Target-triggered assembly of plasmon resonance nanostructures for quantitative detection of lncRNA in liver cancer cells via surface enhanced Raman spectroscopy

Long-stranded non-coding RNAs (lncRNA) have important roles in disease as transcriptional regulators, mRNA processing regulators and protein synthesis factors. However, traditional methods for detecting lncRNA are time-consuming and labor-intensive, and the functions of lncRNA are still being explored. Here, we present a surface enhanced Raman spectroscopy (SERS) based biosensor for the detection of lncRNA associated with liver cancer (LC) as well as in situ cellular imaging. Using the dual SERS probes, quantitative detection of lncRNA (DAPK1-215) can be achieved with an ultra-low detection limit of 952 aM by the target-triggered assembly of core-satellite nanostructures. And the reliability of this assay can be further improved with the R2 value of 0.9923 by an internal standard probe that enables the signal dynamic calibration. Meanwhile, the high expression of DAPK1-215 mainly distributed in the cytoplasm was observed in LC cells compared with the normal ones using the SERS imaging method. Moreover, results of cellular function assays showed that DAPK1-215 promoted the migration and invasion of LC by significantly reducing the expression of the structural domain of death associated protein kinase. The development of this biosensor based on SERS can provide a sensitive and specific method for exploring the expression of lncRNA that would be a potential biomarker for the screening of LC.

DNA Adductomics: A Narrative Review of Its Development, Applications, and Future

DNA adductomics is the global study of all DNA adducts and was first proposed in 2006 by the Matsuda group. Its development has been greatly credited to the advances in mass spectrometric techniques, particularly tandem and multiple-stage mass spectrometry. In fact, liquid chromatography-mass spectrometry (LC-MS)-based methods are virtually the sole technique with practicality for DNA adductomic studies to date. At present, DNA adductomics is primarily used as a tool to search for DNA adducts, known and unknown, providing evidence for exposure to exogenous genotoxins and/or for the molecular mechanisms of their genotoxicity. Some DNA adducts discovered in this way have the potential to predict cancer risks and/or to be associated with adverse health outcomes. DNA adductomics has been successfully used to identify and determine exogenous carcinogens that may contribute to the etiology of certain cancers, including bacterial genotoxins and an N-nitrosamine. Also using the DNA adductomic approach, multiple DNA adducts have been observed to show age dependence and may serve as aging biomarkers. These achievements highlight the capability and power of DNA adductomics in the studies of medicine, biological science, and environmental science. Nonetheless, DNA adductomics is still in its infancy, and great advances are expected in the future.

Plasmonic nanoparticle sensors: current progress, challenges, and future prospects

Plasmonic nanoparticles (NPs) have played a significant role in the evolution of modern nanoscience and nanotechnology in terms of colloidal synthesis, general understanding of nanocrystal growth mechanisms, and their impact in a wide range of applications. They exhibit strong visible colors due to localized surface plasmon resonance (LSPR) that depends on their size, shape, composition, and the surrounding dielectric environment. Under resonant excitation, the LSPR of plasmonic NPs leads to a strong field enhancement near their surfaces and thus enhances various light-matter interactions. These unique optical properties of plasmonic NPs have been used to design chemical and biological sensors. Over the last few decades, colloidal plasmonic NPs have been greatly exploited in sensing applications through LSPR shifts (colorimetry), surface-enhanced Raman scattering, surface-enhanced fluorescence, and chiroptical activity. Although colloidal plasmonic NPs have emerged at the forefront of nanobiosensors, there are still several important challenges to be addressed for the realization of plasmonic NP-based sensor kits for routine use in daily life. In this comprehensive review, researchers of different disciplines (colloidal and analytical chemistry, biology, physics, and medicine) have joined together to summarize the past, present, and future of plasmonic NP-based sensors in terms of different sensing platforms, understanding of the sensing mechanisms, different chemical and biological analytes, and the expected future technologies. This review is expected to guide the researchers currently working in this field and inspire future generations of scientists to join this compelling research field and its branches.

Label-free plasmonic spectral profiling of serum DNA

Genetic and epigenetic modifications are linked to the activation of oncogenes and inactivation of tumor suppressor genes. Likewise, the associated molecular alternations can best inform precision medicine for personalized tumor treatment. Therefore, performing characterization of genetic and epigenetic alternations at the molecular level represents a crucial step in early diagnosis and/or therapeutics of cancer. However, the prevailing methods for DNA analysis involve a series of tedious and complicated steps, in which important genetic and epigenetic information could be lost or altered. To provide a potential approach for non-invasive, direct, and efficient DNA analysis, herein, we present a promising strategy for label-free molecular profiling of serum DNA in its pristine form by fusing surface-enhanced Raman spectroscopy with machine learning on a superior plasmonic nanostructured platform. Using DNA methylation and single-point mutation as two case studies, the presented strategy allows a well-balanced sensitive and specific detection of epigenetic and genetic changes at the single-nucleotide level in serum. We envision the presented label-free strategy could serve as a versatile tool for direct molecular profiling in pristine forms of a wide range of biological markers and aid biomedical diagnostics as well as therapeutics.

DOX-DNA Interactions on the Nanoscale: In Situ Studies Using Tip-Enhanced Raman Scattering

Chemotherapeutic anthracyclines, like doxorubicin (DOX), are drugs endowed with cytostatic activity and are widely used in antitumor therapy. Their molecular mechanism of action involves the formation of a stable anthracycline-DNA complex, which prevents cell division and results in cell death. It is known that elevated DOX concentrations induce DNA chain loops and overlaps. Here, for the first time, tip-enhanced Raman scattering was used to identify and localize intercalated DOX in isolated double-stranded calf thymus DNA, and the correlated near-field spectroscopic and morphologic experiments locate the DOX molecules in the DNA and provide further information regarding specific DOX-nucleobase interactions. Thus, the study provides a tool specifically for identifying intercalation markers and generally analyzing drug-DNA interactions. The structure of such complexes down to the molecular level provides mechanistic information about cytotoxicity and the development of potential anticancer drugs.

Confined-Enhanced Raman Spectroscopy

In 1997, the discovery of single molecule-surface enhanced Raman spectroscopy (SM-SERS) rekindled broad interests owing to its ultrahigh enhancement factor up to the 1014-1015 level. However, regretfully, the advantage of SM-SERS with an ultralow detection limit has not yet been fully utilized in commercialized applications. Here, we report a strategy, which we name confined-enhanced Raman spectroscopy, in which the overall Raman properties can be remarkably improved with in situ-formed active nanoshell on the surface of silver or gold nanoparticles. The nanoshell can confine and anchor molecules onto the surface of plasmonic nanoparticles and avoid desorption from hot spots so that the "on and off" blinking effect can be eliminated. It is the first time the single-molecule detection of analytes with super sensitivity, high stability, and reproducibility based on gold nanoparticles has been realized. In addition, this strategy is suitable for SERS detection in diverse molecule systems, including biomedical diagnosis, catalytic reaction, etc.

Combined analytical approach empowers precise spectroscopic interpretation of subcellular components of pancreatic cancer cells

The lack of specific and sensitive early diagnostic options for pancreatic cancer (PC) results in patients being largely diagnosed with late-stage disease, thus inoperable and burdened with high mortality. Molecular spectroscopic methodologies, such as Raman or infrared spectroscopies, show promise in becoming a leader in screening for early-stage cancer diseases, including PC. However, should such technology be introduced, the identification of differentiating spectral features between various cancer types is required. This would not be possible without the precise extraction of spectra without the contamination by necrosis, inflammation, desmoplasia, or extracellular fluids such as mucous that surround tumor cells. Moreover, an efficient methodology for their interpretation has not been well defined. In this study, we compared different methods of spectral analysis to find the best for investigating the biomolecular composition of PC cells cytoplasm and nuclei separately. Sixteen PC tissue samples of main PC subtypes (ductal adenocarcinoma, intraductal papillary mucinous carcinoma, and ampulla of Vater carcinoma) were collected with Raman hyperspectral mapping, resulting in 191,355 Raman spectra and analyzed with comparative methodologies, specifically, hierarchical cluster analysis, non-negative matrix factorization, T-distributed stochastic neighbor embedding, principal components analysis (PCA), and convolutional neural networks (CNN). As a result, we propose an innovative approach to spectra classification by CNN, combined with PCA for molecular characterization. The CNN-based spectra classification achieved over 98% successful validation rate. Subsequent analyses of spectral features revealed differences among PC subtypes and between the cytoplasm and nuclei of their cells. Our study establishes an optimal methodology for cancer tissue spectral data classification and interpretation that allows precise and cognitive studies of cancer cells and their subcellular components, without mixing the results with cancer-surrounding tissue. As a proof of concept, we describe findings that add to the spectroscopic understanding of PC.

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.

Label-Free Human Disease Characterization through Circulating Cell-Free DNA Analysis Using Raman Spectroscopy

Circulating cell-free DNA (ccfDNA) is a liquid biopsy biomaterial attracting significant attention for the implementation of precision medicine diagnostics. Deeper knowledge related to its structure and biology would enable the development of such applications. In this study, we employed Raman spectroscopy to unravel the biomolecular profile of human ccfDNA in health and disease. We established reference Raman spectra of ccfDNA samples from healthy males and females with different conditions, including cancer and diabetes, extracting information about their chemical composition. Comparative observations showed a distinct spectral pattern in ccfDNA from breast cancer patients taking neoadjuvant therapy. Raman analysis of ccfDNA from healthy, prediabetic, and diabetic males uncovered some differences in their biomolecular fingerprints. We also studied ccfDNA released from human benign and cancer cell lines and compared it to their respective gDNA, confirming it mirrors its cellular origin. Overall, we explored for the first time Raman spectroscopy in the study of ccfDNA and provided spectra of samples from different sources. Our findings introduce Raman spectroscopy as a new approach to implementing liquid biopsy diagnostics worthy of further elaboration.

Selectivity of natural isoquinoline alkaloid assembler in programming poly(dA) into parallel duplex by polyvalent synergy

Ligand-induced assembly of disordered DNAs attracts much attention due to its potential action in transcription regulation and molecular switches-based sensors. Among natural isoquinoline alkaloids (NIAs), we screened out nitidine (NIT) as polyvalent-binding assembler to program poly(dA) into a parallel duplex assembly at neutral pH. The molecule planarity of NIAs was believed to be a determinant factor in programming the parallel poly(dA) assembly. Poly(dA) with more than six adenines can initiate the synergistic binding of NIT to generate the parallel assembly. It is expected that one A-A pair in duplex can bind one NIT molecule provided that poly(dA) is long enough, suggesting the pivotal role of the polyvalent synergy of NIT in programming the parallel poly(dA) assembly. A gold nanoparticles-based colorimetric method was also developed to screen NIT out of NIAs having the potential to construct the poly(dA) assembly. Our work will inspire more interest in developing polyadenine-based switches and sensors by concentrating NIT within the polyadenine parallel assembly.

Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis?

Pancreatic cancer (PC) is an aggressive and lethal neoplasm, ranking seventh in the world for cancer deaths, with an overall 5-year survival rate of below 10%. The knowledge about PC pathogenesis is rapidly expanding. New aspects of tumor biology, including its molecular and morphological heterogeneity, have been reported to explain the complicated “cross-talk” that occurs between the cancer cells and the tumor stroma or the nature of pancreatic ductal adenocarcinoma-associated neural remodeling. Nevertheless, currently, there are no specific and sensitive diagnosis options for PC. Vibrational spectroscopy (VS) shows a promising role in the development of early diagnosis technology. In this review, we summarize recent reports about improvements in spectroscopic methodologies, briefly explain and highlight the drawbacks of each of them, and discuss available solutions. The important aspects of spectroscopic data evaluation with multivariate analysis and a convolutional neural network methodology are depicted. We conclude by presenting a study design for systemic verification of the VS-based methods in the diagnosis of PC.

Correlation coefficient-directed label-free characterization of native proteins by surface-enhanced Raman spectroscopy

Investigation of proteins in their native state is the core of proteomics towards better understanding of their structures and functions. Surface-enhanced Raman spectroscopy (SERS) has shown its unique advantages in protein characterization with fingerprint information and high sensitivity, which makes it a promising tool for proteomics. It is still challenging to obtain SERS spectra of proteins in the native state and evaluate the native degree. Here, we constructed 3D physiological hotspots for a label-free dynamic SERS characterization of a native protein with iodide-modified 140 nm Au nanoparticles. We further introduced the correlation coefficient to quantitatively evaluate the variation of the native degree, whose quantitative nature allows us to explicitly investigate the Hofmeister effect on the protein structure. We realized the classification of a protein of SARS-CoV-2 variants in 15 min, which has not been achieved before. This study offers an effective tool for tracking the dynamic structure of proteins and biomedical research.

Optimization of Gonyautoxin1/4-Binding G-Quadruplex Aptamers by Label-Free Surface-Enhanced Raman Spectroscopy

Nucleic acids with G-quadruplex (G4) structures play an important role in physiological function, analysis and detection, clinical diagnosis and treatment, and new drug research and development. Aptamers obtained using systematic evolution of ligands via exponential enrichment (SELEX) screening technology do not always have the best affinity or binding specificity to ligands. Therefore, the establishment of a structure-oriented experimental method is of great significance. To study the potential of surface-enhanced Raman spectroscopy (SERS) in aptamer optimization, marine biotoxin gonyautoxin (GTX)1/4 and its G4 aptamer obtained using SELEX were selected. The binding site and the induced fit of the aptamer to GTX1/4 were confirmed using SERS combined with two-dimensional correlation spectroscopy. The intensity of interaction between GTX1/4 and G4 was also quantified by measuring the relative intensity of SERS bands corresponding to intramolecular hydrogen bonds. Furthermore, the interaction between GTX1/4 and optimized aptamers was analyzed. The order of intensity change in the characteristic bands of G4 aptamers was consistent with the order of affinity calculated using microscale thermophoresis and molecular dynamics simulations. SERS provides a rapid, sensitive, and economical post-SELEX optimization of aptamers. It is also a reference for future research on other nucleic acid sequences containing G4 structures.

An antigen-targeting assay for Lyme disease: Combining aptamers and SERS to detect the OspA protein

Lyme disease is the fastest growing vector-borne disease in the United States. However, current testing modalities are ill suited to detection of Lyme disease, leading to the diagnosis of many cases after treatment is effective. We present an improved, direct method Lyme disease diagnosis, where the Lyme specific biomarker Outer Surface Protein A (OspA) in clinical serum samples is identified using a diagnostic platform combining surface enhanced Raman scattering (SERS) and aptamers. Employing orthogonal projections to latent structures discriminant analysis, the system accurately identified 91% of serum samples from Lyme patients, and 96% of serum samples from symptomatic controls. In addition, the OspA limit-of-detection, determined to be 1 × 10^-4 ng/mL, is greater than four orders of magnitude lower than that found in serum samples from early Lyme disease patients. The application of this platform to detect this difficult-to-diagnose disease suggests its potential for detecting other diseases that present similar difficulties.

Nanoplatform to Investigate Tumor-Initiating Cancer Stem Cells: Breaking the Diagnostic Barrier

Drug-resistant capacity in a small population of tumor-initiating cancer stem cells (tiCSCs) can be due to aberrant epigenetic changes. However, currently available conventional detection methods are inappropriate and cannot be applied to investigate the scarce population (tiCSCs). In addition, selective inhibitor drugs are shown to reverse epigenetic changes; however, each cancer type is discrete. Hence, it is essential to probe the resultant changes in tiCSCs even after therapy. Therefore, we have developed a multimode nanoplatform to investigate tiCSCs, detect epigenetic changes, and subsequently explore their transformation signals following drug therapy. We performed this by developing a surface-enhanced Raman scattering (SERS)-active nanoplatform integrated with n-dopant using an ultrafast laser ionization technique. The dopant functionalization enhances Raman scattering ability and permits label-free analysis of biomarkers in tiCSCs with the resolution down to the cellular level. Here, we investigated epigenetic biomarkers of tiCSCs in pancreatic and lung cancers. An extended study using inhibitor drugs demonstrates an unexpected increase of tiCSCs from lung cancer; this difference can be attributed to transformation changes in lung tiCSC. Thus, our work brings new insight into the differentiation abilities of CSCs upon epigenetic reversal, emphasizing unique perceptions in cancer treatment.

Recent advances in antibiotic resistance diagnosis using SERS: focus on the “Big 5” challenges

SERS for antibiotic resistance diagnosis.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

Spatial Separation of Plasmonic Hot-Electron Generation and a Hydrodehalogenation Reaction Center Using a DNA Wire

Using hot charge carriers far from a plasmonic nanoparticle surface is very attractive for many applications in catalysis and nanomedicine and will lead to a better understanding of plasmon-induced processes, such as hot-charge-carrier- or heat-driven chemical reactions. Herein we show that DNA is able to transfer hot electrons generated by a silver nanoparticle over several nanometers to drive a chemical reaction in a molecule nonadsorbed on the surface. For this we use 8-bromo-adenosine introduced in different positions within a double-stranded DNA oligonucleotide. The DNA is also used to assemble the nanoparticles into nanoparticles ensembles enabling the use of surface-enhanced Raman scattering to track the decomposition reaction. To prove the DNA-mediated transfer, the probe molecule was insulated from the source of charge carriers, which hindered the reaction. The results indicate that DNA can be used to study the transfer of hot electrons and the mechanisms of advanced plasmonic catalysts.

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.

Biophysics is reshaping our perception of the epigenome: from DNA-level to high-throughput studies

Epigenetic research holds great promise to advance our understanding of biomarkers and regulatory processes in health and disease. An increasing number of new approaches, ranging from molecular to biophysical analyses, enable identifying epigenetic changes on the level of a single gene or the whole epigenome. The aim of this review is to highlight how the field is shifting from completely molecular-biology-driven solutions to multidisciplinary strategies including more reliance on biophysical analysis tools. Biophysics not only offers technical advancements in imaging or structure analysis but also helps to explore regulatory interactions. New computational methods are also being developed to meet the demand of growing data volumes and their processing. Therefore, it is important to capture these new directions in epigenetics from a biophysical perspective and discuss current challenges as well as multiple applications of biophysical methods and tools. Specifically, we gradually introduce different biophysical research methods by first considering the DNA-level information and eventually higher-order chromatin structures. Moreover, we aim to highlight that the incorporation of bioinformatics, machine learning, and artificial intelligence into biophysical analysis allows gaining new insights into complex epigenetic processes. The gained understanding has already proven useful in translational and clinical research providing better patient stratification options or new therapeutic insights. Together, this offers a better readiness to transform bench-top experiments into industrial high-throughput applications with a possibility to employ developed methods in clinical practice and diagnostics.

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.

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.

New insight into the aptamer conformation and aptamer/protein interaction by surface-enhanced Raman scattering and multivariate statistical analysis

We study the interaction between one aptamer and its analyte (the MnSOD protein) by the combination of surface-enhanced Raman scattering and multivariate statistical analysis. We observe the aptamer structure and its evolution during the interaction under different experimental conditions (in air or in buffer). Through the spectral treatment by principal component analysis of a large set of SERS data, we were able to probe the aptamer conformations and orientations relative to the surface assuming that the in-plane nucleoside modes are selectively enhanced. We demonstrate that the aptamer orientation and thus its flexibility rely strongly on the presence of a spacer of 15 thymines and on the experimental conditions with the aptamer lying on the surface in air and standing in the buffer. We reveal for the first time that the interaction with MnSOD induces a large loss of flexibility and freezes the aptamer structure in a single conformation.

Microfluidic In Situ Patterning of Silver Nanoparticles for Surface-Enhanced Raman Spectroscopic Sensing of Biomolecules

This work integrates the advantages of microfluidic devices, nanoparticle synthesis, and on-chip sensing of biomolecules. The concept of microreactors brings new opportunities in chemical synthesis, especially for metallic nanoparticles favorable in surface-enhanced Raman spectroscopy (SERS) for high-resolution and low-limit detection of biomolecules. However, still missing is our understanding of reactions at the microscale and how microsystems can be exploited in biosensing applications via precise control of nanomaterial synthesis. We investigate how microfluidic geometry affects nanoparticle patterning for high-resolution SERS-based sensing and propose a spiral-shaped microchannel that can achieve enhanced mixing, rapid reaction at room temperature, and uniform in situ patterning. The roles of channel geometry as the key parameter on patterning have been studied systematically to provide insight into the rational design of continuous microfluidic systems for SERS applications. We also demonstrate potential applications of this integrated system in label-free on-chip detection of 1 pM rhodamine B (enhancement factor, ∼4.3 × 10¹¹) and a 1 nM 41-base single-stranded deoxyribonucleic acid (DNA) sequence (enhancement factor, ∼1.5 × 10⁸). Our ready-to-use multifunctional system provides an alternative strategy for the facile fabrication of SERS-active substrates and promotes system integration, miniaturization, and on-site biological applications.

Ion-exchanged glass microrods as hybrid SERS/fluorescence substrates for molecular beacon-based DNA detection

Ion-exchange in molten nitrate salts containing metal ions (i.e. silver, copper, etc.) represents a well-established technique able to modify the chemical-physical properties of glass materials. It is widely used not only in the field of integrated optics (IO) but also, more recently, in plasmonics due to the possibility to induce the formation of metal nanoparticles in the glass matrix by an ad hoc thermal post-process. In this work, the application of this technology for the realisation of low-cost and stable surface-enhanced Raman scattering (SERS) active substrates, based on soda-lime glass microrods, is reported. The microrods, with a radius of a few tens of microns, were obtained by cutting the end of an ion-exchanged soda-lime fibre for a length less than 1 cm. As ion source, silver nitrate was selected due to the outstanding SERS properties of silver. The ion-exchange and thermal annealing post-process parameters were tuned to expose the embedded silver nanoparticles on the surface of the glass microrods, avoiding the use of any further chemical etching step. In order to test the combined SERS/fluorescence response of these substrates, labelled molecular beacons (MBs) were immobilised on their surface for deoxyribonucleic acid (DNA) detection. Our experiments confirm that target DNA is attached on the silver nanoparticles and its presence is revealed by both SERS and fluorescence measurements. These results pave the way towards the development of low-cost and stable hybrid fibres, in which SERS and fluorescence interrogation techniques are combined in the same optical device.

Targets and Tools: Nucleic Acids for Surface-Enhanced Raman Spectroscopy

Surface-enhanced Raman spectroscopy (SERS) merges nanotechnology with conventional Raman spectroscopy to produce an ultrasensitive and highly specific analytical tool that has been exploited as the optical signal read-out in a variety of advanced applications. In this feature article, we delineate the main features of the intertwined relationship between SERS and nucleic acids (NAs). In particular, we report representative examples of the implementation of SERS in biosensing platforms for NA detection, the integration of DNA as the biorecognition element onto plasmonic materials for SERS analysis of different classes of analytes (from metal ions to microorgniasms) and, finally, the use of structural DNA nanotechnology for the precise engineering of SERS-active nanomaterials.

A Versatile DNA Origami-Based Plasmonic Nanoantenna for Label-Free Single-Molecule Surface-Enhanced Raman Spectroscopy

DNA origami technology allows for the precise nanoscale assembly of chemical entities that give rise to sophisticated functional materials. We have created a versatile DNA origami nanofork antenna (DONA) by assembling Au or Ag nanoparticle dimers with different gap sizes down to 1.17 nm, enabling signal enhancements in surface-enhanced Raman scattering (SERS) of up to 10¹¹. This allows for single-molecule SERS measurements, which can even be performed with larger gap sizes to accommodate differently sized molecules, at various excitation wavelengths. A general scheme is presented to place single analyte molecules into the SERS hot spots using the DNA origami structure exploiting covalent and noncovalent coupling schemes. By using Au and Ag dimers, single-molecule SERS measurements of three dyes and cytochrome c and horseradish peroxidase proteins are demonstrated even under nonresonant excitation conditions, thus providing long photostability during time-series measurement and enabling optical monitoring of single molecules.

A new method towards the detection of DNA mutation by Surface-Enhanced Raman Spectroscopy

It is generally believed that the self-folding of single-stranded DNA depends on the hydrophobic effect of its internal bases, but the folding of a single-stranded DNA in a solution was not disordered and would be affected by the stacking effect of adjacent bases. In this work, we developed a new method to explore the stacking between adjacent bases using Surface-Enhanced Raman Spectroscopy (SERS) for the first time. Acidic titanium ions were introduced into silver nanoparticles as an aggregating agent (Ag@ITNPs), and obtained a symmetrical spectrum by normalizing the peak to deoxyribose at 955 cm^-1. Based on the influence of adjacent base stacking on the spectrum, we first identified the point mutation sites accurately by SERS. Also, the base content and the DNA frameshift mutations in ssDNA were precisely analyzed. This new method has a simple experimental process and can accurately capture the changes in the base ring breathing peak intensity caused by different adjacent bases, and thus will provide potential application value in the field of gene diagnosis.

Vibrational Spectra of Nucleotides in the Presence of the Au Cluster Enhancer in MD Simulation of a SERS Sensor

Surface-enhanced Raman scattering (SERS) nanoprobes have shown tremendous potential in in vivo imaging. The development of single oligomer resolution in the SERS promotes experiments on DNA and protein identification using SERS as a nanobiosensor. As Raman scanners rely on a multiple spectrum acquisition, faster imaging in real-time is required. SERS weak signal requires averaging of the acquired spectra that erases information on conformation and interaction. To build spectral libraries, the simulation of measurement conditions and conformational variations for the nucleotides relative to enhancer nanostructures would be desirable. In the molecular dynamic (MD) model of a sensing system, we simulate vibrational spectra of the cytosine nucleotide in FF2/FF3 potential in the dynamic interaction with the Au20 nanoparticles (NP) (EAM potential). Fourier transfer of the density of states (DOS) was performed to obtain the spectra of bonds in reaction coordinates for nucleotides at a resolution of 20 to 40 cm-1. The Au20 was optimized by ab initio density functional theory with generalized gradient approximation (DFT GGA) and relaxed by MD. The optimal localization of nucleotide vs. NP was defined and the spectral modes of both components vs. interaction studied. Bond-dependent spectral maps of nucleotide and NP have shown response to interaction. The marker frequencies of the Au20-nucleotide interaction have been evaluated.

Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy

Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar–phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.

Droplet array for open-channel high-throughput SERS biosensing

Open-channel and high throughput are two important aspects of clinical diagnosis, correlation biochemical analysis, cell culture techniques and food safety. Here, we propose the mini-pillar based array for open-channel and high-throughput SERS detection of miRNA. The polydimethylsiloxane (PDMS) mini-pillars are used as a high-throughput platform, which have good anchoring and aggregation effects on microdroplets, greatly reducing the amount of analytical solution and facilitate the homogeneous sample distribution after evaporation. The deposited gold nanorods (Au NRs) on the pillars with optimized diameter served as SERS-active substrate, can greatly improve the sensitivity of SERS signal compared to other planar substrates. On the open-channel biological chip, sensitive, simultaneous, and specific detection of breast cancer marker miRNA-1246 can be performed. In this mini-pillar array SERS system, the limit of detection (LOD) is 10^-12 M. The mini-pillar array shows enormous potential for open channel, high-throughput biomolecular detection, providing an opportunity for biomedical point-of-care testing (POCT) and drug screening.

Surface-Enhanced Raman Scattering Detection of Nucleic Acids Exhibiting Sterically Accessible Guanines Using Ruthenium-Polypyridyl Reagents

Here, we report the application of surface-enhanced Raman scattering (SERS) spectroscopy as a rapid and practical tool for assessing the formation of coordinative adducts between nucleic acid guanines and ruthenium polypyridyl reagents. The technology provides a practical approach for the wash-free and quick identification of nucleic acid structures exhibiting sterically accessible guanines. This is demonstrated for the detection of a quadruplex-forming sequence present in the promoter region of the c-myc oncogene, which exhibits a nonpaired, reactive guanine at a flanking position of the G-quartets.

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.

Highly reusable nanoporous silver sheet for sensitive SERS detection of pesticides

Surface-enhanced Raman spectroscopy (SERS) enables pesticide detection at the point-of-need, but its practical application is limited by expensive and disposable SERS substrates. Here, we report a reusable nanoporous silver (NPAg) sheet for the SERS detection of organochlorine pesticides, aiming to maximize the cost-efficiency of substrate regeneration. The NPAg sheet is prepared by a reduction-induced decomposition method without chemical induced random aggregations. This SERS substrate is sensitive to various analytes regardless of their affinity to a metal surface such as rhodamine B, dichlorodiphenyl-trichloroethane (DDT), and lindane due to its large surface area and the coral rock-like morphology. The SERS signal of lindane, a typical organochlorine pesticide, is identified and quantified with a minimum detectable concentration of 3 × 10^-7 M (87 ppb), which is below the maximum residue limits in various foods set by the regulators across the world. More importantly, after a few minutes of ultrasonic cleaning in water, the NPAg sheet can be reused at least 20 times with a reproducible SERS activity. Furthermore, the NPAg sheet remains stable in terms of its sensitivity and reusability after several months of bare strorage. Therefore, the NPAg sheet as a SERS substrate holds great promise for mass production and convenient applications in low-cost pesticide analysis.

Application of surface-enhanced Raman spectroscopy in fast detection of toxic and harmful substances in food

Surface-enhanced Raman spectroscopy (SERS) is being considered as a powerful technique in the area of food safety due to its rapidity, sensitivity, portability, and non-destructive features. This review aims to provide a comprehensive understanding of SERS applications in fast detection of toxic and harmful substances in food matrix. The enhancement mechanism of SERS, classification of active substrates, detection methods, and their advantages and disadvantages are briefly discussed in the review. The latest research progress of fast SERS detection of food-borne pathogens, mycotoxins, shellfish toxins, illegal food additives, and drug residues are highlighted in sections of the review. According to the current status of SERS detection of food-derived toxic and harmful substances, the review comes up with certain problems to be urgently resolved in SERS and brings up the perspectives on the future directions of SERS based biosensors.

Surface dynamics of genomic DNAs upon lowering the pH, in the presence of graphene/AgNPs-based SERS detection platform

Graphene/AgNPs-based surface dynamics of native DNA functional groups at different acidic pH values was discussed using surface-enhanced Raman spectroscopy (SERS). Also, ab initio dynamics of Verlet type was investigated for nucleic acid nitrogenous bases adsorbed on a graphene surface, respectively. The experimental dynamical parameters were given in terms of full widths at half-maximum (FWHMs) and (sub)picosecond global relaxation times, associated with SERS bands. Furthermore, using density functional theory (DFT) as implemented in SIESTA and the velocity autocorrelation function (VACF), we have obtained the vibrational density of states (VDOS) for each of the four DNA bases placed on a pristine graphene layer. Graphical abstract Top: computed VbDOS for guanine. Bottom: Verlet temperature as a function of time.

Gold Nanocylinders on Gold Film as a Multi-spectral SERS Substrate

The surface enhanced Raman scattering (SERS) efficiency of gold nanocylinders deposited on gold thin film is studied. Exploiting the specific plasmonic properties of such substrates, we determine the influence of the nanocylinder diameter and the film thickness on the SERS signal at three different excitation wavelengths (532, 638 and 785 nm). We demonstrate that the highest signal is reached for the highest diameter of 250 nm due to coupling between the nanocylinders and for the lowest thickness (20 nm) as the excited plasmon is created at the interface between the gold and glass substrate. Moreover, even if we show that the highest SERS efficiency is obtained for an excitation wavelength of 638 nm, a large SERS signal can be obtained at all excitation wavelengths and on a wide spectral range. We demonstrate that it can be related with the nature of the plasmon (propagative plasmon excited through the nanocylinder grating) and with its angular dependence (tuning of the plasmon position with the excitation angle). Such an effect allows the excitation of plasmon on nearly the whole visible range, and paves the way to multispectral SERS substrates.

Surface-enhanced Raman spectroscopy: benefits, trade-offs and future developments

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopy technique with sensitivity down to the single molecule level that provides fine molecular fingerprints, allowing for direct identification of target analytes. Extensive theoretical and experimental research, together with continuous development of nanotechnology, has significantly broadened the scope of SERS and made it a hot research field in chemistry, physics, materials, biomedicine, and so on. However, SERS has not been developed into a routine analytical technique, and continuous efforts have been made to address the problems preventing its real-world application. The present minireview focuses on analyzing current and potential strategies to tackle problems and realize the SERS performance necessary for translation to practical applications.

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

Efficient DNA mutation detection methods are required for diagnosis, personalized therapy development, and prognosis assessment for diseases such as cancer. To address this issue, we proposed a straightforward approach by combining active plasmonic nanostructures, surface-enhanced Raman spectroscopy (SERS), and polymerase chain reaction (PCR) with a statistical tool to identify and classify BRAF wild type (WT) and V600E mutant genes. The nanostructures provide enhanced sensitivity, while PCR offers high specificity toward target DNA. A series of positively charged plasmonic nanostructures including gold/silver nanospheres, nanoshells, nanoflowers, and nanostars were synthesized with a one-pot strategy and characterized. By changing the shape of nanostructures, we are able to vary the surface plasmon resonance from 551 to 693 nm. The gold/silver nanostar showed the highest SERS activity, which was employed for DNA mutation detection. We reproducibly analyzed as few as 100 copies of target DNA sequences using gold/silver nanostars, thus demonstrating the high sensitivity of the direct SERS detection. By means of statistical analysis (principal component analysis-linear discriminant analysis), this method was successfully applied to differentiate the WT and V600E mutant both from whole genome DNA lysed from cell line and from cell-free DNA collected from cell culture media. We further proved that this assay is capable of specifically amplifying and accurately classifying a real plasma sample. Thus, this direct SERS strategy combined with the active plasmonic nanostructures has the potential for wide applications as an alternative tool for sensitively monitoring and evaluating important clinical nucleotide biomarkers.

Cancer Diagnosis through SERS and Other Related Techniques

Cancer heterogeneity increasingly requires ultrasensitive techniques that allow early diagnosis for personalized treatment. In addition, they should preferably be non-invasive tools that do not damage surrounding tissues or contribute to body toxicity. In this context, liquid biopsy of biological samples such as urine, blood, or saliva represents an ideal approximation of what is happening in real time in the affected tissues. Plasmonic nanoparticles are emerging as an alternative or complement to current diagnostic techniques, being able to detect and quantify novel biomarkers such as specific peptides and proteins, microRNA, circulating tumor DNA and cells, and exosomes. Here, we review the latest ideas focusing on the use of plasmonic nanoparticles in coded and label-free surface-enhanced Raman scattering (SERS) spectroscopy. Moreover, surface plasmon resonance (SPR) spectroscopy, colorimetric assays, dynamic light scattering (DLS) spectroscopy, mass spectrometry or total internal reflection fluorescence (TIRF) microscopy among others are briefly examined in order to highlight the potential and versatility of plasmonics.

Quantum scale organic semiconductors for SERS detection of DNA methylation and gene expression

Cancer stem cells (CSC) can be identified by modifications in their genomic DNA. Here, we report a concept of precisely shrinking an organic semiconductor surface-enhanced Raman scattering (SERS) probe to quantum size, for investigating the epigenetic profile of CSC. The probe is used for tag-free genomic DNA detection, an approach towards the advancement of single-molecule DNA detection. The sensor detected structural, molecular and gene expression aberrations of genomic DNA in femtomolar concentration simultaneously in a single test. In addition to pointing out the divergences in genomic DNA of cancerous and non-cancerous cells, the quantum scale organic semiconductor was able to trace the expression of two genes which are frequently used as CSC markers. The quantum scale organic semiconductor holds the potential to be a new tool for label-free, ultra-sensitive multiplexed genomic analysis.

Raman Scattering: From Structural Biology to Medical Applications

This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.

Surface Enhanced Raman Spectroscopy for DNA Biosensors-How Far Are We?

A sensitive and accurate identification of specific DNA fragments (usually containing a mutation) can influence clinical decisions. Standard methods routinely used for this type of detection are PCR (Polymerase Chain Reaction, and its modifications), and, less commonly, NGS (Next Generation Sequencing). However, these methods are quite complicated, requiring time-consuming, multi-stage sample preparation, and specially trained staff. Usually, it takes weeks for patients to obtain their results. Therefore, different DNA sensors are being intensively developed by many groups. One technique often used to obtain an analytical signal from DNA sensors is Raman spectroscopy. Its modification, surface-enhanced Raman spectroscopy (SERS), is especially useful for practical analytical applications due to its extra low limit of detection. SERS takes advantage of the strong increase in the efficiency of Raman signal generation caused by a local electric field enhancement near plasmonic (typically gold and silver) nanostructures. In this condensed review, we describe the most important types of SERS-based nanosensors for genetic studies and comment on their potential for becoming diagnostic tools.

A review on recent advances in the applications of surface-enhanced Raman scattering in analytical chemistry

This review is focused on recent developments of surface-enhanced Raman scattering (SERS) applications in Analytical Chemistry. The work covers advances in the fabrication methods of SERS substrates, including nanoparticles immobilization techniques and advanced nanopatterning with metallic features. Recent insights in quantitative and sampling methods for SERS implementation and the development of new SERS-based approaches for both qualitative and quantitative analysis are discussed. The advent of methods for pre-concentration and new approaches for single-molecule SERS quantification, such as the digital SERS procedure, has provided additional improvements in the analytical figures-of-merit for analysis and assays based on SERS. The use of metal nanostructures as SERS detection elements integrated in devices, such as microfluidic systems and optical fibers, provided new tools for SERS applications that expand beyond the laboratory environment, bringing new opportunities for real-time field tests and process monitoring based on SERS. Finally, selected examples of SERS applications in analytical and bioanalytical chemistry are discussed. The breadth of this work reflects the vast diversity of subjects and approaches that are inherent to the SERS field. The state of the field indicates the potential for a variety of new SERS-based methods and technologies that can be routinely applied in analytical laboratories.

Multiplex SERS Chemosensing of Metal Ions via DNA-Mediated Recognition

The combination of molecular sensors and plasmonic materials is emerging as one of the most promising approaches for ultrasensitive SERS-based detection of metal ions in complex fluids. However, only a very small fraction of the large pool of potential chemosensors described in classical analytical chemistry has been successfully implemented into viable SERS platforms for metal ion determination. This is due to the molecular restrictions that require the chemosensor to adhere onto the plasmonic surface while retaining the capability to undergo large structural alterations upon metal ion binding. In this work, we demonstrate that the structural and functional plasticity of DNA for interacting with small aromatic molecules can be exploited to this end. DNA coating of silver nanoparticles modulates the interaction of the commercially available alizarin red S (ARS) chemosensor with the nanomaterial, translating its recognition capabilities from bulk solution onto the plasmonic surface, while simultaneously directing the particle assembling into highly efficient SERS clusters. The sensing approach was successfully applied to the multiplex, quantitative determination of Al(III) and Fe(III) in tap water in the subppb level.

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.