Label-Free Surface-Enhanced Raman Spectroscopy Detection of DNA with Single-Base Sensitivity

Confocal Raman Microscopy Enables Label-Free, Quantitative, and Structurally Informative Detection of DNA Hybridization at Porous Silica Surfaces

Characterization of DNA at solid/liquid interfaces remains a challenge because most surface-sensitive techniques are unable to provide quantitative insight into the base content, length, or structure. Surface-enhanced Raman scattering measurements of DNA hybridization on plasmonic-metal substrates have been used to overcome small Raman-scattering cross-sections; however, surface-enhanced Raman spectroscopy measurements are not generally quantitative due to the fall-off in the scattering signal with the decay of the electric field enhancement from the surface, which also limits the length of oligonucleotides that can be investigated. In this work, we introduce an experimental methodology in which confocal Raman microscopy is used to characterize hybridization reactions of ssDNA immobilized at the solid/liquid interface of porous silica particles. By focusing the femtoliter confocal probe volume within a single porous particle, signal enhancement arises from the ∼1500-times greater surface area detected compared to a planar substrate. Because the porous support is a purely dielectric material, the scattering signal is independent of the proximity of the oligonucleotide to the silica surface. With this technique, we characterize a 19-mer capture strand and determine its hybridization efficiency with 9-mer and 16-mer target sequences from the scattering of a structurally insensitive phosphate-stretching mode. Changes in polarizability and frequency of scattering from DNA bases were observed, which are consistent with Watson-Crick base pairing. Quantification of base content from their duplex scattering intensities allows us to discriminate between hybridization of two target strands of equivalent length but with different recognition sequences. A duplex having a single-nucleotide polymorphism could be distinguished from hybridization of a fully complementary strand based on differences in base content and duplex conformation.

Frequency Shift Surface-Enhanced Raman Spectroscopy Sensing: An Ultrasensitive Multiplex Assay for Biomarkers in Human Health

The sensitive and selective detection of biomarkers for human health remains one of the grand challenges of the analytical sciences. Compared to established methods (colorimetric, (chemi) luminescent), surface-enhanced Raman spectroscopy (SERS) is an emerging alternative with enormous potential for ultrasensitive biological detection. Indeed even attomolar (10^-18 M) detection limits are possible for SERS due to an orders-of-magnitude boosting of Raman signals at the surface of metallic nanostructures by surface plasmons. However, challenges remain for SERS assays of large biomolecules, as the largest enhancements require the biomarker to enter a "hot spot" nanogap between metal nanostructures. The frequency-shift SERS method has gained popularity in recent years as an alternative assay that overcomes this drawback. It measures frequency shifts in intense SERS peaks of a Raman reporter during binding events on biomolecules (protein coupling, DNA hybridization, etc.) driven by mechanical transduction, charge transfer, or local electric field effects. As such, it retains the excellent multiplexing capability of SERS, with multiple analytes being identifiable by a spectral fingerprint in a single read-out. Meanwhile, like refractive index surface plasmon resonance methods, frequency-shift SERS measures the shift of an intense signal rather than resolving a peak above noise, easing spectroscopic resolution requirements. SERS frequency-shift assays have proved particularly suitable for sensing large, highly charged biomolecules that alter hydrogen-bonding networks upon specific binding. Herein we discuss the frequency-shift SERS method and promising applications in (multiplex) biomarker sensing as well as extensions to ion and gas sensing and much more.

Metformin hydrochloride action on cell membrane N-cadherin expression and cell nucleus revealed by SERS nanoprobes

The anti-tumor effects of metformin hydrochloride (MH), an initial pharmacologic agent for type 2 diabetes, were reexamined by surface-enhanced Raman scattering (SERS) spectroscopy. A SERS immuno-tag fabricated by decorating silver nanoparticles (AgNPs) with a specific antibody was employed to trace the dynamic expression of the tumor metastasis-related N-cadherin. With the MH action, the N-cadherin expression on the cell membranes decreases, proving that MH has a pharmacological effect on prohibiting cancer cell metastasis. Another AgNP-based nucleus targeting nanoprobe was adopted to culture with the MH acted cells, which can help the label-free SERS collection of the cell nuclei to explore the MH influences on intranuclear genes and proteins. By analyzing the intranuclear SERS spectra, the find is that MH has impacts on the transcription and translation of genes, thus regulates the expression of tumor metastasis-related proteins (N-cadherins). This study presents a proof-of-concept for MH as a potential drug for diabetes patients associated with tumors. The developed plasmonic immune analytical platform can be extended to assess other substances of the cell membrane and applicable for the SERS-based screening of membrane receptor-related drugs at the cellular level.

Ultrasensitive Characterization of the Prion Protein by Surface-Enhanced Raman Scattering: Selective Enhancement via Electrostatic Tethering of the Intrinsically Disordered Domain with Functionalized Silver Nanoparticles

Surface-enhanced Raman scattering (SERS) circumvents the inherent insensitivity of Raman spectroscopy and offers a powerful tool for the ultrasensitive detection and characterization of biomolecules at low concentrations. Here we show that SERS via electrostatic tethering between surface-modified negatively charged silver nanoparticles and highly positively charged intrinsically disordered N-terminal domain of the prion protein allows highly sensitive and reproducible protein detection and characterization at as low as hundreds of nanomolar protein concentrations. These measurements preferentially illuminate a selective part of the protein due to a sharp dependence of the near-field intensity on the distance between the nanoparticle surface and the protein. We also demonstrate that by shortening the length of the disordered tail it is possible to achieve a domain-selective Raman enhancement to study the C-terminal globular domain. Our tether-length-dependent SERS methodology will serve as a potent, noninvasive, and label-free strategy to detect and characterize a wide range of proteins possessing disordered segments.

Response of HPRT Gene Fragment Functionalized Gold Nanoparticles to Gamma Ray Irradiation

Radiation-sensitive biomolecules are highly significant for studying biological effects of radiation and developing ionizing radiation detectors based on biomolecules. In this work, we selected hypoxanthine phosphoribosyl transferase gene fragments sensitive to gamma-ray irradiation as a sensing element for radiation detection. The end was modified with thiol groups. The thiol-modified oligonucleotide sequences were coupled to the surface of gold nanoparticles by Au-S covalent bonds. The DNA attached to the surface of gold nanoparticles forms a DNA-AuNPs assembly through base pairing. The assembly was irradiated by gamma rays. And its response to radiation was studied with ultraviolet-visible spectroscopy and surface-enhanced Raman scattering (SERS) spectroscopy techniques. SERS spectroscopy and ultraviolet spectroscopy can detect the response of the DNA-AuNPs assembly to gamma-ray irradiation below 100 and 100 - 250 Gy, respectively. The results indicated that it was feasible to develop a new approach of gamma-ray detectors using biomolecular assemblies of gold nanoparticles.

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.

DNA-Origami-Based Assembly of Au@Ag Nanostar Dimer Nanoantennas for Label-Free Sensing of Pyocyanin

Early-stage detection of diseases caused by pathogens is a prerequisite for expedient patient care. Due to the limited signal-to-noise ratio, molecular diagnostics needs molecular signal amplification after recognition of the target molecule. In this present study, we demonstrate the design of plasmonically coupled bimetallic Ag coated Au nanostar dimers with controlled nanogap using rectangular DNA origami. We further report the utility of the designed nanostar dimer structures as efficient SERS substrate for the ultrasensitive and label-free detection of the pyocyanin molecule, which is a biomarker of the opportunistic pathogenic bacteria, Pseudomonas aeruginosa. The experimental results showed that the detection limit of pyocyanin with such nanoantenna based biosensor was 335 pM, which is much lower than the clinical range of detection. Thus, fast, sensitive and label-free detection of pyocyanin at ultralow concentration in an infected human body can pave a facile route for early stage warning for severe bacterial infections.

DNA-assisted synthesis of Ortho-NanoDimer with sub-nanoscale controllable gap for SERS application

Nanostructure with precisely controllable narrow gap width remains a great challenge, especially at the sub-nanoscale level. Here, a versatile strategy named as DNA-assisted synthesis of ortho-nanodimer (DaSON) is proposed to fabricate Ag (Au) nanodimers with a uniform gap width from nanometers to angstroms. In such a strategy, two nanoparticles are constrained by the equilibrium state of the DNA hybridization and electrostatic repulsion to form zipper-like ortho-nanostructures with an extremely uniform gap whose width can be finely adjusted at nanoscale or sub-nanoscale by changing the DNA sequence and the surface charge of nanoparticles. The inherent strong electromagnetic coupling in the uniform sub-nanometer gap can generates an unparalleled SERS enhancement together with an extraordinary reproducibility. Compared with conventional DNA-based nano-gap fabrication strategy, the DaSON strategy enhances the SERS intensity for more than two orders of magnitude with a detection limit of 100 aM for DNA, and significantly improves the reproducibility in both labeled and label-free SERS sensing applications. Moreover, the DaSON strategy holds wide applicability for arbitrary kinds of DNA-modifiable nanoparticles. Therefore, we believe that the DaSON strategy provides an innovative method for the synthesis of nanostructures with controllable nanogaps and has a promising future in multiple fields including nanotechnology, catalysis and photonics.

Quantitative PCR based detection system for cyanobacterial geosmin/2-methylisoborneol (2-MIB) events in drinking water sources: Current status and challenges

Taste and odor (T&O) are an important issue in drinking water, aquaculture, recreation and a few other associated industries, and cyanobacteria-relevant geosmin and 2-methylisoborneol (2-MIB) are the two most commonly detected T&O compounds worldwide. A rise in the cyanobacterial blooms and associated geosmin/2-MIB episodes due to anthropogenic activities as well as climate change has led to global concerns for drinking water quality. The increasing awareness for the safe drinking, aquaculture or recreational water systems has boost the demand for rapid, robust, on-site early detection and monitoring system for cyanobacterial geosmin/2-MIB events. In past years, research has indicated quantitative PCR (qPCR) as one of the promising tools for detection of geosmin/2-MIB episodes. It offers advantages of detecting the source organism even at very low concentrations, distinction of odor-producing cyanobacterial strains from non-producers and evaluation of odor producing potential of the cyanobacteria at much faster rates compared to conventional techniques.The present review aims at examining the current status of developed qPCR primers and probes in identifying and detecting the cyanobacterial blooms along with geosmin/2-MIB events. Among the more than 100 articles about cyanobacteria associated geosmin/2-MIB in drinking water systems published after 1990, limited reports (approx. 10 each for geosmin and 2-MIB) focused on qPCR detection and its application in the field. Based on the review of literature, a comprehensive open access global cyanobacterial geosmin/2-MIB events database (CyanoGM Explorer) is curated. It acts as a single platform to access updated information related to origin and geographical distribution of geosmin/2-MIB events, cyanobacterial producers, frequency, and techniques associated with the monitoring of the events. Although a total of 132 cyanobacterial strains from 21 genera and 72 cyanobacterial strains from 13 genera have been reported for geosmin and 2-MIB production, respectively, only 58 geosmin and 28 2-MIB synthesis regions have been assembled in the NCBI database. Based on the identity, geosmin sequences were found to be more diverse in the geosmin synthase conserved/primer design region, compared to 2-MIB synthesis region, hindering the design of universal primers/probes. Emerging technologies such as the bioelectronic nose, Surface Enhanced Raman Scattering (SERS), and nanopore sequencing are discussed for future applications in early on-site detection of geosmin/2-MIB and producers. In the end, the paper also highlights various challenges in applying qPCR as a universal system of monitoring and development of response system for geosmin/2-MIB episodes.

Microfluidic synthesis of high-valence programmable atom-like nanoparticles for reliable sensing

Synthesis of programmable atom-like nanoparticles (PANs) with high valences and high yields remains a grand challenge. Here, a novel synthetic strategy of microfluidic galvanic displacement (μ-GD) coupled with microfluidic DNA nanoassembly is advanced for synthesis of single-stranded DNA encoder (SSE)-encoded PANs for reliable surface-enhanced Raman scattering (SERS) sensing. Notably, PANs with high valences (e.g., n-valence, n = 12) are synthesized with high yields (e.g., >80%) owing to the effective control of interfacial reactions sequentially occurring in the microfluidic system. On the basis of this, we present the first demonstration of a PAN-based automatic analytical platform, in which sensor construction, sample loading and on-line monitoring are carried out in the microfluidic system, thus guaranteeing reliable quantitative measurement. In the proof-of-concept demonstration, accurate determination of tetracycline (TET) in serum and milk samples with a high recovery close to 100% and a low relative standard deviation (RSD) less than 5.0% is achieved by using this integrated analytical platform.

A disposable paper-based hydrophobic substrate for highly sensitive surface-enhanced Raman scattering detection

Detection of target analytes with high sensitivity and reproducibility remains a challenge for surface-enhanced Raman scattering (SERS) due to the lack of cost-effective and highly sensitive substrates. In this study, a hydrophobic SERS substrate capable of concentrating nanoparticles and analytes was prepared by spin-coating lubricating liquid onto commercial paper. The condensation effect of the paper-based hydrophobic substrate induced aggregation of gold nanoparticles (Au NPs) to generate ''hot spots'' for SERS and to drive analytes to the hot-spot areas for more sensitive detection. The obtained SERS signal intensity was 5-fold higher than that obtained using common paper, and a detection limit (LOD) of 4.3 × 10^-10 M for rhodamine 6G (R6G) was achieved. Randomly selected points on the substrate and different batches of substrates all exhibited high reproducibility, and the relative standard deviation (RSD) at 1362 cm^-1 is approximately 11%. A further application of the hydrophobic substrate was demonstrated by the detection of cytochrome C within a linear detection range of 3.90 × 10^-8 M-1.25 × 10^-6 M. In addition, the prepared substrate can obtain identifiable SERS spectra of cancer cells and non-cancer cells because a large number of AuNP or Au NPs clusters can adhere to cells, resulting in the construction of a 3D hotspot matrix. The disposable hydrophobic paper substrate eliminates the problem of solution diffusion, and also provides an effective platform for biomolecular screening detection.

Proximity hybridization-triggered DNA assembly for label-free surface-enhanced Raman spectroscopic bioanalysis

We have developed a versatile label-free surface-enhanced Raman spectroscopic platform for detecting various biotargets via proximity hybridization-triggered DNA assembly based on the 736 cm^-1 Raman peak of adenine breathing mode. We initially immobilized the first probe to AuNPs and modified the second with poly adenine. Presence of target DNA or protein molecules assembled a sandwich complex that brought the poly adenine close to the AuNPs surface, generating Raman signals, that were proportional to target molecule concentration. These approach exhibits high sensitivity, with a detection limit of 5.4 pM, 47 fM, and 0.51 pg/mL for target DNA, thrombin and CEA, respectively. Owing to a one step proximity dependent complex formation, this technique is simple and can be completed within 40 min, making it a promising candidate for point-of-care testing applications.

Multifunctional Flexible SERS Sensor on a Fixate Gel Pad: Capturing, Derivation, and Selective Picogram Indirect Detection of Explosive 2,2',4,4',6,6'-Hexanitrostilbene

2,2',4,4',6,6'-Hexanitrostilbene (HNS) is an explosive with better explosion performance than the well-known 2,4,6-trinitrotoluene (TNT). Surprisingly, unlike other nitroaromatic explosives, there are limited reports regarding the detection of the HNS, let alone sensing reports on surface residues. In this work, a multifunctional flexible SERS sensor was proposed for the indirect detection of HNS based on the transparent fixate gel pads. The sticky and flexible gel pad can effectively collect any HNS surface residues. The inherent amine groups within the gel pad of which the main ingredient is polyurethane can react with HNS to form the orange Meisenheimer-alike complex. The modification of Ag NPs with halide ions was screened for the best SERS performance. KI-modified-citrate-reduced Ag NPs showed selective but enormous SERS enhancement for the HNS derivative. The detection of HNS in the solution phase was explored, and a linear range of 0.01-25 ppm was achieved. The lowest detectable amount (LDA) of HNS was found to be 50 pg, making it one of the most sensitive methods in literature. It was successfully utilized for the HNS residues sensing on fingerprints and bags with LDAs of 5 and 200 ng, respectively. In addition, other explosives including TATB, LLM-105, RDX, HMX, FOX-7, and TNT were also examined to assess the selectivity of the fixate. It was found that the fixate showed excellent selectivity for HNS.

Acceleration of Biomolecule Enrichment and Detection with Rotationally Motorized Opto-Plasmonic Microsensors and the Working Mechanism

Vigorous research efforts have advanced the state-of-the-art nanosensors with ultrahigh sensitivity for bioanalysis. However, a dilemmatic challenge remains: it is extremely difficult to obtain nanosensors that are both sensitive and high-speed for the detection of low-concentration molecules in aqueous samples. Herein, we report how the controlled mechanical rotation (or rotary motorization) of designed opto-plasmonic microsensors can substantially and robustly accelerate the enrichment and detection speed of deoxyribonucleic acid (DNA) with retained high sensitivity. At least 4-fold augmentation of the capture speed of DNA molecules is obtained from a microsensor rotating at 1200 rpm. Theoretical analysis and modeling shed light on the underlying working mechanism, governed by the molecule-motor-flow interaction as well as its application range and limitation. This work provides a device scheme that alleviates the dilemmatic challenge in biomolecule sensing and offers the understanding of the complex interactions of molecules and moving microobjects in suspension. The results may assist the rational design of efficient microrobotic systems for the capture, translocation, sensing, and release of biocargoes.

Dual platform based sandwich assay surface-enhanced Raman scattering DNA biosensor for the sensitive detection of food adulteration

Surface enhanced Raman scattering (SERS) DNA biosensing is an ultrasensitive, selective, and rapid detection technique with the ability to produce molecule-specific distinct fingerprint spectra. It supersedes the long amplicon based PCR assays, the fluorescence and spectroscopic techniques with their quenching and narrow spectral bandwidth, and the electrochemical detection techniques using multiplexing. However, the performance of the SERS DNA biosensor relies on the DNA probe length, platform composition, both the presence and position of Raman tags and the chosen sensing strategy. In this context, we herein report a SERS biosensor based on dual nanoplatforms with a uniquely designed Raman tag (ATTO Rho6G) intercalated short-length DNA probe for the sensitive detection of the pig species Sus scrofa. In the design of the signal probe (SP), a Raman tag was incorporated adjacent to the spacer arm, followed by a terminal thiol modifier, which consequently had a strong influence on the SERS signal enhancement. The detection strategy involves the probe-target DNA hybridization mediated coupling of the two platforms, i.e., the graphene oxide-gold nanorod (GO-AuNR) functionalized capture probe (CP) and SP-conjugated gold nanoparticles (AuNPs), consequently enhancing the SERS intensity by both the electromagnetic hot spots generated at the junctions or interstices of the two platforms and the chemical enhancement between the AuNPs and the adsorbed intercalated Raman tag. This dual platform based SERS DNA biosensor exhibited outstanding sensitivity in detecting pork DNA with a limit of detection (LOD) of 100 aM validated with DNA extracted from a pork sample (LOD 1 fM). Moreover, the fabricated SERS biosensor showed outstanding selectivity and specificity for differentiating the DNA sequences of six closely related non-target species from the target DNA sequences with single and three nucleotide base-mismatches. Therefore, the developed short-length DNA linked dual platform based SERS biosensor could replace the less sensitive traditional methods of pork DNA detection and be adopted as a universal detection approach for the qualitative and quantitative detection of DNA from any source.

Extracellular Vesicle Identification Using Label-Free Surface-Enhanced Raman Spectroscopy: Detection and Signal Analysis Strategies

Extracellular vesicles (EVs) have been widely investigated as promising biomarkers for the liquid biopsy of diseases, owing to their countless roles in biological systems. Furthermore, with the notable progress of exosome research, the use of label-free surface-enhanced Raman spectroscopy (SERS) to identify and distinguish disease-related EVs has emerged. Even in the absence of specific markers for disease-related EVs, label-free SERS enables the identification of unique patterns of disease-related EVs through their molecular fingerprints. In this review, we describe label-free SERS approaches for disease-related EV pattern identification in terms of substrate design and signal analysis strategies. We first describe the general characteristics of EVs and their SERS signals. We then present recent works on applied plasmonic nanostructures to sensitively detect EVs and notable methods to interpret complex spectral data. This review also discusses current challenges and future prospects of label-free SERS-based disease-related EV pattern identification.

Ultrasensitive SERS detection of antitumor drug methotrexate based on modified Ag substrate

Methotrexate (MTX) is a drug with broad-spectrum antitumor activity that is of great importance in therapeutic drug monitoring applications. In this essay, the two-step modified concentrated Ag colloid with the assistance of KF and MgSO₄ was used as the SERS active substrate for the ultrasensitive detection of MTX and its commercial formulations (tablets). It can be found that the two-step modification of the samples is a crucial procedure to remove the by-products in the synthesis of Ag colloid and further concentrate the Ag colloid. Under the optimal detection conditions, the minimum detection concentration of MTX is 1 × 10^-16 mol/L. And, there is a good linear relationship over a wide concentration range of 1 × 10^-16-1 × 10^-6 mol/L. The labelled amounts of the two manufacturers of MTX commercial tablets are in the range of 96.4-104.3% with the RSDs between 1.8% and 3.5% by this method, which are in accordance with the methodological requirements. These results prove that the proposed SERS method exhibits a good reproducibility and ultra-high sensitivity for the detection of the antitumor drug MTX.

Detection of Buried Explosives Using a Surface-Enhanced Raman Scattering (SERS) Substrate Tailored for Miniaturized Spectrometers

The advent of miniaturized, fiber-based, Raman spectrometers provides a clear path for the wide implementation of surface-enhanced Raman scattering (SERS) in analytical chemistry. For instance, miniaturized systems are especially useful in field applications due to their simplicity and low cost. However, traditional SERS substrates are generally developed and optimized using expensive Raman microscope systems equipped with high numerical aperture (NA) objective lenses. Here, we introduced a new type of SERS substrate with intrinsic Raman photon directing capability that compensates the relatively low signal collection power of fiber-based Raman spectrometers. The substrate was tested for the detection of buried 2,4-dinitrotoluene in simulated field conditions. A linear calibration curve (R² = 0.98) for 2,4-dinitrotoluene spanning 3 orders of magnitude (from μg kg^-1 to mg kg^-1) was obtained with a limit of detection of 10 μg kg^-1 within a total volume of 10 μL. This detection level is 2 orders of magnitude lower than that possible with the current state-of-the-art technologies, such as ion mobility spectrometry-mass spectrometry. The approach reported here demonstrated a high-performance detection of 2,4-dinitrotoluene in field conditions by a SERS platform optimized for miniaturized Raman systems that can be deployed for a routine inspection of landmine-contaminated sites and homeland security applications.

Machine learning for composition analysis of ssDNA using chemical enhancement in SERS

Surface-enhanced Raman spectroscopy (SERS) is an attractive method for bio-chemical sensing due to its potential for single molecule sensitivity and the prospect of DNA composition analysis. In this manuscript we leverage metal specific chemical enhancement effect to detect differences in SERS spectra of 200-base length single-stranded DNA (ssDNA) molecules adsorbed on gold or silver nanorod substrates, and then develop and train a linear regression as well as neural network models to predict the composition of ssDNA. Our results indicate that employing substrates of different metals that host a given adsorbed molecule leads to distinct SERS spectra, allowing to probe metal-molecule interactions under distinct chemical enhancement regimes. Leveraging this difference and combining spectra from different metals as an input for PCA (Principal Component Analysis) and NN (Neural Network) models, allows to significantly lower the detection errors compared to manual feature-choosing analysis as well as compared to the case where data from single metal is used. Furthermore, we show that NN model provides superior performance in the presence of complex noise and data dispersion factors that affect SERS signals collected from metal substrates fabricated on different days.

Equipment-free and visualized biosensor for transcription factor rapid assay based on dopamine-functionalized cellulose paper

A cellulose paper-based biosensor was developed for the equipment-free and naked-eye detection of a transcription factor (TF) using dopamine as the signal-responsive material based on exonuclease III-assisted cycling amplification. Compared with other TF biosensors, the proposed biosensor demonstrates low-cost, portable, disposable, and naked-eye detection features.

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.

Reliable Quantification of pH Variation in Live Cells Using Prussian Blue-Caged Surface-Enhanced Raman Scattering Probes

Intracellular pH is an important parameter that is highly associated with diverse physiological processes. The reliable measurement of pH values inside cells remains a formidable challenge because of the complexity of cytoplasm. Herein, we report a robust Prussian blue (PB)-caged pH-responsive surface-enhanced Raman scattering (SERS) probe for precisely mapping the dynamic pH values in live cells. The PB shell has a subnanoscale porous structure that allows only very small biospecies such as H⁺ or OH^- to pass freely through the shell and react with the encased pH-responsive SERS probe, while physically resisting the entry of large biomolecules. This probe achieved unmatched detection linearity (R² > 0.999) for pH measurements in diverse complex biological samples. Moreover, the nitrile (C≡N) in PB shows a sharp band in the cellular Raman-silent region, which serves as a background-free internal standard for accurate profiling of the probe distribution inside the cells. We applied the proposed probe to monitor the dynamic pH changes during cellular autophagy induced by different stimuli and thereby demonstrated that the PB-caged probe can reliably quantify subtle intracellular pH variations, providing an effective tool for revealing the relationship between abnormal intracellular pH and cellular functions.

Plasmonics meets super-resolution microscopy in biology

Super-resolution microscopy can reveal the subtle biological processes hidden behind the optical diffraction barrier. Plasmonics is a key nanophotonic that combines electronics and photonics through the interaction of light with the metallic nanostructure. In this review, we survey the recent progresses on plasmonic-assisted super-resolution microscopy. The strong electromagnetic field enhancement trapped near metallic nanostructures offers a unique opportunity to manipulate the illumination scheme for overcoming the diffraction limit. Plasmonic nanoprobes, exploited as surface-enhanced Raman scattering (SERS) and plasmon-enhanced fluorescence nanoparticles, are a major category of contrast agent in super-resolution microscopy. The outstanding challenges, future developments, and potential biological applications are also discussed.

Profiling DNA mutation patterns by SERS fingerprinting for supervised cancer classification

Profiling DNA mutation patterns for cancer classification plays an essential role in precision and personalized medicine. Conventional PCR-based mutation assay is limited by the extensive labour on target amplification. We herein create an amplification-free surface enhanced Raman spectroscopy (SERS) biochip which enables direct and simultaneous identification of multiple point mutations in tumor cells. Without pre-amplifying the target sequences, the SERS assay reads out the presence of cellular mutations through the interpretation of Raman fingerprints. The SERS sensor is integrated into a microfluidic chip, achieving one-step multiplex analysis within 40 min. Importantly, by combining SERS spectra encoding technique with supervised learning algorithm, a panel of nucleotide mixtures can be well distinguished according to their mutation profiles. We initially demonstrate an excellent levels of classification in samples from colorectal cancer and melanoma cell lines. For final clinical validation, the system performance is verified by classifying cancer patient samples, which shows an accuracy above 90%. Due to the simplicity and rapidness, the SERS biosensor is expected to become a promising tool for clinical point-of-care diagnosis towards precision medicine.

Elucidation of leak-resistance DNA hybridization chain reaction with universality and extensibility

Hybridization chain reaction (HCR) was a significant discovery for the development of nanoscale materials and devices. One key challenge for HCR is the vulnerability to background leakage in the absence of the initiator. Here, we systematically analyze the sources of leakage and refine leak-resistant rule by using molecular thermodynamics and dynamics, biochemical and biophysical methods. Transient melting of DNA hairpin is revealed to be the underlying cause of leakage and that this can be mitigated through careful consideration of the sequence thermodynamics. The transition threshold of the energy barrier is proposed as a testing benchmark of leak-resistance DNA hairpins. The universal design of DNA hairpins is illustrated by the analysis of hsa-miR-21-5p as biomarker when used in conjunction with surface-enhanced Raman spectroscopy. We further extend the strategy for specific signal amplification of miRNA homologs. Significantly, it possibly provides a practical route to improve the accuracy of DNA self-assembly for signal amplification, and that could facilitate the development of sensors for the sensitive detection of interest molecules in biotechnology and clinical medicine.

Identifying conformational changes of aptamer binding to theophylline: A combined biolayer interferometry, surface-enhanced Raman spectroscopy, and molecular dynamics study

Theophylline is a potent bronchodilator for the treatment of asthma, bronchitis, and emphysema. Its narrow therapeutic window (20-100 μM) demands that the blood concentration of theophylline be monitored carefully, which can be achieved by aptamer capture. Thus, an understanding of what occurs when aptamers bind to theophylline is critical for identifying a high-affinity and high-specificity aptamer, which improve the sensitivity and selectivity of theophylline detection. Consequently, there is an urgent need to develop a simple, convenient, and nondestructive method to monitor conformational changes during the binding process. Here, we report the determination of the affinity of a selected aptamer and theophylline via biolayer interferometry (BLI) experiments. Additionally, using surface-enhanced Raman spectroscopy (SERS), the conformational changes on theophylline-aptamer binding were identified from differences in the SER spectra. Finally, molecular dynamics (MD) simulations were used to identify the specific conformational changes of the aptamer during the binding process. Such a combined BLI-SERS-MD method provides an in-depth understanding of the theophylline-aptamer binding processes and a comprehensive explanation for conformational changes, which helps to select, design, and modify an aptamer with high affinity and specificity. It can also be used as a scheme for the study of other aptamer-ligand interactions, which can be applied to the detection, sensing, clinical diagnosis, and treatment of diseases.

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.

Phosphorylation-Dependent SERS Readout for Activity Assay of Protein Kinase A in Cell Extracts

Protein kinases are key regulators of cell function, the abnormal activity of which may induce several human diseases, including cancers. Therefore, it is of great significance to develop a sensitive and reliable method for assaying protein kinase activities in real biological samples. Here, we report the phosphorylation-dependent surface-enhanced Raman scattering (SERS) readout of spermine-functionalized silver nanoparticles (AgNPs) for protein kinase A (PKA) activity assay in cell extracts. In this assay, the presence of PKA would phosphorylate and alter the net charge states of Raman dye-labeled substrate peptides, and the resulting anionic products could absorb onto the AgNPs with cationic surface charge through electrostatic attraction. Meanwhile, the Raman signals of dyes labeled on peptides were strongly enhanced by the aggregated AgNPs with interparticle hot spots formed in assay buffer. The SERS readout was directly proportional to the PKA activity in a wide range of 0.0001-0.5 U·μL^-1 with a detection limit as low as 0.00003 U·μL^-1. Moreover, the proposed SERS-based assay for the PKA activity was successfully applied to monitoring the activity and inhibition of PKA in real biological samples, particularly in cell extracts, which would be beneficial for kinase-related disease diagnostics and inhibitor screening.

A Self-Calibrating Surface-Enhanced Raman Scattering-Active System for Bacterial Phenotype Detection

Pathogen detection is of significant importance in human health and safety due to the high morbidity and mortality induced by bacterial infections. Therefore, the development of rapid, sensitive, and selective methods for the discrimination of pathogens is the key to improve the patient survival rates. In this work, we develop a new self-calibrating surface-enhanced Raman scattering (SERS)-based sensor that enables sensitive and reproducible pathogen detection in practical samples. The assay makes use of gold nanoflowers (AuNFs) consisting of three components: a solid Au core of ∼15 nm, a hollow gap of ∼1 nm, and a flower-like Au shell. We have demonstrated that the sensitive and quantitative analysis of biomolecules can be achieved by the target-dependent, sequence-specific DNA hybridization assembly between AuNFs with a built-in internal standard. We further demonstrate that this kind of reliable SERS sensor is able to distinguish different bacteria with sensitivity down to single bacterium. We expect that the established quantitative SERS technique could provide a promising tool for widespread applications in biomedical research and clinical diagnostics.

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.

DNA Nanofirecrackers Assembled through Hybridization Chain Reaction for Ultrasensitive SERS Immunoassay of Prostate Specific Antigen

Isothermal nucleic acid amplification technology has been widely adopted for analytical chemistry with the purpose of sensitivity improvement. Herein we present an ultrasensitive concatenated hybridization chain reaction (C-HCR) based surface-enhanced Raman scattering (SERS) immunoassay by forming antibody-antigen-aptamer heterosandwich structures with the model analyte of total prostate specific antigens (tPSA). In the C-HCR, two HCRs, one proceeds with two hairpins and the other with four biotin-modified hairpins, are coupled, making the formation of DNA nanofirecrackers with the lengths longer than 200 nm and more than four hundred million binding sites of streptavidin modified enzymes. These types of DNA nanofirecrackers through the aptamer encoded linker strand to form heterosandwich structures could provide a general signal application platform such as enzyme catalysis with high amplification efficiency. As a proof of concept, the Au@Ag core-shell nanostructure based SERS immunoassay with excellent signal amplification has been developed by employing the streptavidin modified alkaline phosphatase (SA-ALP) through its catalysis of 2-phospho-l-ascorbic acid trisodium salt (AAP) to form Au@Ag core-shell nanostructures via the formation of ascorbic acid (AA) to reduce AgNO₃ and deposition of silver element on gold nanorods (AuNRs). The newly developed method has a detection limit as low as 0.94 fg/mL and has successfully achieved the detection of serum samples from clinical patients, which was consistent with the clinical test results, showing that this C-HCR strategy to form DNA nanofirecrackers has great potential in clinical applications.

Key Role of Direct Adsorption on SERS Sensitivity: Synergistic Effect among Target, Aggregating Agent, and Surface with Au or Ag Colloid as Surface-Enhanced Raman Spectroscopy Substrate

It is widely accepted that the sensitivity of surface-enhanced Raman spectroscopy (SERS) is mainly manipulated by the electromagnetic enhancement mechanism (EM). Herein, we determined that the direct adsorption of the target on the SERS active surface is vital as well, through the systematic investigation of the SERS behavior of three positively charged molecules on negatively charged gold (Au) or silver nanoparticles (Ag NPs). Facilitated by the synergistic effect among the molecule, the surface, and the specific adsorbed halide ions (Cl^-, Br^-, and I^-), high SERS sensitivity for trace target was realized, which was mainly from the directly adsorbed molecules. Noteworthy, little contribution from the nondirectly adsorbed molecules was discernible, although the EM enhancement was at the same level for these two surface species dwelling within a distance significantly less than 1 nm from the surface. Further, the related strategy for trace detection sheds light on how to realize sensitive SERS detection of new targets.

DNA-Driven Nanoparticle Assemblies for Biosensing and Bioimaging

DNA molecules with superior flexibility, affinity and programmability have garnered considerable attention for the controllable assembly of nanoparticles (NPs). By controlling the density, length and sequences of DNA on NPs, the configuration of NP assemblies can be rationally designed. The specific recognition of DNA enables changes to be made to the spatial structures of NP assemblies, resulting in differences in tailorable optical signals. Comprehensive information on the fabrication of DNA-driven NP assemblies would be beneficial for their application in biosensing and bioimaging. This review analyzes the progress of DNA-driven NP assemblies, and discusses the tunable configurations determined by the structural parameters of DNA skeletons. The collective optical properties, such as chirality, fluorescence and surface enhanced Raman resonance (SERS), etc., of DNA-driven NP assemblies are explored, and engineered tailorable optical properties of these spatial structures are achieved. We discuss the development of DNA-directed NP assemblies for the quantification of DNA, toxins, and heavy metal ions, and demonstrate their potential application in the biosensing and bioimaging of tumor markers, RNA, living metal ions and phototherapeutics. We hihghlight possible challenges in the development of DNA-driven NP assemblies, and further direct potential prospects in the practical applications of macroscopical materials and photonic devices.

Beehive-Inspired Macroporous SERS Probe for Cancer Detection through Capturing and Analyzing Exosomes in Plasma

The protein phosphorylation status of exosomes can regulate the activity and function of proteins related to cancer development, and it is highly possible to diagnose cancers through analyzing the protein phosphorylation status. However, monitoring the protein phosphorylation status with a simple and label-free method is still clinically challenging. Here, inspired by beehives, we developed an Au-coated TiO₂ macroporous inverse opal (MIO) structure with an engineered "slow light effect" and thus with outstanding surface-enhanced Raman scattering (SERS) performance. The MIO structure can capture and analyze the exosomes from plasma of cancer patients without any labeling processes. It was found that the SERS intensity of exosomes at 1087 cm^-1 arising from the P-O bond within the phosphoproteins can be used as a criterion for tumor liquid biopsies. The intensity of the 1087 cm^-1 SERS peak from exosomes extracted from the plasma of cancer patients (prostate, lung, liver, and colon) is at least two times of that from healthy people. This indicates the simplicity and versatility of this method in cancer diagnostics. Our method has obvious advantages (noninvasive and time-saving) over currently clinically used tumor liquid biopsy techniques (such as western blot), which has great potentials to make vitro cancer diagnostics/monitoring as simple as diagnostics/monitoring of common diseases.

Polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) method for gene methylation level detection in plasma

Gene promoter hypermethylation is a vital step in tumorigenesis. This paper set out to explore the use of polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) for the detection of gene methylation levels, with a focus on cancer diagnosis. Methods: PCR with methylation independent primers were used on DNA samples to amplify target genes regardless of their methylation states. SERS was used on the obtained PCR products to generate spectra that contained peak changes belonging to CG and AT base pairs. Multiple linear regression (MLR) was then used to deconvolute the SERS spectra so that the CG/AT ratios of the sample could be obtained. These MLR results were used to calculate methylation levels of the target genes. For protocol verification, three sets of seven reference DNA solutions with known methylation levels (0%, 1%, 5%, 25%, 50%, 75%, and 100%) were analysed. Clinically, blood plasma samples were taken from 48 non-small-cell lung cancer (NSCLC) patients and 51 healthy controls. The methylation levels of the genes p16, MGMT, and RASSF1 were determined for each patient using this method. Results: Verification experiment on the mixtures with known methylation levels resulted in an error of less than 6% from the actual levels. When applied to our clinical samples, the frequency of methylation in at least one of the three target genes among the NSCLC patients was 87.5%, but this percentage decreased to 11.8% for the control group. The methylation levels of p16 were found to be significantly higher in NSCLC patients with more pack-years smoked (p=0.04), later cancer stages (p=0.03), and cancer types of squamous cell and large cell versus adenocarcinoma (p=0.03). Prediction accuracy of 88% was achieved from classification and regression trees (CART) based on methylation levels and states, respectively. Conclusion: This research showed that the PCR-SERS protocol could quantitatively measure the methylation levels of genes in plasma. The methylation levels of the genes p16, MGMT, and RASSF1 were higher in NSCLC patients than in controls.

SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.

Semen analysis and sperm characteristics of Karan Fries cattle

Karan Fries is an Indian composite breed of cattle with superior milk production with a greater disease resistance than many other cattle. Understanding of the basic sperm and semen characteristics is necessary to develop the artificial insemination and sperm sexing methods. This study was conducted to evaluate the morphological, rheological and biochemical characteristics of Karan Fries (Indian composite breed) bull semen. Semen analysis was conducted using Computer Assisted Sperm Analysis (CASA) and rheological methods. Results from correlation assessments indicated there was a positive correlation among values for sperm velocity variables. Motility of bull sperm movements in a linear path were the important variables evaluated in this study. There was also characterization of the individual spermatozoa using scanning electron microscopy (SEM) and Raman spectroscopy. The sperm head length and width were 8.8 ± 0.8 and 3.9 ± 0.6 μm, respectively, and the approximate flagellum length was 59.4 ± 4.5 μm. There was a difference in the Raman intensity among the individual spermatozoa. Results of this study could be important in designing and developing methods of artificial insemination, cryopreservation of semen and semen sexing.