blocked the amplification of the wild-type sequences while substantially amplifying the mutated ones, which was visualized by both colorimetric and fluorescence assays. We then checked the mutation profile of KRAS codon 12 in the DNA derived from tumor tissue samples (number of samples, n = 30) and circulating tumor cells (n = 24) from CRC patients. Finally, we validated the results by comparing them with the data obtained from DNA sequencing of colon tumors (n = 21) of the same CRC patients. This method showed excellent sensitivity (1 DNA copy/μl), reproducibility [relative standard deviation (%RSD) < 5%, for n = 3], and linear dynamic range (1 ag/μl-10 pg/μl, R2 = 0.94). This platform is significantly faster, relatively cheaper, has superior sensitivity and specificity, and does not require any high-end equipment. To conclude, this method has the potential to be translated into clinical settings for the detection of mutations in diverse diseases and conditions.

SERSomes for metabolic phenotyping and prostate cancer diagnosis

Molecular phenotypic variations in metabolites offer the promise of rapid profiling of physiological and pathological states for diagnosis, monitoring, and prognosis. Since present methods are expensive, time-consuming, and still not sensitive enough, there is an urgent need for approaches that can interrogate complex biological fluids at a system-wide level. Here, we introduce hyperspectral surface-enhanced Raman spectroscopy (SERS) to profile microliters of biofluidic metabolite extraction in 15 min with a spectral set, SERSome, that can be used to describe the structures and functions of various molecules produced in the biofluid at a specific time via SERS characteristics. The metabolite differences of various biofluids, including cell culture medium and human serum, are successfully profiled, showing a diagnosis accuracy of 80.8% on the internal test set and 73% on the external validation set for prostate cancer, discovering potential biomarkers, and predicting the tissue-level pathological aggressiveness. SERSomes offer a promising methodology for metabolic phenotyping.

SERS biosensors for liquid biopsy towards cancer diagnosis by detection of various circulating biomarkers: current progress and perspectives

Liquid biopsy has emerged as a promising non-invasive strategy for cancer diagnosis, enabling the detection of various circulating biomarkers, including circulating tumor cells (CTCs), circulating tumor nucleic acids (ctNAs), circulating tumor-derived small extracellular vesicles (sEVs), and circulating proteins. Surface-enhanced Raman scattering (SERS) biosensors have revolutionized liquid biopsy by offering sensitive and specific detection methodologies for these biomarkers. This review comprehensively examines the application of SERS-based biosensors for identification and analysis of various circulating biomarkers including CTCs, ctNAs, sEVs and proteins in liquid biopsy for cancer diagnosis. The discussion encompasses a diverse range of SERS biosensor platforms, including label-free SERS assay, magnetic bead-based SERS assay, microfluidic device-based SERS system, and paper-based SERS assay, each demonstrating unique capabilities in enhancing the sensitivity and specificity for detection of liquid biopsy cancer biomarkers. This review critically assesses the strengths, limitations, and future directions of SERS biosensors in liquid biopsy for cancer diagnosis.

Multiplex detection of bacterial pathogens by PCR/SERS assay

Bacterial infections are a leading cause of death globally. The detection of DNA sequences correlated to the causative pathogen has become a vital tool in medical diagnostics. In practice, PCR-based assays for the simultaneous detection of multiple pathogens currently rely on probe-based quantitative strategies that require expensive equipment but have limited sensitivity or multiplexing capabilities. Hence, novel approaches to address the limitations of the current gold standard methods are still in high demand. In this study, we propose a simple multiplex PCR/SERS assay for the simultaneous detection of four bacterial pathogens, namely P. aeruginosa, S. aureus, S. epidermidis, and M. smegmatis. Wherein, specific primers for amplifying each target gDNA were applied, followed by applying SERS nanotags functionalized with complementary DNA probes and Raman reporters for specific identification of the target bacterial pathogens. The PCR/SERS assay showed high specificity and sensitivity for genotyping bacterial pathogen gDNA, whereby as few as 100 copies of the target gDNA could be detected. With high sensitivity and the convenience of standard PCR amplification, the proposed assay shows great potential for the sensitive detection of multiple pathogen infections to aid clinical decision-making.

Ultrafast and Highly Specific Detection of One-Base Mutated Cell-Free DNA at a Very Low Abundance

Liquid biopsy as well as genotyping plays important roles in guiding the use of tumor-targeted drugs and monitoring the generation of drug resistance. However, current methods, such as next-generation sequencing (NGS) and pyrosequencing, require long analysis time and complicated steps. To achieve ultrafast and highly specific detection of cell-free DNA (cfDNA) from blood, we improved our recently developed FEN1-aided RPA (FARPA), which combined flap endonuclease 1 (FEN1)-catalyzed invasive reactions with recombinase polymerase amplification (RPA) by inactivating the RPA enzymes before invasive reactions, designing short RPA primers, and changing invasive reaction conditions. Using the L858R and T790M mutations as examples, FARPA was sensitive to detect 5 copies of targeted mutants, specific to sense the mutants with an abundance as low as 0.01% from blood, and ultrafast to get results within 40 min. The method was readily expended to genotyping, and 15 min was enough to report the allele species directly from oral swab samples by coupling quick DNA extraction reagents. Validation was carried out by detecting clinical samples, including 20 cfDNA from patients with non-small cell lung cancer (NSCLC) for liquid biopsy and 43 human genomic DNA (gDNA) purified from blood (33) or lysed from oral swabs (10) for genotyping, giving 100% agreement with NGS and pyrosequencing, respectively. Furthermore, a portable battery-driven device with dual-channel fluorescence detection was successfully constructed to facilitate point-of-care testing (POCT) of liquid biopsy and genotyping, providing doctors with a potential tool to achieve genotyping- or mutant-guided personalized medicine at emergency or source-limited regions.

Surface-enhanced Raman scattering sensing for detection and mapping of key cellular biomarkers

Cellular biomarkers mainly contain proteins, nucleic acids, glycans and many small molecules including small biomolecule metabolites, reactive oxygen species and other cellular chemical entities. The detection and mapping of the key cellular biomarkers can effectively help us to understand important cellular mechanisms associated with physiological and pathological processes, which greatly promote the development of clinical diagnosis and disease treatment. Surface-enhanced Raman scattering (SERS) possesses high sensitivity and is free from the influence of strong self-fluorescence in living systems as well as the photobleaching of the dyes. It exhibits rich and narrow chemical fingerprint spectra for multiplexed detection, and has become a powerful tool to detect and map cellular biomarkers. In this review, we present an overview of recent advances in the detection and mapping of different classes of cellular biomarkers based on SERS sensing. These advances fully confirm that the SERS-based sensors and sensing methods have great potential for the exploration of biological mechanisms and clinical applications. Additionally, we also discuss the limitations of present research and the future developments of the SERS technology in this field.

Nanoplasmonic biosensors for precision medicine

Nanoplasmonic biosensors have a huge boost for precision medicine, which allows doctors to better understand diseases at the molecular level and to improve the earlier diagnosis and develop treatment programs. Unlike traditional biosensors, nanoplasmonic biosensors meet the global health industry's need for low-cost, rapid and portable aspects, while offering multiplexing, high sensitivity and real-time detection. In this review, we describe the common detection schemes used based on localized plasmon resonance (LSPR) and highlight three sensing classes based on LSPR. Then, we present the recent applications of nanoplasmonic in other sensing methods such as isothermal amplification, CRISPR/Cas systems, lab on a chip and enzyme-linked immunosorbent assay. The advantages of nanoplasmonic-based integrated sensing for multiple methods are discussed. Finally, we review the current applications of nanoplasmonic biosensors in precision medicine, such as DNA mutation, vaccine evaluation and drug delivery. The obstacles faced by nanoplasmonic biosensors and the current countermeasures are discussed.

Plasmonic surface-enhanced Raman scattering nano-substrates for detection of anionic environmental contaminants: Current progress and future perspectives

Surface-enhanced Raman scattering spectroscopy (SERS) is a powerful technique of vibrational spectroscopy based on the inelastic scattering of incident photons by molecular species. It has unique properties such as ultra-sensitivity, selectivity, non-destructivity, speed, and fingerprinting properties for analytical and sensing applications. This enables SERS to be widely used in real-world sample analysis and basic plasmonic mechanistic studies. However, the desirable properties of SERS are compromised by the high cost and low reproducibility of the signals. The development of multifunctional, stable and reusable nano-engineered SERS substrates is a viable solution to circumvent these drawbacks. Recently, plasmonic SERS active nano-substrates with various morphologies have attracted the attention of researchers due to promising properties such as the formation of dense hot spots, additional stability, tunable and controlled morphology, and surface functionalization. This comprehensive review focused on the current advances in the field of SERS active nanosubstrates suitable for the detection and quantification of anionic environmental pollutants. The common fabrication methods, including the techniques for morphological adjustments and surface modification, substrate categories, and the design of nanotechnologically fabricated plasmonic SERS substrates for anion detection are systematically presented. Here, the need for the design, synthesis, and functionalization of SERS nano-substrates for anions of great environmental importance is explained in detail. In addition, the broad categories of SERS nano-substrates, namely colloid-based SERS substrates and solid-support SERS substrates are discussed. Moreover, a brief discussion of SERS detection of certain anionic pollutants in the environment is presented. Finally, the prospects in the fabrication and commercialization of pilot-scale handheld SERS sensors and the construction of smart nanosubstrates integrated with novel amplifying materials for the detection of anions of environmental and health concern are proposed.

Nanosupernova: a new anisotropic nanostructure for SERS

Gold and/or silver nanostars are interesting anisotropic nanoparticles that have been used in surface-enhanced Raman scattering (SERS). In particular SERS nanotags consisting of gold nanostars and Raman reporter molecules have been widely utilised in biosensing and bioimaging. To improve the SERS activity of gold/silver nanostars, this paper details the development of a simple synthesis method that results in the formation of quasi-spherical SERS nanotags and larger highly anisotropic nanoparticles with a novel structure, which we have designated nanosupernova. The resulting SERS nanotags and nanosupernova contain gold/silver nanostars at their core, a self-assembled monolayer of Raman reporter molecules, and a final silver coating. The silver coating is the essential step responsible for the formation of the two types of particles, with incubation time, and type of Raman reporter molecule, the defining factor as to which forms. We discovered that the Raman reporter molecule, 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), plays a crucial role in controlling the morphology of nanosupernova. We believe the larger highly anisotropic nanoparticles will open new applications in material sciences and in optical and electronic devices in the future.

The Application of Nanotechnology for Quantification of Circulating Tumour DNA in Liquid Biopsies: A Systematic Review

Technologies for quantifying circulating tumour DNA (ctDNA) in liquid biopsies could enable real-time measurements of cancer progression, profoundly impacting patient care. Sequencing methods can be too complex and time-consuming for regular point-of-care monitoring, but nanotechnology offers an alternative, harnessing the unique properties of objects tens to hundreds of nanometres in size. This systematic review was performed to identify all examples of nanotechnology-based ctDNA detection and assess their potential for clinical use. Google Scholar, PubMed, Web of Science, Google Patents, Espacenet and Embase/MEDLINE were searched up to 23rd March 2021. The review identified nanotechnology-based methods for ctDNA detection for which quantitative measures (e.g., limit of detection, LOD) were reported and biologically relevant samples were used. The pre-defined inclusion criteria were met by 66 records. LODs ranged from 10 zM to 50nM. 25 records presented an LOD of 10fM or below. Nanotechnology-based approaches could provide the basis for the next wave of advances in ctDNA diagnostics, enabling analysis at the point-of-care, but none are currently used clinically. Further work is needed in development and validation; trade-offs are expected between different performance measures e.g., number of sequences detected and time to result.

SERS combined with PCR as a potent tool for detecting mutations: a case study of tomato plants

Conventional methods of detecting economically essential mutations have several disadvantages. Even though fluorescence-based methods are still the best option, Surface-Enhanced Raman Spectroscopy (SERS) may soon emerge as an alternative to the current techniques for detecting these mutations, because of its ability to detect molecular vibrational signatures. We were able to identify and develop a PCR-based SERS assay that can relentlessly differentiate between different types of indels, and SNPs as demonstrated in the case of tomato genome related to tomato yellow leaf curl virus and root-knot nematodes, diseases that are economically significant to the global agriculture industry and where the selection of resistant crops is the best solution. This tri-primer assay utilizes mutation-specific forward primers and SERS probes tagged with FAM and Cy3 dyes, specific for each allele of a particular gene (Ty-3 and Mi-1). The unique Raman spectral features of these dyes enabled to perform of multiplexing, which made it possible to detect not only the indel type but also the zygosity in a single experiment. Moreover, this technique successfully differentiated between two different SNP-based alleles. Therefore, due to its efficient multiplexing capability and lack of the need for quenchers, it has the potential to become a powerful onsite and offsite screening tool in the not-too-distant future.

Accurate assembly and direct characterization of DNA nanogels crosslinked by G-quadruplex, i-motif and duplex with surface-enhanced Raman spectroscopy

The direct characterization of DNA nanogels at the atomic level is desirable and of great significance, however, has been challenging because of structural complexity and the larger size of nanogels. Herein, we demonstrated a simple, sensitive and reliable SERS (Surface-enhanced Raman spectroscopy)-based approach towards direct monitoring microstructures, such as three types of nanogels crosslinked by DNA G-quadruplex, i-motif and GC duplex. The achievement is attributed to the detection of featured Raman bands corresponding to the formation of Watson-Crick and Hoogsteen hydrogen bonds as well as C·C⁺ base pairs. Importantly, this work reveals that the silver nanoparticles attaching on the surface of nanogels can form local 'hotspots' and produce high-quality of Raman spectra under the assistance of iodide, aluminum ions and dichloromethane, therefore, shows great potential for wide applications in accurate characterization of various DNA nanostructures.

SERS characterization of colorectal cancer cell surface markers upon anti-EGFR treatment

Colorectal cancer (CRC) is the third most diagnosed and the second lethal cancer worldwide. Approximately 30-50% of CRC are driven by mutations in the KRAS oncogene, which is a strong negative predictor for response to anti-epidermal growth factor receptor (anti-EGFR) therapy. Examining the phenotype of KRAS mutant and wild-type (WT) CRC cells in response to anti-EGFR treatment may provide significant insights into drug response and resistance. Herein, surface-enhanced Raman spectroscopy (SERS) assay was applied to phenotype four cell surface proteins (EpCAM, EGFR, HER2, HER3) in KRAS mutant (SW480) and WT (SW48) cells over a 24-day time course of anti-EGFR treatment with cetuximab. Cell phenotypes were obtained using Raman reporter-coated and antibody-conjugated gold nanoparticles (SERS nanotags), where a characteristic Raman spectrum was generated upon single laser excitation, reflecting the presence of the targeted surface marker proteins. Compared to the KRAS mutant cells, KRAS WT cells were more sensitive to anti-EGFR treatment and displayed a significant decrease in HER2 and HER3 expression. The SERS results were validated with flow cytometry, confirming the SERS assay is promising as an alternative method for multiplexed characterization of cell surface biomarkers using a single laser excitation system.

Revealing the effect of intramolecular interactions on DNA SERS detection: SERS capability for structural analysis

Intramolecular interactions are key factors for constructing the secondary conformations of biomolecules and they are also vital for biomolecular functions. Their effect on the surface-enhanced Raman spectroscopy (SERS) spectra is also important for reliable label-free detection. The current work focuses on three GCGC-quadruplexes as model molecules for SERS studies, which contain both the G-quartet and the GCGC-quartet. Their spectra are compared with the ones of the G-quadruplex and the duplex. The present work presents the specific effect of intramolecular interactions, including various Watson-Crick and Hoogsteen hydrogen bonds as well as base stacking, on the SERS signals of closely-related secondary conformations. The overall results indicated a significant influence on the direct label-free detection of DNA molecules and the SERS capability for secondary structural analysis.

Plasmonic nanosensors for point-of-care biomarker detection

Advancement of materials along with their fascinating properties play increasingly important role in facilitating the rapid progress in medicine. An excellent example is the recent development of biosensors based on nanomaterials that induce surface plasmon effect for screening biomarkers of various diseases ranging from cancer to Covid-19. The recent global pandemic re-confirmed the trend of real-time diagnosis in public health to be in point-of-care (POC) settings that can screen interested biomarkers at home, or literally anywhere else, at any time. Plasmonic biosensors, thanks to its versatile designs and extraordinary sensitivities, can be scaled into small and portable devices for POC diagnostic tools. In the meantime, efforts are being made to speed up, simplify and lower the cost of the signal readout process including converting the conventional heavy laboratory instruments into lightweight handheld devices. This article reviews the recent progress on the design of plasmonic nanomaterial-based biosensors for biomarker detection with a perspective of POC applications. After briefly introducing the plasmonic detection working mechanisms and devices, the selected highlights in the field focusing on the technology's design including nanomaterials development, structure assembly, and target applications are presented and analyzed. In parallel, discussions on the sensor's current or potential applicability in POC diagnosis are provided. Finally, challenges and opportunities in plasmonic biosensor for biomarker detection, such as the current Covid-19 pandemic and its testing using plasmonic biosensor and incorporation of machine learning algorithms are discussed.

Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications

In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.

Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers

During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.

Positively-charged plasmonic nanostructures for SERS sensing applications

Surface-enhanced Raman (SERS) spectroscopy has been establishing itself as an ultrasensitive analytical technique with a cross-disciplinary range of applications, which scientific growth is triggered by the continuous improvement in the design of advanced plasmonic materials with enhanced multifunctional abilities and tailorable surface chemistry. In this regard, conventional synthetic procedures yield negatively-charged plasmonic materials which can hamper the adhesion of negatively-charged species. To tackle this issue, metallic surfaces have been modified via diverse procedures with a broad array of surface ligands to impart positive charges. Cationic amines have been preferred because of their ability to retain a positive zeta potential even at alkaline pH as well as due to their wide accessibility in terms of structural features and cost. In this review, we will describe and discuss the different approaches for generating positively-charged plasmonic platforms and their applications in SERS sensing.

60-nt DNA Direct Detection without Pretreatment by Surface-Enhanced Raman Scattering with Polycationic Modified Ag Microcrystal Derived from AgCl Cube

Direct detection of long-strand DNA by surface-enhanced Raman scattering (SERS) is a valuable method for diagnosis of hereditary diseases, but it is currently limited to less than 25-nt DNA strand in pure water, which makes this approach unsuitable for many real-life applications. Here, we report a 60-nt DNA label-free detection strategy without pretreatment by SERS with polyquaternium-modified Ag microcrystals derived from an AgCl cube. Through the reduction-induced decomposition, the size of the about 3 × 3 × 3 μm³ AgCl cube is reduced to Ag, and the surface is distributed with the uniform size of 63 nm silver nanoparticles, providing a large area of a robust and highly electromagnetic enhancement region. The modified polycationic molecule enhances the non-specific electrostatic interaction with the phosphate group, thereby anchoring DNA strands firmly to the SERS enhanced region intactly. As a result, the single-base recognition ability of this strategy reaches 60-nt and is successfully applied to detect thalassemia-related mutation genes.

Gold Nanostars with Reduced Fouling Facilitate Small Molecule Detection in the Presence of Protein

Gold nanoparticles have the potential to be used in biomedical applications from diagnostics to drug delivery. However, interactions of gold nanoparticles with different biomolecules in the cellular environment result in the formation of a “protein corona”—a layer of protein formed around a nanoparticle, which induces changes in the properties of nanoparticles. In this work we developed methods to reproducibly synthesize spheroidal and star-shaped gold nanoparticles, and carried out a physico-chemical characterization of synthesized anionic gold nanospheroids and gold nanostars through transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential (ZP), nanoparticles tracking analysis (NTA), ultraviolet-visible (UV–Vis) spectroscopy and estimates of surface-enhanced Raman spectroscopy (SERS) signal enhancement ability. We analyzed how they interact with proteins after pre-incubation with bovine serum albumin (BSA) via UV–Vis, DLS, ZP, NTA, SERS, cryogenic TEM (cryo-TEM) and circular dichroism (CD) spectroscopy. The tests demonstrated that the protein adsorption on the particles’ surfaces was different for spheroidal and star shaped particles. In our experiments, star shaped particles limited the protein corona formation at SERS “hot spots”. This benefits the small-molecule sensing of nanostars in biological media. This work adds more understanding about protein corona formation on gold nanoparticles of different shapes in biological media, and therefore guides design of particles for studies in vitro and in vivo.

Quantitative detection of crystal violet using a surface-enhanced Raman scattering based on a flower-like HAp/Ag nanocomposite

Herein, we proposed a simple one-pot sol-thermal strategy to prepare a highly sensitive and reproducible SERS substrate. The silver-doped hydroxyapatite nanocomposite (HAp/Ag) could suppress the oxidation of silver nanoparticles, which endow the SERS substrate with good stability and reproducibility. Due to the strong interaction between the HAp/Ag substrate and the analytes, a stronger Raman signal generated during the process of SERS detection. In particular, the HAp/Ag substrate enabled the determination of rhodamine 6G (R6G) and crystal violet (CV), and the limits of detection (LOD) were low at 10^-6 M and 10^-5 M, respectively. In addition, the HAp/Ag substrate could be used for the quantitative analysis of CV in wastewater with a good linear relationship between 10^-2 and 10^-5 M. In this context, the HAp/Ag substrate combines the superior properties of both Ag NPs and HAp particles, providing a potential method for monitoring the environment and building a convenient SERS platform to detect pollutants in wastewater.

Highly specific detection of KRAS single nucleotide polymorphism by asymmetric PCR/SERS assay

The molecular diagnosis of KRAS mutations has become crucial for clinical decision-making in colorectal cancer (CRC) treatments. Currently, the common methods for detecting mutations are based on quantitative PCR, DNA sequencing and droplet digital PCR (ddPCR), which require expensive specialized equipment and testing reagents. Herein, we propose a simple and specific strategy by integrating asymmetric PCR with surface-enhanced Raman spectroscopy (Asy-PCR/SERS) for the detection of KRAS G12V mutation, one of the most common driver mutations in CRC. To discriminate mutant targets from non-targets, Asy-PCR was applied to obtain single-stranded DNA (ssDNA) with unequal amounts of forward and reverse primers, subsequently, detection of the target mutant ssDNA amplicons was attempted by hybridization with Raman reporter-coded and allele-specific oligonucleotide-functionalized gold nanoparticles (SERS nanotags). The oligo encoding of the KRAS G12V mutant sequence could be identified by using a portable Raman spectrometer where the characteristic spectra of SERS nanotags indicate the presence of mutant targets. The Asy-PCR/SERS method showed high specificity and sensitivity for identifying as few as 0.1% mutant alleles of KRAS G12V mutation from non-target sequences. Using colorectal polyp biopsies, we demonstrated that Asy-PCR/SERS assay could distinguish KRAS G12V (c.35G > T) and KRAS G12D (c.35G > A) which occur at the same nucleotide location. As KRAS G12V is a driver oncogene in other cancers including lung, pancreatic, ovarian and endometrial cancers, the proposed assay shows great potential for application in additional tumor streams.

DNA Studies: Latest Spectroscopic and Structural Approaches

This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

Rational design of on-chip gold plasmonic nanoparticles towards ctDNA screening

This paper demonstrates the design, synthesis, simulation, and testing of three distinct geometries of plasmonic gold nanoparticles for on-chip DNA screening towards liquid biopsy. By employing a seed-mediated growth method, we have synthesized gold nanospheres, nanorods, and nanobipyramids. In parallel, we developed numerical simulations to understand the effects of nanoparticle geometry on the resonance features and refractive index sensitivity. Both experimental and simulation results were compared through a series of studies including in-solution and on-chip tests. We have thoroughly characterized the impact of nanoparticle geometry on the sensitivity to circulating tumor DNA, with immediate implications for liquid biopsy. The results agree well with theoretical predictions and simulations, including both bulk refractive index sensitivity and thin film sensitivity. Importantly, this work quantitatively establishes the link between nanoparticle geometry and efficacy in detecting rare circulating biomarkers. The nanobipyramids provided the highest sensitivity, approximately doubling the sensitivity compared to nanorods. To the best of our knowledge this is the first report carrying through geometric effects of simulation to clinically relevant biosensing. We put forth here synthesis and testing of three nanoparticle geometries, and a framework for both experimental and theoretical validation of plasmonic sensitivities towards liquid biopsy.

Microfluidic Magnetic Analyte Delivery Technique for Separation, Enrichment, and Fluorescence Detection of Ultratrace Biomarkers

A microfluidic magnetic analyte delivery (μMAD) technique was developed to realize sample preparation and ultrasensitive biomarker detection. A simply designed microfluidic device was employed to carry out this technique, including a poly(dimethylsiloxane)-glass hybrid microchip having four straight rectangular channels and a permanent magnet. In the μMAD process, functionalized magnetic beads (MBs) were used to recognize and isolate analytes from a complex sample matrix, deliver analytes into tiny microchannels, and preconcentrate analytes in the magnetic trapping/detection region for in situ fluorescence detection. In the feasibility study and sensitivity optimization, horseradish peroxidase-labeled MBs were used, and critical parameters for the signal amplification performance of μMAD were carefully evaluated. At optimized conditions, a sensitivity improvement of at least 2 orders of magnitude was achieved. As a proof of concept, μMAD was combined with the enzyme-linked immunosorbent assay (ELISA), while carcinoembryonic antigen (CEA), prostate-specific antigen (PSA), and interleukin 6 (IL-6) were selected as model biomarkers. The limits of detection (LODs) of μMAD-ELISA were as low as 0.29 pg/mL for CEA, 0.047 pg/mL for PSA, and 0.021 pg/mL for IL-6, which corresponded to an over 200-fold reduction compared to their commercial ELISA results. Meanwhile, μMAD-ELISA revealed high selectivity and reproducibility. In clinical sample analysis, good accuracy was acquired for human serum analysis relative to commercial ELISA kits, and satisfied recoveries of 85.1-102% with RSDs of 1.7-9.8% for IL-6 and 84.7-113% with RSDs of 3.2-8.3% for interferon-γ were obtained. This ultrasensitive and easy operation technique provides a valuable approach for trace-level biomarker detection for practical applications.

Liquid biopsy genotyping by a simple lateral flow strip assay with visual detection

Liquid biopsy, as a minimally invasive method that allows real-time monitoring of the tumor genome, represents a competing approach for cancer diagnosis, prognosis and therapy decision making. Liquid biopsy in cancer patients mainly includes analysis of circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA). ctDNA is the tumor-derived fraction of the cell-free DNA present in the blood. ctDNA is detected based on cancer-specific genomic aberrations (mainly mutations) and represents a challenging analyte due to high fragmentation and low concentration. Several methodologies have been developed for ctDNA analysis in cancer patients but many of these technologies are too time-intensive, complicated and expensive for implementation in diagnostic testing. Herein, we developed a novel lateral flow strip assay for mutational analysis of ctDNA in blood samples and visual detection that is based on gold nanoparticles as reporters. As a model, common single-point mutations of the KRAS gene, related to colorectal cancer (CRC), have been selected for method development. The proposed DNA biosensor has been successfully applied for the detection of three KRAS mutations (KRAS G12D/A/V), along with the wild-type KRAS gene in synthetic DNA targets, cancer cell lines and cfDNA from blood samples of healthy individuals and CRC patients. The main advantages of the proposed lateral flow assay are simplicity, rapid analysis time (∼10 min) and visual detection without the requirement of special instrumentation. The assay is also cost-effective with high detectability, specificity and reproducibility and has the potential to be used as a portable and universal device. In conclusion, the proposed assay offers a rapid diagnostic strip test for visual genotyping, as an alternative approach for liquid biopsy applications.

Effect of Cetuximab-Conjugated Gold Nanoparticles on the Cytotoxicity and Phenotypic Evolution of Colorectal Cancer Cells

Epidermal growth factor receptor (EGFR) is estimated to be overexpressed in 60~80% of colorectal cancer (CRC), which is associated with a poor prognosis. Anti-EGFR targeted monoclonal antibodies (cetuximab and panitumumab) have played an important role in the treatment of metastatic CRC. However, the therapeutic response of anti-EGFR monoclonal antibodies is limited due to multiple resistance mechanisms. With the discovery of new functions for gold nanoparticles (AuNPs), we hypothesize that cetuximab-conjugated AuNPs (cetuximab-AuNPs) will not only improve the cytotoxicity for cancer cells, but also introduce expression change of the related biomarkers on cancer cell surface. In this contribution, we investigated the size-dependent cytotoxicity of cetuximab-AuNPs to CRC cell line (HT-29), while also monitored the expression of cell surface biomarkers in response to treatment with cetuximab and cetuximab-AuNPs. AuNPs with the size of 60 nm showed the highest impact for cell cytotoxicity, which was tested by cell counting kit-8 (CCK-8) assay. Three cell surface biomarkers including epithelial cell adhesion molecule (EpCAM), melanoma cell adhesion molecule (MCAM), and human epidermal growth factor receptor-3 (HER-3) were found to be expressed at higher heterogeneity when cetuximab was conjugated to AuNPs. Both surface-enhanced Raman scattering/spectroscopy (SERS) and flow cytometry demonstrated the correlation of cell surface biomarkers in response to the drug treatment. We thus believe this study provides powerful potential for drug-conjugated AuNPs to enhance cancer prognosis and therapy.

Positively charged gold-silver nanostar enabled molecular characterization of cancer associated extracellular vesicles

Direct surface-enhanced Raman scattering (SERS) has contributed to characterizing extracellular vesicles (EVs) by providing molecular signatures. However, little work has been carried out to understand the heterogeneity of EVs created by different methods or from different biological sources. Herein, we pioneered the use of positively charged gold-silver nanostars to explore the SERS profiles of different EVs. The physical features of EVs from cancer cells including the size, concentration, morphology and surface potential have been characterized via nanoparticle tracking analysis, transmission electron microscopy and zeta potential analysis. The results show that negatively charged EVs are attracted to positively charged gold-silver nanostar surfaces via electrostatic forces resulting in SERS spectra showing characteristic vibrational modes of the different components of EVs (i.e. proteins, lipids and nucleic acids). SERS data were complemented by other spectroscopic techniques including atomic force microscopy-infrared spectroscopy, UV-visible absorbance spectroscopy and fluorescence spectroscopy providing a more complete molecular picture of EVs. SERS signatures of EVs from different origins, batches, and isolation approaches were compared and analyzed. A statistical method (principal component analysis-linear discriminant analysis) was utilized to differentiate EV subtypes. Consequently, a desirable discrimination outcome for blind samples was obtained. This study provides novel insights to deepen our understanding of EV heterogeneity.

Plasmonic SERS Biosensor Based on Multibranched Gold Nanoparticles Embedded in Polydimethylsiloxane for Quantification of Hematin in Human Erythrocytes

This work reports a plasmonic surface-enhanced Raman scattering (SERS) biosensor that allows for quantitative analysis of hematin in erythrocytes without the need of separating it from hemoglobin (Hb). The biosensor exploits the tunable localized surface plasmon resonance (LSPR) characteristics of multibranched gold nanoparticles (M-AuNPs) and the strong plasmon coupling between an Au thin film and a flexible substrate consisting of M-AuNPs embedded in polydimethylsiloxane (PDMS) (i.e., M-AuNP-embedded PDMS substrate). In the assay, the hematin (or hematin-containing erythrocyte hemolysate) was deposited on Au film surface and covered with M-AuNP-embedded PDMS. Strong SERS signals were generated under excitation at 785 nm; the signals were sensitive to hematin concentration but not to several common coexisting biological substances. The intensities of the SERS signal (at 1623 cm^-1) displayed a wide linear range using hematin concentrations in a range of at least ∼1.5 nM-1.1 μM; the limit of detection (LOD) was ∼0.03 ± 0.01 nM at a signal/noise (S/N) of 3. This assay is simple and sensitive without tedious separation procedures, thereby saving time and enhancing efficiency. This biosensor can be used to determine hematin concentration in human erythrocyte cytosols giving concentrations of ∼18.5 ± 4.5 (by averaging eight samples) and 51.5 ± 6.2 μM (by averaging three samples) for healthy and sickle erythrocytes, respectively, making it a potential application in clinical detection.

Applications of surface-enhanced Raman spectroscopy in detection fields

Surface-enhanced Raman spectroscopy (SERS) is a Raman spectroscopy technique that has been widely used in food safety, environmental monitoring, medical diagnosis and treatment and drug monitoring because of its high selectivity, sensitivity, rapidness, simplicity and specificity in identifying molecular structures. This review introduces the detection mechanism of SERS and summarizes the most recent progress concerning the use of SERS for the detection and characterization of molecules, providing references for the later research of SERS in detection fields.

Metal Nanoparticles-Enhanced Biosensors: Synthesis, Design and Applications in Fluorescence Enhancement and Surface-enhanced Raman Scattering

Metal nanoparticles (NP) that exhibit localized surface plasmon resonance play an important role in metal-enhanced fluorescence (MEF) and surface-enhanced Raman scattering (SERS). Among the optical biosensors, MEF and SERS stand out to be the most sensitive techniques to detect a wide range of analytes from ions, biomolecules to macromolecules and microorganisms. Particularly, anisotropic metal NPs with strongly enhanced electric field at their sharp corners/edges under a wide range of excitation wavelengths are highly suitable for developing the ultrasensitive plasmon-enhanced biosensors. In this review, we first highlight the reliable methods for the synthesis of anisotropic gold NPs and silver NPs in high yield, as well as their alloys and composites with good control of size and shape. It is followed by the discussion of different sensing mechanisms and recent advances in the MEF and SERS biosensor designs. This includes the review of surface functionalization, bioconjugation and (directed/self) assembly methods as well as the selection/screening of specific biorecognition elements such as aptamers or antibodies for the highly selective bio-detection. The right combinations of metal nanoparticles, biorecognition element and assay design will lead to the successful development of MEF and SERS biosensors targeting different analytes both in-vitro and in-vivo. Finally, the prospects and challenges of metal-enhanced biosensors for future nanomedicine in achieving ultrasensitive and fast medical diagnostics, high-throughput drug discovery as well as effective and reliable theranostic treatment are discussed.

A blueprint for performing SERS measurements in tissue with plasmonic nanofibers

Plasmonic nanostructures have found increasing utility due to the increased popularity that surface-enhanced Raman scattering (SERS) has achieved in recent years. SERS has been incorporated into an ever-growing list of applications, with bioanalytical and physiological analyses having emerged as two of the most popular. Thus far, the transition from SERS studies of cultured cells to SERS studies involving tissue has been gradual and limited. In most cases, SERS measurements in more intact tissue have involved nanoparticles distributed throughout the tissue or localized to specific regions via external functionalization. Performing highly localized measurements without the need for global nanoparticle uptake or specialized surface modifications would be advantageous to the expansion of SERS measurements in tissue. To this end, this work provides critical insight with supporting experimental evidence into performing SERS measurements with nanosensors inserted in tissues. We address two critical steps that are otherwise underappreciated when other approaches to performing SERS measurements in tissue are used. Specifically, we demonstrate two mechanical routes for controlled positioning and inserting the nanosensors into the tissue, and we discuss two means of focusing on the nanosensors both before and after they are inserted into the tissue. By examining the various combinations of these steps, we provide a blueprint for performing SERS measurements with nanosensors inserted in tissue. This blueprint could prove useful for the general development of SERS as a tool for bioanalytical and physiological studies and for more specialized techniques such as SERS-optophysiology.

Multiplex detection of ctDNA mutations in plasma of colorectal cancer patients by PCR/SERS assay

Molecular diagnostic testing of KRAS and BRAF mutations has become critical in the management of colorectal cancer (CRC) patients. Some progress has been made in liquid biopsy detection of mutations in circulating tumor DNA (ctDNA), which is a fraction of circulating cell-free DNA (cfDNA), but slow analysis for DNA sequencing methods has limited rapid diagnostics. Other methods such as quantitative PCR and more recently, droplet digital PCR (ddPCR), have limitations in multiplexed capacity and the need for expensive specialized equipment. Hence, a robust, rapid and facile strategy is needed for detecting multiple ctDNA mutations to improve the management of CRC patients. To address this significant problem, herein, we propose a new application of multiplex PCR/SERS (surface-enhanced Raman scattering) assay for the detection of ctDNA in CRC, in a fast and non-invasive manner to diagnose and stratify patients for effective treatment.

Methods: To discriminate ctDNA mutations from wild-type cfDNA, allele-specific primers were designed for the amplification of three clinically important DNA point mutations in CRC including KRAS G12V, KRAS G13D and BRAF V600E. Surface-enhanced Raman scattering (SERS) nanotags were labelled with a short and specific sequence of oligonucleotide, which can hybridize with the corresponding PCR amplicons. The PCR/SERS assay was implemented by firstly amplifying the multiple mutations, followed by binding with multicolor SERS nanotags specific to each mutation, and subsequent enrichment with magnetic beads. The mutation status was evaluated using a portable Raman spectrometer where the fingerprint spectral peaks of the corresponding SERS nanotags indicate the presence of the mutant targets. The method was then applied to detect ctDNA from CRC patients under a blinded test, the results were further validated by ddPCR.

Results: The PCR/SERS strategy showed high specificity and sensitivity for genotyping CRC cell lines and plasma ctDNA, where as few as 0.1% mutant alleles could be detected from a background of abundant wild-type cfDNA. The blinded test using 9 samples from advanced CRC patients by PCR/SERS assay was validated with ddPCR and showed good consistency with pathology testing results.

Conclusions: With ddPCR-like sensitivity yet at the convenience of standard PCR, the proposed assay shows great potential in sensitive detection of multiple ctDNA mutations for clinical decision-making.

Tunable plasmonics of hollow raspberry-like nanogold for the robust Raman scattering detection of antibiotics on a portable Raman spectrometer

It is important to develop novel sensors for the simple, rapid, and quantitative detection of residual antibiotics in food, considering their potential threats to human health. Herein, we report the successful fabrication of raspberry-like nanogold (R-like Au) structures with rough surfaces and partially hollow structures for the rapid and sensitive detection of antibiotics in duck meats on a portable Raman spectrometer. The R-like Au with tunable plasmonic wavelengths was fabricated by a two-step method. Ag particles as seeds were substituted by Au particles through a replacement reaction; moreover, the surface plasmon resonances (SPRs) of R-like Au red-shifted with the increase in the Au ion concentration. The R-like Au with a diameter of about 120 nm that matched well with the 785 nm laser on the portable Raman spectrometer was used as an excellent surface-enhanced Raman spectroscopy (SERS) active platform for detecting two kinds of antibiotics, namely, nitrofurantoin (NFT) and nitrofurazone (NFZ), in spiked duck meats. Both of them have sufficient sensitivity (0.05-10 mg L-1), good linear relationship (R2 > 0.99) and high recovery in quantitative SERS analysis. The platform is simple without the need for complex pretreatment of the food samples or use of large scale Raman spectrometers, promising easy implementation for the on-site analysis of residuals of antibiotics in food.

Plasmonic SERS Au Nanosunflowers for Sensitive and Label-Free Diagnosis of DNA Base Damage in Stimulus-Induced Cell Apoptosis

Molecular diagnosis and accurate damage analysis of complex genomic DNAs in tumor cells are crucial to the theranostics of cancers but still a huge challenge. Herein, by designed preparation of a uniform plasmonic sunflower-like assembly gold (Au) nanostructure that is capable of efficient DNA capture and providing high-density gap-plasmon "hot spots" for adequate surface-enhanced Raman spectroscopy (SERS) enhancement, we succeeded in sensitive and reliable label-free SERS detection of DNA damage in electrostimulus-induced apoptotic cancer cells at the DNA base level for the first time. The SERS results showed that the external electrostimulus (at 1.2 V, for 5 min) was almost harmless to normal healthy cells, but it caused pronounced double strand break and adenine base damage in cancer cell DNAs, which effectively destroyed the reproduction and transcription of DNAs and ultimately induced cell apoptosis. The developed sensing platform and method are promising for cell study of genetically related diseases.

Real-time and label-free detection of VKORC1 genes based on a magnetoelastic biosensor for warfarin therapy

Various thrombotic disorders have been treated with the anticoagulant warfarin. However, a small change in warfarin concentration may lead to drug adverse reactions or therapeutic failure due to its narrow therapeutic index. Therefore, the dose of warfarin must be monitored for each patient during therapy in real-time and in a sensitive and stable manner. In this work, we designed a magnetoelastic (ME) biosensor using Metglas alloy 2826 to detect VKORC1 genotypes, which is one of the most important known genetic determinants of warfarin dosing. The sensor enabled both fast responses to DNA binding and wireless transmission of signals. Specifically in the target recognition layer, the sensor introduced an avidin-biotin interaction system for signal amplification by increasing the surface load mass. The resonance frequency shift of the signal was linear to the concentration of the target in the range of 0.1 fM to 10 pM, with a detection limit (LOD) of 0.00389 fM (S/N = 3) and a sensitivity of 45.7 Hz pM^-1. Importantly, this ME-based biosensor was small and portable without the use of any optical labels, which has high potential to be applied in advanced biomedical diagnosis of nucleic acids and proteins.