A reusable laser wrapped graphene-Ag array based SERS sensor for trace detection of genomic DNA methylation

Ultrasensitive detection of 5-hydroxymethylcytosine in genomic DNA using a graphene-based sensor modified with biotin and gold nanoparticles

Ten-eleven translocation (TET) proteins orchestrate deoxyribonucleic acid (DNA) methylation-demethylation dynamics by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and are frequently inactivated in various cancers. Due to the significance of 5hmC as an epigenetic biomarker for cancer diagnosis, pathogenesis, and treatment, its rapid and precise quantification is essential. Here, we report a highly sensitive electrochemical method for quantifying genomic 5hmC using graphene sheets that were electrochemically exfoliated and functionalized with biotin and gold nanoparticles (Bt-AuNPs) through a single-step electrical method. The attachment of Bt-AuNPs to graphene enhances the specificity of 5hmC-containing DNA and augments the oxidation of 5hmC to 5-formylcytosine in DNA. When coupled to a gold electrode, the Bt-AuNP-graphene-based sensor exhibits exceptional sensitivity and specificity for detecting 5hmC, with a detection limit of 63.2 fM. Furthermore, our sensor exhibits a remarkable capacity to measure 5hmC levels across a range of biological samples, including preclinical mouse tissues with varying 5hmC levels due to either TET gene disruption or oncogenic transformation, as well as human prostate cancer cell lines. Therefore, our sensing strategy has substantial potential for cancer diagnostics and prognosis.

Nanoimprinted Plasmonic Crystals for Cost-Effective SERS Identification of Methylated DNAs

The development of a cost-effective and rapid assay technique for the identification of DNA methylation is one of the most crucial issues in the field of biomedical diagnosis because DNA methylation plays key roles in human health. The plasmonic crystal-based surface-enhanced Raman spectroscopy (SERS) technique is promising for the realization of such an assay method owing to its capability of generating uniformly enhanced electric fields to achieve high reproducibility and accuracy in SERS assays. However, the time and technical costs of fabricating plasmonic crystals are high, owing to the need for nanofabrication equipment. In this study, we developed nanoimprinted plasmonic crystals for cost-effective and rapid DNA methylation assays. Our plasmonic crystals identified methylated DNA with the 40-base pair adenomatous polyposis coli (APC) gene sequence, which is correlated with cell growth and cancer cells.

Optical nanomaterial-based detection of biomarkers in liquid biopsy

Liquid biopsy, which is a minimally invasive procedure as an alternative to tissue biopsy, has been introduced as a new diagnostic/prognostic measure. By screening disease-related markers from the blood or other biofluids, it promises early diagnosis, timely prognostication, and effective treatment of the diseases. However, there will be a long way until its realization due to its conceptual and practical challenges. The biomarkers detected by liquid biopsy, such as circulating tumor cell (CTC) and circulating tumor DNA (ctDNA), are extraordinarily rare and often obscured by an abundance of normal cellular components, necessitating ultra-sensitive and accurate detection methods for the advancement of liquid biopsy techniques. Optical biosensors based on nanomaterials open an important opportunity in liquid biopsy because of their enhanced sensing performance with simple and practical properties. In this review article, we summarized recent innovations in optical nanomaterials to demonstrate the sensitive detection of protein, peptide, ctDNA, miRNA, exosome, and CTCs. Each study prepares the optical nanomaterials with a tailored design to enhance the sensing performance and to meet the requirements of each biomarker. The unique optical characteristics of metallic nanoparticles (NPs), quantum dots, upconversion NPs, silica NPs, polymeric NPs, and carbon nanomaterials are exploited for sensitive detection mechanisms. These recent advances in liquid biopsy using optical nanomaterials give us an opportunity to overcome challenging issues and provide a resource for understanding the unknown characteristics of the biomarkers as well as the mechanism of the disease.

All laser direct writing process for temperature sensor based on graphene and silver

A highly sensitive temperature sensing array is prepared by all laser direct writing (LDW) method, using laser induced silver (LIS) as electrodes and laser induced graphene (LIG) as temperature sensing layer. A finite element analysis (FEA) photothermal model incorporating a phase transition mechanism is developed to investigate the relationship between laser parameters and LIG properties, providing guidance for laser processing parameters selection with laser power of 1-5 W and laser scanning speed (greater than 50 mm/s). The deviation of simulation and experimental data for widths and thickness of LIG are less than 5% and 9%, respectively. The electrical properties and temperature responsiveness of LIG are also studied. By changing the laser process parameters, the thickness of the LIG ablation grooves can be in the range of 30-120 μm and the resistivity of LIG can be regulated within the range of 0.031-67.2 Ω·m. The percentage temperature coefficient of resistance (TCR) is calculated as - 0.58%/°C. Furthermore, the FEA photothermal model is studied through experiments and simulations data regarding LIS, and the average deviation between experiment and simulation is less than 5%. The LIS sensing samples have a thickness of about 14 μm, an electrical resistivity of 0.0001-100 Ω·m is insensitive to temperature and pressure stimuli. Moreover, for a LIS-LIG based temperature sensing array, a correction factor is introduced to compensate for the LIG temperature sensing being disturbed by pressure stimuli, the temperature measurement difference is decreased from 11.2 to 2.6 °C, indicating good accuracy for temperature measurement.

SERS-based methods for the detection of genomic biomarkers of cancer

Genomic biomarkers of cancer are based on changes in nucleic acids, which include abnormal expression levels of some miRNAs, point mutations in DNA sequences, and altered levels of DNA methylation. The presence of tumor-related nucleic acids in body fluids (blood, saliva, or urine) makes it possible to achieve a non-invasive early-stage cancer diagnosis. Currently existing techniques for the discovery of nucleic acids require complex, time-consuming, costly assays and have limited multiplexing abilities. Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique that is able to provide molecular specificity combined with trace sensitivity. SERS has gained research attention as a tool for the detection of nucleic acids because of its promising potential: label-free SERS can decrease the complexity of assays currently used with fluorescence-based detection due to the absence of the label, while labeled SERS may outperform the gold standard in terms of the multiplexing ability. The first papers about SERS-based methods for the measurement of genomic biomarkers were written in 2008, and since then, more than 150 papers have been published. The aim of this paper is to review and evaluate the proposed SERS-based methods in terms of their level of development and their potential for liquid biopsy application, as well as to contribute to their further evolution by attracting research attention to the field. This goal will be reached by grouping, on the basis of their experimental protocol, all the published manuscripts on the topic and evaluating each group in terms of its limit of detection and applicability to real body fluids. Thus, the methods are classified according to their working principles into five main groups, including capture-based, displacement-based, sandwich-based, enzyme-assisted, and specialized protocols.

The Convenience of Polydopamine in Designing SERS Biosensors with a Sustainable Prospect for Medical Application

Polydopamine (PDA) is a multifunctional biomimetic material that is friendly to biological organisms and the environment, and surface-enhanced Raman scattering (SERS) sensors have the potential to be reused. Inspired by these two factors, this review summarizes examples of PDA-modified materials at the micron or nanoscale to provide suggestions for designing intelligent and sustainable SERS biosensors that can quickly and accurately monitor disease progression. Undoubtedly, PDA is a kind of double-sided adhesive, introducing various desired metals, Raman signal molecules, recognition components, and diverse sensing platforms to enhance the sensitivity, specificity, repeatability, and practicality of SERS sensors. Particularly, core-shell and chain-like structures could be constructed by PDA facilely, and then combined with microfluidic chips, microarrays, and lateral flow assays to provide excellent references. In addition, PDA membranes with special patterns, and hydrophobic and strong mechanical properties can be used as independent platforms to carry SERS substances. As an organic semiconductor material capable of facilitating charge transfer, PDA may possess the potential for chemical enhancement in SERS. In-depth research on the properties of PDA will be helpful for the development of multi-mode sensing and the integration of diagnosis and treatment.

DNA Methylation Signatures of Tumor-Associated Natural Killer Cells with Self-Functionalized Nanosensor Enable Colorectal Cancer Diagnosis

Natural killer (NK) cells undergo multiple DNA genomic alterations, especially methylation-based modifications that affect activation and function. Several epigenetic modifier markers have been targeted for immunotherapy to date, but the possibility of cancer diagnosis using NK cell's DNA has been overlooked. Here, we investigated the potential use of NK cell DNA genome modifications as markers for the diagnosis of colorectal cancer (CRC) and validated their efficacy in CRC patients. Using Raman spectroscopy as the detection methodology, we identified CRC-specific methylation signatures by comparing CRC-interacted NK cells to healthy circulating NK cells. Subsequently, we identified methylation-dependent alterations in these NK cell populations. These markers were then utilized by a machine learning algorithm to develop a diagnostic model with predictive capabilities. The diagnostic prediction model accurately differentiated CRC patients from normal controls. Our findings demonstrated the utility of NK DNA markers in the diagnosis of CRC.

Label-free and sensitive fluorescent sensing of ten-eleven translocation enzyme via cascaded recycling signal amplifications

The sensitive detection of ten-eleven translocation (TET) dioxygenase is of significance for understanding the demethylation mechanism of 5-methylocytosine (5mC), which is responsible for a wide range of biological functions that can affect gene expression in eukaryotic species. Here, a non-label and sensitive fluorescence biosensing method for TET assay using TET1 as the model target molecule is established on the basis of target-triggered Mg²⁺-dependent DNAzyme and catalytic hairpin assembly (CHA)-mediated multiple signal amplification cascades. 5mC sites in the hairpin DNA probe are first oxidized by TET1 into 5-carboxycytosine, which are further reduced by pyridine borane into dihydrouracil, followed by its recognition and cleavage by the USER enzyme to liberate active DNAzyme and G-quadruplex sequences from the probe. The DNAzyme further cyclically cleaves the substrate hairpins to trigger subsequent CHA reaction and DNAzyme cleavage cycles for yielding many G-quadruplex strands. Thioflavin T dye then intercalates into G-quadruplexes to cause a magnificent increase of fluorescence for high sensitivity assay of TET1 with 47 fM detection limit. And, application of this method for TET1 monitoring in diluted serum has also been confirmed.

Label-free DNA detection using silver nanoprism decorated silicon nanoparticles: Effect of silicon nanoparticle size and doping levels

In the present work, we have fabricated silver nanoprism (AgNPrs)/silicon nanoparticle (SiNPs) hybrid arrays for highly sensitive detection of biomolecules via surface-enhanced Raman spectroscopy (SERS) technique. SiNPs having 7 to 37 nm in size and with phosphorous doping varying from 1 × 10¹⁹ to 1 × 10²⁰ cm^-3 were synthesized in nonthermal plasma synthesis. SiNPs were further immobilized on glass substrates using spin-coating, followed by deposition of AgNPrs using the drop-casting method. SERS studies showed that AgNPrs/SiNPs hybrid arrays exhibit substantial amplification of fingerprint bands of rhodamine 6G (R6G) compared to bare silicon as the reference. Raman signal intensity was found to be dependent on the size of SiNPs, with the largest nanoparticles exhibiting the highest SERS enhancement. In addition, an increase in phosphorous doping concentration was found to reduce R6G peak intensities. AgNPrs/SiNPs hybrid arrays showed excellent stability over time and high spot-to-spot reproducibility as well. Moreover, hybrid arrays enabled DNA detection through intense vibrational modes of human genomic DNA, with a lower detection limit of 1.5 pg/µL; indicating that AgNPrs/SiNPs sensors can serve as a reliable and cost-effective biosensing platform for rapid and label-free analysis of biomolecules.

Traceability of bilberries (Vaccinium myrtillus L.) of the Baltic-Nordic region using surface-enhanced Raman spectroscopy (SERS): DFT simulation-based DNA analysis

Food traceability is a major issue in the industry. We investigated whether bilberries (Vaccinium myrtillus L.) from 4 different locations within the Baltic-Nordic region could be effectively differentiated using surface-enhanced Raman scattering (SERS) based spectral data and chemometric analyses. Furthermore, we aimed to determine if nucleobase (adenine and cytosine) methylation could be responsible for any observed variation. Our experiment was successful in that both principal component (PCA) and discriminant function analyses (DFA) showed differentiation between bilberry DNA from all 4 geographical regions. Density functional theory (DFT) based simulations allowed us to analyze whether DNA's spectral data dissimilarities may be due to nucleobase methylation. Although results were inconclusive on this, our investigation provides valuable data on simulated versus experimental DNA and DNA component spectra. Further research will be directed towards understanding what other epigenetic changes could be responsible for the observed DNA variation as well as determining the optimal parameters for using DFT simulations in upcoming projects.

Nucleotide detection mechanism and comparison based on low-dimensional materials: A review

The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.

Phase separation enabled silver nano-array

The surface-supported silver nanoparticles have been studied and applied in various applications. Many unique nanostructures have been introduced into this field to improve the functionalities of the surfaces depending on application purposes. We created featured silver nano-array surfaces by utilizing the solvent-mediated phase transition on the surface grafted with poly (acrylic) acids polymer chains and taking advantage of the low temperature of argon gas discharged plasma as a reducing agent. The applied solvents and grafted polymer chain densities affected the phase transition and thus determined the outcome of surface nano-array patterns. However, the total loaded silver ions on the surface affected silver nano-array structures at the sub-micron levels. The featured silver patterned surfaces made in the optimal conditions present a favorable surface-enhanced Raman spectroscopy enhancement as well as recyclability for detection re-usage. This novel method prepares tunable silver nanopatterned surfaces and provides a new approach to various potential applications.

Ultra-sensitive detection of streptomycin in foods using a novel SERS switch sensor fabricated by AuNRs array and DNA hydrogel embedded with DNAzyme

Detrimental health effects caused by the intake of food contaminated with streptomycin have drawn concerns on effective monitoring using sensitive and selective methods. In this work, a DNA hydrogel surface enhanced Raman spectroscopy (SERS) sensor was successfully developed for the ultrasensitive determination of streptomycin residues in foods. The sensor used a DNA hydrogel containing DNAzyme (Pb-DNAzyme), triggering release of the Raman reporter 4-mercaptobenzonitrile, which was detected using a gold nanorods (AuNRs) array. The linear range of the sensor was 0.01-150 nM and the limit of detection was 4.85 × 10^-3 nM. Tests conducted with four streptomycin structural analogues confirmed the sensor was specific. Milk and honey samples spiked with streptomycin were analysed, resulting in standard recoveries in the range 98.2-117.3%. These findings demonstrated that such a sensor can be used for ultrasensitive detection of streptomycin in foods.

The Wavelength-Dependent SERS Template Based on a Nanopillar Array

Surface-enhanced Raman spectroscopy (SERS) can be regarded as a powerful tool for probing chemical molecules by effectively enhancing Raman signals. However, the enhancement factors depend on the SERS template, the probed molecular structures, and the excitation laser wavelength. Herein, we proposed a simple and easily fabricated nanostructured template for SERS and analyzed the wavelength-dependent factors. Three types of golden nanopillar arrays on silicon wafers were designed and manufactured. The SERS signals of the Rhodamine 6G (R6G) molecules were extracted. Three laser sources, a blue 17 mW 458 nm diode laser, a green 20 mW 532 nm laser, and a red 6 mW 633 nm laser, were employed as the excitation laser sources. The 458 nm laser was located far from the resonate spectrum of R6G. The optical intensity distributions for the different SERS templates excited by three laser beams were also simulated. The enhancement factors (EFs) of R6G on the three nanostructured templates were measured and compared. The photoluminescence spectrum of the nanostructured templates and SERS signals of R6G were also measured. In addition, the experimental results concerned optical simulations. The analysis tool that was used was a convolution profile of multiple Lorentzian line shapes with a Gaussian profile. It is helpful to understand the SERS signals when the excitation laser wavelength is located out of the resonance region of molecules. It can also provide a new design approach to fabricate an SERS Template with a nanopillar array for different excitation wavelengths.

Ultrasensitive Simultaneous Detection of Multiple Rare Modified Nucleosides as Promising Biomarkers in Low-Put Breast Cancer DNA Samples for Clinical Multi-Dimensional Diagnosis

Early cancer diagnosis is essential for successful treatment and prognosis, and modified nucleosides have attracted widespread attention as a promising group of cancer biomarkers. However, analyzing these modified nucleosides with an extremely low abundance is a great challenge, especially analyzing multiple modified nucleosides with a different abundance simultaneously. In this work, an ultrasensitive quantification method based on chemical labeling, coupled with LC-MS/MS analysis, was established for the simultaneous quantification of 5hmdC, 5fdC, 5hmdU and 5fdU. Additionally, the contents of 5mdC and canonical nucleosides could be obtained at the same time. Upon derivatization, the detection sensitivities of 5hmdC, 5fdC, 5hmdU and 5fdU were dramatically enhanced by several hundred times. The established method was further applied to the simultaneous detection of nine nucleosides with different abundances in about 2 μg genomic DNA of breast tissues from 20 breast cancer patients. The DNA consumption was less than other overall reported quantification methods, thereby providing an opportunity to monitor rare, modified nucleosides in precious samples and biology processes that could not be investigated before. The contents of 5hmdC, 5hmdU and 5fdU in tumor tissues and normal tissues adjacent to the tumor were significantly changed, indicating that these three modified nucleosides may play certain roles in the formation and development of tumors and be potential cancer biomarkers. While the detection rates of 5hmdC, 5hmdU and 5fdU alone as a biomarker for breast cancer samples were 95%, 75% and 85%, respectively, by detecting these three cancer biomarkers simultaneously, two of the three were 100% consistent with the overall trend. Therefore, simultaneous detection of multiple cancer biomarkers in clinical samples greatly improved the accuracy of cancer diagnosis, indicating that our method has great application potential in clinical multidimensional diagnosis.

Arrays of Ag-nanoparticles decorated TiO2 nanotubes as reusable three-dimensional surface-enhanced Raman scattering substrates for molecule detection

Three-dimensional surface-enhanced Raman scattering (SERS) substrates usually provide more hot spots in the excitation light beam and higher sensitivity when compared with the two-dimensional counterpart. Here a simple approach is presented for the fabrication of arrays of Ag-nanoparticles decorated TiO2 nanotubes. Arrays of ZnO nanorods were fabricated in advance by a hydrothermal method. Then TiO2 nanotube arrays were achieved by immersing the arrays of ZnO nanorods in an aqueous solution of (NH4)2TiF6 for 1.5 h. Vertically aligned TiO2 nanotube arrays were modified with dense Ag nanoparticles by Ag mirror reaction. High density of Ag nanoparticles decorated on the fabricated TiO2 nanotubes provide plenty of hotspots for Raman enhancement. In addition, the fabricated array of Ag nanoparticles modified TiO2 nanotubes can serve as a reusable SERS substrate because of the photocatalytic activity of the TiO2 nanotubes. The SERS substrate adsorbed with analyte molecules can realize self-cleaning in deionized water after UV irradiation for 2.5 h. The sensitivity of the fabricated SERS substrate was investigated by the detection of organic dye molecules. The detectable concentration limits of rhodamine 6G (R6G), malachite green (MG) and methylene blue (MB) were found to be 10−12 M, 10−9 M and 10−8 M, respectively. The enhancement factor (EF) of the three-dimensional SERS substrate was estimated to be as high as ∼1.4×108. Therefore, the prepared Ag nanoparticles modified TiO2 nanotube arrays have promising potentials to be applied to rapid and trace SERS detection of organic chemicals.

Reduced graphene oxide on silver nanoparticle layers-decorated titanium dioxide nanotube arrays as SERS-based sensor for glyphosate direct detection in environmental water and soil

When glyphosate, a widely used organophosphate herbicide in agricultural applications, contaminates the environment, it could lead to chronic harm to human health. Herein, an efficient, air-stable and reusable surface-enhanced Raman scattering (SERS) substrate was designed to be an analytical tool for direct determination of glyphosate. A vertical heterostructure of reduced graphene oxide (rGO)-wrapped dual-layers silver nanoparticles (AgNPs) on titania nanotube (TiO2 NTs) arrays was constructed as a SERS substrate. The TiO2 NTs/AgNPs-rGO exhibited high SERS performance for methylene blue detection, offering an analytical enhancement factor (AEF) as large as 7.1 × 108 and the limit of detection (LOD) as low as 10-14 M with repeatability of 4.4 % relative standard deviation (RSD) and reproducibility of 2.0 % RSD. The sensor was stable in ambient and was reusable after photo-degradation. The designed sensor was successfully applied for glyphosate detection with a LOD of 3 µg/L, which is below the maximum contaminant level of glyphosate in environmental water, as recommended by the U.S. EPA and the European Union. A uniqueness of this study is that there is no significant difference between the real-world applications of the SERS sensor on direct glyphosate analysis in environmental samples compared to an analysis using ultra-high performance liquid chromatography.

A fast and label-free detection of hydroxymethylated DNA using a nozzle-jet printed AuNPs@Ti3C2 MXene-based electrochemical sensor

5-hydroxymethylcytosine (5hmC) is a key epigenetic mark in the mammalian genome that has been proposed as a promising cancer biomarker with diagnostic and prognostic potentials. A new type of two-dimensional (2D) material called MXene includes transition metal carbides and nitrides and possesses unique physico-chemical properties suitable for diverse applications, including electrochemical sensors. Here, we report a new nozzle-jet printed electrochemical sensor using gold nanoparticles (AuNPs)@Ti₃C₂ MXene nanocomposite for the real-time and label-free detection of 5hmC in the genome. We utilized Ti₃C₂ MXene as a platform to immobilize AuNPs, which have been shown to exhibit different affinity interactions toward 5-methylcytosine (5 mC) and 5hmC, and thus produce distinct electrochemical responses. To fabricate the electrode, a highly conductive and adhesive silver ink was prepared to generate a silver line onto polyethylene terephthalate (PET) substrate using nozzle-jet printing, followed by deposition of AuNPs@Ti₃C₂ MXene ink at one end via dropcasting. Analyses of morphology and chemical composition showed that all steps of the sensor fabrication were successful. The fabricated sensor coupled with cyclic voltammetry showed excellent performance in distinguishing 5 mC- or 5hmC-enriched cellular genomic DNAs. As a proof-of-concept investigation, we confirmed that our sensor readily and consistently detected 5hmC diminution in multiple tumors, compared to the paired normal tissues. Thus, our simple and cost-effective sensing strategy using printable AuNPs@Ti₃C₂ MXene ink holds promise for a wide range of practical applications in epigenetic studies as well as clinical settings.

A Multilayer Interlaced Ag Nanosheet Film Prepared by an Electrodeposition Method on a PPy@PEDOT:PSS Film: A Strategy to Prepare Sensitive Surface-Enhanced Raman Scattering Substrates

A highly sensitive multilayer interlaced silver (Ag) nanosheet (MISN) film was prepared on a PPy@PEDOT:PSS film via an electrodeposition method for surface-enhanced Raman scattering (SERS) applications. After the PPy@PEDOT:PSS film was pretreated with ascorbic acid solution, many sparse Ag nanoparticles (NPs) could be directly reduced on the surface of the PPy@PEDOT:PSS film in AgNO₃ solution. Then, the MISN film was directionally grown along the surface of sparse Ag NPs by using an electrochemical galvanostatic method to form a Ag/PPy@PEDOT:PSS film for a SERS substrate. The results indicated that with the increase in electrodeposition time, the density of Ag nanosheets was also increased for boosting the SERS effect. Accordingly, owing to the directional growth of Ag NPs, the increase in the length-width ratio of single Ag nanosheets would further promote the SERS signal of the substrate. Moreover, the maximum enhancement factor of the SERS substrate could reach to 12,478, and the minimum limit of detection of melamine solution was down to 5.42 ng/mL. The SERS sensitivity of the Ag nanosheet film reached 100.65. This method of preparing the SERS substrate provides a novel and robust strategy for the low-cost and high-sensitivity detection in biomedicine, drugs, and food.

Effect of Graphene vs. Reduced Graphene Oxide in Gold Nanoparticles for Optical Biosensors-A Comparative Study

Aiming to develop a nanoparticle-based optical biosensor using gold nanoparticles (AuNPs) synthesized using green methods and supported by carbon-based nanomaterials, we studied the role of carbon derivatives in promoting AuNPs localized surface plasmon resonance (LSPR), as well as their morphology, dispersion, and stability. Carbon derivatives are expected to work as immobilization platforms for AuNPs, improving their analytical performance. Gold nanoparticles (AuNPs) were prepared using an eco-friendly approach in a single step by reduction of HAuCl₄·3H₂O using phytochemicals (from tea) which act as both reducing and capping agents. UV-Vis spectroscopy, transmission electron microscopy (TEM), zeta potential (ζ-potential), and X-ray photoelectron spectroscopy (XPS) were used to characterize the AuNPs and nanocomposites. The addition of reduced graphene oxide (rGO) resulted in greater dispersion of AuNPs on the rGO surface compared with carbon-based nanomaterials used as a support. Differences in morphology due to the nature of the carbon support were observed and are discussed here. AuNPs/rGO seem to be the most promising candidates for the development of LSPR biosensors among the three composites we studied (AuNPs/G, AuNPs/GO, and AuNPs/rGO). Simulations based on the Mie scattering theory have been used to outline the effect of the phytochemicals on LSPR, showing that when the presence of the residuals is limited to the formation of a thin capping layer, the quality of the plasmonic resonance is not affected. A further discussion of the application framework is presented.

Single polymeric microfiber waveguide platform for sensitive detection and discrimination of DNA methylation

A novel sensitive detection platform for p16 and p16 methylation based on a single polymeric fluorescent microfiber waveguide with sandwich-structured hybridization designs.

Rapid and Label-Free Detection of 5-Hydroxymethylcytosine in Genomic DNA Using an Au/ZnO Nanorods Hybrid Nanostructure-Based Electrochemical Sensor

Ten-eleven-translocation (TET) proteins modify DNA methylation by oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Loss of 5hmC, a widely accepted epigenetic hallmark of cancers, is proposed as a biomarker for early cancer diagnosis and prognosis. Thus, precise quantification of 5hmC holds great potential for diverse clinical applications. DNAs containing 5mC or 5hmC display different adsorption affinity toward the gold surface, thus producing different electrochemical responses. Here a novel, label-free electrochemical sensor based on gold nanoparticles (Au NPs)/zinc oxide nanorods (ZnO NRs) nanostructure for the facile and real-time detection of 5hmC-enriched DNAs is reported. The hybrid structure is fabricated by the vertical hydrothermal growth of ZnO NRs onto indium tin oxide glass substrate, followed by the decoration of ZnO NRs with Au NPs via sputtering. Successful fabrication is confirmed by analyzing the morphology and chemical composition of the sensor. By coupling the fabricated sensor with cyclic voltammetry, its functionality in distinguishing genomic DNAs containing different levels of 5hmC is validated. Notably, the sensor device successfully and consistently detects 5hmC loss in primary hepatocellular carcinoma, compared to the normal tissues. Thus, the novel sensing strategy to assess DNA hydroxymethylation will likely find broad applications in early cancer diagnosis and prognosis evaluation.

A facile wet-chemistry approach to engineer an Au-based SERS substrate and enhance sensitivity down to ppb-level detection

A two-dimensional flexible surface-enhanced Raman scattering (SERS) filter substrate provides an alternative strategy for the highly sensitive portable detection of various toxic molecules and biomaterials. Herein, we developed a solid-liquid interfacial reduction reaction to post-engineer a solid Au nanostructure surface on filter paper to improve the SERS effect. Among four reductants (ascorbic acid, l-dopamine, hydroquinone (HQ), and formaldehyde), HQ possessed a larger oxidation overpotential and facilitated homogeneous growth, forming small Au branch-structure nanoparticles from HAuCl4 solution. Due to the surface effect by exposing abundant -OH groups and intrinsic aromatic rings from TNA/HQ on nano-gold, the SERS effect on positively charged analytes near the plasmonic Au surface was enhanced, while forming a protective layer against severe water interruption. The resulting SERS substrate with branched nano-gold provided several SERS-enhanced sites, increased the enhancement by more than 6 times compared to original SERS sensing, and displayed a 1.4-7.4 × 105 analytical enhancement factor, which leads to a limit of detection down to several ppb. Less than 6% of deviation in the SERS intensity at different sensing sites was observed. We successfully improved the primary SERS substrate using a high overpotential reductant. Owing to its soft and flexible properties, the paper-based SERS substrate can be used conveniently in different sizes, pasting on curved materials, detecting additives in fish, and preventing the coffee-ring effect, showing high practicality and potential commercial value in the future.

Graphene and its Derivatives-Based Optical Sensors

Being the first successfully prepared two-dimensional material, graphene has attracted extensive attention from researchers due to its excellent properties and extremely wide range of applications. In particular, graphene and its derivatives have displayed several ideal properties, including broadband light absorption, ability to quench fluorescence, excellent biocompatibility, and strong polarization-dependent effects, thus emerging as one of the most popular platforms for optical sensors. Graphene and its derivatives-based optical sensors have numerous advantages, such as high sensitivity, low-cost, fast response time, and small dimensions. In this review, recent developments in graphene and its derivatives-based optical sensors are summarized, covering aspects related to fluorescence, graphene-based substrates for surface-enhanced Raman scattering (SERS), optical fiber biological sensors, and other kinds of graphene-based optical sensors. Various sensing applications, such as single-cell detection, cancer diagnosis, protein, and DNA sensing, are introduced and discussed systematically. Finally, a summary and roadmap of current and future trends are presented in order to provide a prospect for the development of graphene and its derivatives-based optical sensors.

A Quest for New Cancer Diagnosis, Prognosis and Prediction Biomarkers and Their Use in Biosensors Development

Traditional techniques for cancer diagnosis, such as nuclear magnetic resonance, ultrasound and tissue analysis, require sophisticated devices and highly trained personnel, which are characterized by elevated operation costs. The use of biomarkers has emerged as an alternative for cancer diagnosis, prognosis and prediction because their measurement in tissues or fluids, such as blood, urine or saliva, is characterized by shorter processing times. However, the biomarkers used currently, and the techniques used for their measurement, including ELISA, western-blot, polymerase chain reaction (PCR) or immunohistochemistry, possess low sensitivity and specificity. Therefore, the search for new proteomic, genomic or immunological biomarkers and the development of new noninvasive, easier and cheaper techniques that meet the sensitivity and specificity criteria for the diagnosis, prognosis and prediction of this disease has become a relevant topic. The purpose of this review is to provide an overview about the search for new cancer biomarkers, including the strategies that must be followed to identify them, as well as presenting the latest advances in the development of biosensors that possess a high potential for cancer diagnosis, prognosis and prediction, mainly focusing on their relevance in lung, prostate and breast cancers.

Graphene and Graphene Oxide Applications for SERS Sensing and Imaging

Surface Enhanced Raman Spectroscopy (SERS) has a long history as an ultrasensitive platform for the detection of biological species from small aromatic molecules to complex biological systems as circulating tumor cells. Thanks to unique properties of graphene, the range of SERS applications has largely expanded. Graphene is efficient fluorescence quencher improving quality of Raman spectra. It contributes also to the SERS enhancement factor through the chemical mechanism. In turn, the chemical flexibility of Reduced Graphene Oxide (RGO) enables tunable adsorption of molecules or cells on SERS active surfaces. Graphene oxide composites with SERS active nanoparticles have been also applied for Raman imaging of cells. This review presents a survey of SERS assays employing graphene or RGO emphasizing the improvement of SERS enhancement brought by graphene or RGO. The structure and physical properties of graphene and RGO will be discussed too.

A Review of Chinese Raman Spectroscopy Research Over the Past Twenty Years

This paper introduces the major Chinese research groups in the fields of biomedicine, food safety, environmental testing, material research, archaeological and cultural relics, gem identification, forensic science, and other research areas of Raman spectroscopy and combined methods spanning the two decades from 1997 to 2017. Briefly summarized are the research directions and contents of the major Chinese Raman spectroscopy research groups, giving researchers engaged in Raman spectroscopy research a more comprehensive understanding of the state of Chinese Raman spectroscopy research and future development trends to further develop Raman spectroscopy and its applications.

Plasmonic Gold Nanohole Array for Surface-Enhanced Raman Scattering Detection of DNA Methylation

Surface-enhanced Raman spectroscopy (SERS), which utilizes nanogaps between noble-metal nanostructures as hot spots to yield ultrasensitive SERS signals, is an outstanding label-free and straightforward tool for DNA methylation analysis. Herein, a plasmonic gold nanohole array (PGNA) with well-controlled hot spots and an open surface was designed as a SERS substrate for DNA methylation detection. A finite-difference time-domain (FDTD) simulation was first employed to investigate the electric field distributions of the PGNA as a function of the geometric parameters. The plasmonic response was tuned to 785 cm^-1 to match the ring breathing vibrational band of cytosine, the intensity change of which was revealed to be a marker of DNA methylation. Then, guided by the FDTD simulation results, the PGNA was fabricated via the electron beam lithography (EBL) technique. The fabricated PGNA had an open and easily accessible surface topology, a SERS enhancement factor of ∼10⁶, and a relative standard deviation (RSD) of 7.1% for 500 repetitions over an area of 20 × 20 μm² using 1 μM Rhodamine 6G as the Raman reporter. The fabricated PGNA was further used as a platform for determining DNA methylation. The proposed method exhibited a sensitivity for detecting 1% of methylation changes. Moreover, insight into the dynamic information on methylation events was obtained by combining principal component analysis (PCA) with 2D correlation spectroscopy analysis. Finally, clear discrimination of the different methylation sites, such as 5-methylcytosine and N6-methyladenine, was demonstrated.

DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy

We show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm^-1 and changes in the Raman peaks in the 1200-1700 cm^-1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm^-1 and spectral intensity inversion at 1324 (C₅=C₆) and 1473 cm^-1 (C₄=N₃) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C₅=C₆) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ∼1470 cm^-1 vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ∼1000 cm^-1 peak and distribution of the signal in the 1200-1700 cm^-1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. The Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ∼259 nm excitation wavelength.

New Dual-Spectroscopic Strategy for the Direct Detection of Aristolochic Acids in Blood and Tissue

Aristolochic acids (AAs) contained in herbal plants are implicated in multiple organ injuries and have a high mutational burden in upper tract urothelial cancers. The currently available techniques for monitoring AAs include LC (liquid chromatography) and LC/MS (mass spectrometry), but the application of these approaches are limited due to the complex sample preparation and derivatization steps. Therefore, there is an urgent need to develop efficient methods for identifying and quantifying AAs. Here, we present a new dual-spectroscopic approach for the direct detection of AAs from blood and tissue samples; the detection of aristolochic acid I (AAI) is performed by surface-enhanced Raman spectroscopy (SERS), and its bioproduct, aristololactam (AAT), is detected by fluorescence spectroscopy based on their distinctive spectral response. Furthermore, a graphene assisted enrichment coupled with a magnetic retrieval strategy was developed to enhance SERS sensitivity toward AAI. Our method was successfully applied to directly determine both AAI and AAT from the blood, liver, and kidney of rats. The potential for real-world application was demonstrated by continuously monitoring AAI and AAT in rat blood and tissues after AAI feeding. The results showed that AAI was gradually metabolized to AAT and transported to different organs. It was found that the metabolism of AAI took place in the kidney, but AAT residue was detected in both liver and kidney, which might be related to long-term toxicity and gene mutation. The proposed dual-spectroscopic strategy is applicable to long-term toxicology research and to the direct diagnosis of AAI-induced organ injury.

Multi-hydrogen bond assisted SERS detection of adenine based on multifunctional graphene oxide/poly (diallyldimethyl ammonium chloride)/Ag nanocomposites

Nanocomposites of graphene oxide/poly (diallyldimethyl ammonium chloride)/Ag nanoparticles (GO/PDDA/Ag NPs) were constructed via a self-assembly process as a surface-enhanced Raman scattering (SERS) substrate, in which functional macromolecules PDDA were utilized to load GO and support Ag NPs. Fundamental SERS performance of this SERS substrate was evaluated using rhodamine 6G (R6G), which displayed excellent enhancement effect, transferable nature and high stability of the synthesized GO/PDDA/Ag NPs substrate. Furthermore, the synthesized SERS substrate was employed in the sensitive detection of adenine with a linear range of 0.05-1000 μM and low detection limit of 1 nM. Other than the large surface area of GO, multiple-hydrogen bond interactions between adenine and the modified PDDA were another important factor in capturing adenine molecules and enhancing SERS signal. The hydrogen bond interaction was calculated using quantum mechanical calculations. Moreover, determination of adenine in aqueous solutions was achieved with good anti-interference ability against other nucleic bases with similar structures, such as guanine, cytosine and thymine. Therefore, GO/PDDA/Ag can be anticipated to be a potential substrate for label-free, fast and sensitive SERS detection of adenine in the field of bioanalysis.

Versatile Electroanalytical Bioplatforms for Simultaneous Determination of Cancer-Related DNA 5-Methyl- and 5-Hydroxymethyl-Cytosines at Global and Gene-Specific Levels in Human Serum and Tissues

This paper reports the preparation of versatile electrochemical biosensing platforms for the simple, rapid, and PCR-independent detection of the most frequent DNA methylation marks (5-methylcytosine, 5-mC, and/or 5-hydroxymethylcytosine, 5-hmC) both at global and gene-specific levels. The implemented strategies, relying on the smart coupling of immuno-magnetic beads (MBs), specific DNA probes and amperometric detection at screen-printed carbon electrodes (SPCEs), provided sensitive and selective determination of the target methylated DNAs in less than 90 min with a great reproducibility and demonstrated feasibility for the simultaneous detection of the same or different cytosine epimarks both at global level and in different loci of the same gene or in different genes. The bioplatforms were applied to determine global methylation events in paraffin-embedded colorectal tissues and specific methylation at promoters of tumor suppressor genes in genomic DNA extracted from cancer cells and paraffin-embedded colorectal tissues, and in serum without previous DNA extraction from cancer patients.

Liquid biopsy of circulating tumor DNA and biosensor applications

Circulating tumor DNA (ctDNA) as a class of liquid biopsy is a type of gene fragment that contains tumor-specific gene changes in body fluids such as human peripheral blood. More and more evidences show that ctDNA is an excellent tumor biomarker for diagnosis, prognosis, tumor heterogeneity and so on. ctDNA is a tumor code in the blood. Liquid biopsy of ctDNA is firstly summarized. Compared with the traditional detection technologies of ctDNA, the biosensor is an excellent choice for the detection of ctDNA because of its portability, sensitivity, specificity and ease of use. This review mainly evaluates various biosensors applied to the detection of ctDNA. We discuss the most commonly used bioreceptors to specifically identify and bind ctDNA, including complementary DNA (cDNA), peptide nucleic acid (PNA) and anti-5 MethylCytosines, and the biotransducers which convert biological signals to analysable signs. The review also discusses signal amplification strategies in biosensors to detect ctDNA.

Exploring the margins of SERS in practical domain: An emerging diagnostic modality for modern biomedical applications

Excellent multiplexing capability, molecular specificity, high sensitivity and the potential of resolving complex molecular level biological compositions augmented the diagnostic modality of surface-enhanced Raman scattering (SERS) in biology and medicine. While maintaining all the merits of classical Raman spectroscopy, SERS provides a more sensitive and selective detection and quantification platform. Non-invasive, chemically specific and spatially resolved analysis facilitates the exploration of SERS-based nano probes in diagnostic and theranostic applications with improved clinical outcomes compared to the currently available so called state-of-art technologies. Adequate knowledge on the mechanism and properties of SERS based nano probes are inevitable in utilizing the full potential of this modality for biomedical applications. The safety and efficiency of metal nanoparticles and Raman reporters have to be critically evaluated for the successful translation of SERS in to clinics. In this context, the present review attempts to give a comprehensive overview about the selected medical, biomedical and allied applications of SERS while highlighting recent and relevant outcomes ranging from simple detection platforms to complicated clinical applications.

Recent progress on graphene-based substrates for surface-enhanced Raman scattering applications

Graphene-based SERS substrates are classified and introduced, and their applications in biosensing-related fields are reviewed.

Plasmonic Nanomaterial-Based Optical Biosensing Platforms for Virus Detection

Plasmonic nanomaterials (P-NM) are receiving attention due to their excellent properties, which include surface-enhanced Raman scattering (SERS), localized surface plasmon resonance (LSPR) effects, plasmonic resonance energy transfer (PRET), and magneto optical (MO) effects. To obtain such plasmonic properties, many nanomaterials have been developed, including metal nanoparticles (MNP), bimetallic nanoparticles (bMNP), MNP-decorated carbon nanotubes, (MNP-CNT), and MNP-modified graphene (MNP-GRP). These P-NMs may eventually be applied to optical biosensing systems due to their unique properties. Here, probe biomolecules, such as antibodies (Ab), probe DNA, and probe aptamers, were modified on the surface of plasmonic materials by chemical conjugation and thiol chemistry. The optical property change in the plasmonic nanomaterials was monitored based on the interaction between the probe biomolecules and target virus. After bioconjugation, several optical properties, including fluorescence, plasmonic absorbance, and diffraction angle, were changed to detect the target biomolecules. This review describes several P-NMs as potential candidates of optical sensing platforms and introduces various applications in the optical biosensing field.

Ag Nanorods-Oxide Hybrid Array Substrates: Synthesis, Characterization, and Applications in Surface-Enhanced Raman Scattering

Over the last few decades, benefitting from the sufficient sensitivity, high specificity, nondestructive, and rapid detection capability of the surface-enhanced Raman scattering (SERS) technique, numerous nanostructures have been elaborately designed and successfully synthesized as high-performance SERS substrates, which have been extensively exploited for the identification of chemical and biological analytes. Among these, Ag nanorods coated with thin metal oxide layers (AgNRs-oxide hybrid array substrates) featuring many outstanding advantages have been proposed as fascinating SERS substrates, and are of particular research interest. The present review provides a systematic overview towards the representative achievements of AgNRs-oxide hybrid array substrates for SERS applications from diverse perspectives, so as to promote the realization of real-world SERS sensors. First, various fabrication approaches of AgNRs-oxide nanostructures are introduced, which are followed by a discussion on the novel merits of AgNRs-oxide arrays, such as superior SERS sensitivity and reproducibility, high thermal stability, long-term activity in air, corrosion resistivity, and intense chemisorption of target molecules. Next, we present recent advances of AgNRs-oxide substrates in terms of practical applications. Intriguingly, the recyclability, qualitative and quantitative analyses, as well as vapor-phase molecule sensing have been achieved on these nanocomposites. We further discuss the major challenges and prospects of AgNRs-oxide substrates for future SERS developments, aiming to expand the versatility of SERS technique.

Technical advances in global DNA methylation analysis in human cancers

Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types. Important breakthroughs in the recent years have uncovered further oxidized derivatives of 5mC - 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), thereby expanding our understanding of the DNA methylation dynamics. While the biological roles of these epigenetic derivatives are being extensively characterized, this review presents a perspective on the opportunity of innovation in the global methylation analysis platforms. While multiple methods for global analysis of 5mC in clinical samples exist and have been reviewed elsewhere, two of the established methods - Liquid Chromatography coupled with mass spectrometry (LC-MS/MS) and Immunoquantification have successfully evolved to include the quantitation of 5hmC, 5fC and 5caC. Although the analytical performance of LC-MS/MS is superior, the simplicity afforded by the experimental procedure of immunoquantitation ensures it’s near ubiquity in clinical applications. Recent developments in spectroscopy, nanotechnology and sequencing also provide immense promise for future evaluations and are discussed briefly. Finally, we provide a perspective on the current scenario of global DNA methylation analysis tools and present suggestions to develop the next generation toolset.