Direct detection of DNA using 3D surface enhanced Raman scattering hotspot matrix

Silver nanoparticles (AgNPs) are evaporatively self‐assembled into the 3D surface enhanced Raman scattering (SERS) hotspot matrix with the assistant of glycerol to improve the spectral reproducibility in direct DNA detection. AgNPs and DNA in the glycerol‐stabilized 3D SERS hotspot matrix are found to form flexible sandwich structures through electrostatic interaction where neighboring AgNPs create uniform and homogeneous localized surface plasmon resonance coupling environments for central DNA. Nearly two orders of magnitude extra SERS enhancement, more stable peak frequency and narrower peak full width at half maximum can therefore be obtained in DNA SERS spectra, which ensures highly stable and reproducible SERS signals in direct detection of both single strand DNA and double strand DNA utilizing the 3D SERS hotspot matrix. By normalizing the SERS spectra using phosphate backbone as internal standard, identification of single base variation in oligonucleotides, determination of DNA hybridization events and recognition of chemical modification on bases (hexanethiol‐capped at 5’ end) have been demonstrated experimentally. This proposed 3D SERS hotspot matrix opens a novel perspective in manipulating plasmonic nanoparticles to construct SERS platforms and would make the surface enhanced Raman spectroscopy a more practical and reliable tool in direct DNA detection.     

静电纺纳米复合纤维柔性表面增强拉曼散射传感基底的研究进展

表面增强拉曼散射(Surface enhanced Raman scattering,SERS)是一种分子检测光谱技术,借助SERS基底,可对生物、化学等复杂体系中的痕量分子进行分析。 其中静电纺纳米纤维SERS基底由于具有高比表面积、可透气透水、柔韧可折叠弯曲等特点,在复杂体系中提取、过滤、浓缩痕量分子等应用场景中,其表面结构具有其他刚性SERS基底不可比拟的优势。然而,静电纺纳米纤维SERS基底的发展却受到制备方法的限制,存在检测灵敏度较低、制备过程复杂等问题。 因此,目前的研究工作主要集中在新型制备方法及工艺的开发。 本文综述了静电纺纳米金银复合纤维SERS基底的几种常用制备方法,包括直接混合纺丝法、化学吸附法、静电吸附法、物理沉积法和原位化学还原法,并总结了静电纺纳米纤维SERS基底在复杂体系中提取、过滤、浓缩待测分子的应用,最后对静电纺纳米复合纤维SERS基底的发展进行了展望。     

Rolling‐Circle Amplification Detection of Thrombin Using Surface‐Enhanced Raman Spectroscopy with Core‐Shell Nanoparticle Probe

An ultrasensitive surface‐enhanced Raman spectroscopy (SERS) sensor based on rolling‐circle amplification (RCA)‐increased “hot‐spot” was developed for the detection of thrombin. The sensor contains a SERS gold nanoparticle@Raman label@SiO₂ core‐shell nanoparticle probe in which the Raman reporter molecules are sandwiched between a gold nanoparticle core and a thin silica shell by a layer‐by‐layer method. Thrombin aptamer sequences were immobilized onto the magnetic beads (MBs) through hybridization with their complementary strand. In the presence of thrombin, the aptamer sequence was released; this allowed the remaining single‐stranded DNA (ssDNA) to act as primer and initiate in situ RCA reaction to produce long ssDNAs. Then, a large number of SERS probes were attached on the long ssDNA templates, causing thousands of SERS probes to be involved in each biomolecular recognition event. This SERS method achieved the detection of thrombin in the range from 1.0×10^?12 to 1.0×10^?8 M and a detection limit of 4.2×10^?13 M , and showed good performance in real serum samples.     

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

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

Surface enhanced Raman scattering for multiplexed detection

The multiplexed detection of biological analytes from complex mixtures is of crucial importance for the future of intelligent management and detection of disease. This review focuses on recent advances in the use of surface enhanced Raman scattering (SERS) spectroscopy as an analytical technique that can deliver multiplexed detection for a variety of biological target in increasingly complex media. The use of SERS has developed from the multipelxed detection of custom dye molecules to biomolecules such as DNA and proteins. Recent work has also shown the capability of SERS multiplexing for in vivo as well as in vitro applications.     

Fast and sensitive DNA analysis using changes in the FRET signals of molecular beacons in a PDMS microfluidic channel

A new DNA hybridization analytical method using a microfluidic channel and a molecular beacon-based probe (MB-probe) is described. A stem-loop DNA oligonucleotide labeled with two fluorophores at the 5′ and 3′ termini (a donor dye, TET, and an acceptor dye, TAMRA, respectively) was used to carry out a fast and sensitive DNA analysis. The MB-probe utilized the specificity and selectivity of the DNA hairpin-type probe DNA to detect a specific target DNA of interest. The quenching of the fluorescence resonance energy transfer (FRET) signal between the two fluorophores, caused by the sequence-specific hybridization of the MB-probe and the target DNA, was used to detect a DNA hybridization reaction in a poly(dimethylsiloxane) (PDMS) microfluidic channel. The azoospermia gene, DYS 209, was used as the target DNA to demonstrate the applicability of the method. A simple syringe pumping system was used for quick and accurate analysis. The laminar flow along the channel could be easily controlled by the 3-D channel structure and flow speed. By injecting the MB-probe and target DNA solutions into a zigzag-shaped PDMS microfluidic channel, it was possible to detect their sequence-specific hybridization. Surface-enhanced Raman spectroscopy (SERS) was also used to provide complementary evidence of the DNA hybridization. Our data show that this technique is a promising real-time detection method for label-free DNA targets in the solution phase. Figure FRET-based DNA hybridization detection using a molecular beacon in a zigzag-shaped PDMS microfluidic channel     

Inverse-flow derivatization for capillary electrophoresis of DNA fragments with laser-induced fluorescence detection

A novel method is presented to detect DNA fragments separated by capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection using inverse-flow derivatization. In electrophoresis, the intercalating dye, thiazol orange was only added to the separation buffer at the positive polarity. The negatively charged DNA fragments migrated from the negative polarity to the positive polarity, while the positively charged dye migrated in the opposite direction. When DNA fragments met with dye ions, the DNA–dye complexes were formed. The complexes continued migrating to the positive end, due to their net negative charges. When the complexes passed through the detection window, the fluorescent signals were generated. Importantly, DNA fragments migrated as their native state before DNA–dye complexes were formed. This procedure was used to detect double stranded DNA (dsDNA) and single stranded DNA (ssDNA) fragments, and polymerase chain reaction (PCR) products. The excellent resolution and good reproducibility of DNA fragments were achieved in non-gel sieving medium. This procedure may be useful in genetic mutation/polymorphism detections.     

表面增强拉曼光谱研究小檗碱与DNA的相互作用

用表面增强拉曼光谱研究了小檗碱（BER）与小牛胸腺DNA（ct DNA)的相互作用,并对重要谱峰进行了归属。在Ag胶体系中,小檗碱分子的拉曼信号增强显著,表明小檗碱阳离子键合到银胶粒子的表面。加入ct NA之后,小檗碱分子的大部分SERS带的强度进一步增加,而仅有少数几个带的信号强度趋于消失,可能是小檗碱分子的异喹啉部分键合到DNA的小沟槽,小檗碱与DNA的相互作用模式主要是通过静电力及疏水相互作用,吸收光谱表明,Ag胶体系的存在并未改变小檗碱分子与DNA的相互作用模式。     

Folding and unfolding kinetics of DNA hairpins in flowing solution by multiparameter fluorescence correlation spectroscopy

Dynamic equilibrium between the folded and unfolded conformations of single stranded DNA hairpin molecules containing polythymine hairpin loops was investigated using simultaneous two-beam fluorescence cross-correlation spectroscopy and single beam autocorrelation spectroscopy. The hairpins were end-labeled with a fluorescent dye and a quencher, such that folding and unfolding of the DNA hairpin primary structure caused the dye fluorescence to fluctuate on the same characteristic time scale as the folding and unfolding reaction. These fluctuations were observed as the molecules flowed sequentially between two spatially offset, microscopic detection volumes. Cross-correlation analysis of fluorescence from the two detection volumes revealed the translational diffusion and flow properties of the hairpins, as well as the average molecular occupancy of the two volumes. Autocorrelation analysis of the fluorescence from the individual detection volumes revealed the kinetics of hairpin folding and unfolding, with the parameters relating to diffusion, flow, and molecular occupancy constrained to the values determined from the cross-correlation analysis. This allowed unambiguous characterization of the folding and unfolding kinetics, without the need to determine the hydrodynamic properties by analyzing a separate control sample. The analysis revealed nonexponential relaxation kinetics and DNA size-dependent folding times characteristic of dynamic heterogeneity in the DNA hairpin-forming mechanism.     

Silver Coated Platinum Core–Shell Nanostructures on Etched Si Nanowires: Atomic Layer Deposition (ALD) Processing and Application in SERS

A new method to prepare plasmonically active noble metal nanostructures on large surface area silicon nanowires (SiNWs) mediated by atomic layer deposition (ALD) technology has successfully been demonstrated for applications of surface‐enhanced Raman spectroscopy (SERS)‐based sensing. As host material for the plasmonically active nanostructures we use dense single‐crystalline SiNWs with diameters of less than 100 nm as obtained by a wet chemical etching method based on silver nitrate and hydrofluoric acid solutions. The SERS active metal nanoparticles/islands are made from silver (Ag) shells as deposited by autometallography on the core nanoislands made from platinum (Pt) that can easily be deposited by ALD in the form of nanoislands covering the SiNW surfaces in a controlled way. The density of the plasmonically inactive Pt islands as well as the thickness of noble metal Ag shell are two key factors determining the magnitude of the SERS signal enhancement and sensitivity of detection. The optimized Ag coated Pt islands on SiNWs exhibit great potential for ultrasensitive molecular sensing in terms of high SERS signal enhancement ability, good stability and reproducibility. The plasmonic activity of the core‐shell Pt//Ag system that will be experimentally realized in this paper as an example was demonstrated in numerical finite element simulations as well as experimentally in Raman measurements of SERS activity of a highly diluted model dye molecule. The morphology and structure of the core‐shell Pt//Ag nanoparticles on SiNW surfaces were investigated by scanning‐ and transmission electron microscopy. Optimized core–shell nanoparticle geometries for maximum Raman signal enhancement is discussed essentially based on the finite element modeling.     

Specific detection of DNA through coupling of a TaqMan assay with surface enhanced Raman scattering (SERS)

We have combined the benefits of a TaqMan assay with surface enhanced Raman scattering (SERS), to generate a novel DNA detection method which provides increased sensitivity, with clear applications for disease identification through clinical testing. Target DNA detection limits by SERS were shown to be lower than conventional fluorescence detection and clinically relevant samples of methicillin-resistant Staphylococcus aureus were detected with high specificity.     

Surface-enhanced Raman scattering study of the adsorption of croconate violet on colloidal silver particles

Very stable silver particle suspension has been synthesized for use in surface-enhanced Raman scattering (SERS) spectroscopy with near-infrared exciting radiation. Such citrate-stabilized silver particles were obtained through a suitable control of the nucleation and growth process during the synthesis. The SERS spectra of the bis(dicyanomethylene) croconate dianion or croconate violet (CrocV) were obtained, with excitation in the near-infrared and in the visible region. The differences in the spectral patterns were correlated with a pre-resonance Raman effect of the adsorbate. The vibrational frequencies of CrocV isolated and interacting with silver surface were obtained through theoretical calculations using DFT method that together the surface selection rules allowed to perform the vibrational assignment of the SERS spectra and to infer the adsorption geometry.     

Potential-Averaged Raman Spectroscopy for the Time-Resolved Study

Raman spectroscopy, especially surface enhanced Raman spectroscopy (SERS) has long been used to study the interfacial phenomena, it provides a possible method to characterize a variety of surface and interfacial processes at molecular levels in detail.     

Growth of tetrahedral silver nanocrystals in aqueous solution and their SERS enhancement

Silver nanocrystals with tetrahedral shapes and {111} faces have been synthesized by the light-driven growth method in an aqueous solution. The nanocrystals of T(d) symmetry were formed under the effect of tartrate and citrate as the structural-directing reagents at the appropriate stages of reaction. Further, the nanocrystals may be assembled through electrostatic interaction to develop large-scale particle surfaces with sharp vertexes, which can generate strong localized electromagnetic field for surface-enhanced Raman scattering (SERS) studies. Benzenethiol was used as the probe to evaluate their SERS enhancement, and enhancement factors of up to 10(6) are reached. As a kind of promising material, these novel nanocrystals will be applied in surface enhanced spectroscopy and plasmonics field.     

A “Schizophotonic” All‐In‐One Nanoparticle Coating for Multiplexed SE(R)RS Biomedical Imaging

SERS nanoprobes for in vivo biomedical applications require high quantum yield, long circulation times, and maximum colloidal stability. Traditional synthetic routes require high metal–dye affinities and are challenged by unfavorable electrostatic interactions and limited scalability. We report the synthesis of a new near‐IR active poly(N‐(2‐hydroxypropyl) methacrylamide) (pHPMA). The integration of various SERS reporters into a biocompatible polymeric surface coating allows for controlled dye incorporation, high colloidal stability, and optimized in vivo circulation times. This technique allows the synthesis of very small (<20 nm) SERS probes, which is crucial for the design of excretable and thus highly translatable imaging agents. Depending on their size, the “schizophotonic” nanoparticles can emit both SERS and fluorescence. We demonstrate the capability of this all‐in‐one gold surface coating and SERS reporter for multiplexed lymph‐node imaging.     

A simple filter-based approach to surface enhanced Raman spectroscopy for trace chemical detection

We demonstrate an extremely simple and practical surface enhanced Raman spectroscopy (SERS) technique for trace chemical detection. Filter membranes first trap silver nanoparticles to form a SERS-active substrate and then concentrate analytes from a mL-scale sample into a μL-scale detection volume. We demonstrate a significant improvement in detection limit as compared to colloidal SERS for the pesticide malathion and the food contaminant melamine. The measured SERS intensity exhibits low variation relative to traditional SERS techniques, and the data can be closely fit with a Langmuir isotherm. Thus, due to the simple procedure, the low-cost of the substrates, the quantitative results, and the performance improvement due to analyte concentration, our technique enables SERS to be practical for a broad range of analytical applications, including field-based detection of toxins in large-volume samples.     

Highly sensitive signal detection of duplex dye-labelled DNA oligonucleotides in a PDMS microfluidic chip: confocal surface-enhanced Raman spectroscopic study

Rapid and highly sensitive detection of duplex dye-labelled DNA sequences in a PDMS microfluidic channel was investigated using confocal surface enhanced Raman spectroscopy (SERS). This method does not need either an immobilization procedure or a PCR amplification procedure, which are essential for a DNA microarray chip. Furthermore, Raman peaks of each dye-labelled DNA can be easily resolved since they are much narrower than the corresponding broad fluorescence bands. To find the potential applicability of confocal SERS for sensitive bio-detection in a microfluidic channel, the mixture of two different dye-labelled (TAMRA and Cy3) sex determining Y genes, SRY and SPGY1, was adsorbed on silver colloids in the alligator teeth-shaped PDMS microfluidic channel and its SERS signals were measured under flowing conditions. Its major SERS peaks were observable down to the concentration of 10(-11) M. In the present study, we explore the feasibility of confocal SERS for the highly sensitive detection of duplex dye-labelled DNA oligonucleotides in a PDMS microfluidic chip.     

Detection of structurally similar adulterants in botanical dietary supplements by thin-layer chromatography and surface enhanced Raman spectroscopy combined with two-dimensional correlation spectroscopy

Thin-layer chromatography (TLC) coupled with surface enhanced Raman spectroscopy (SERS) has been widely used for the study of various complex systems, especially for the detection of adulterants in botanical dietary supplements (BDS). However, this method is not sufficient to distinguish structurally similar adulterants in BDS since the analogs have highly similar chromatographic and/or spectroscopic behaviors. Taking into account the fact that higher cost and more time will be required for comprehensive chromatographic separation, more efforts with respect to spectroscopy are now focused on analyzing the overlapped SERS peaks. In this paper, the combination of a TLC–SERS method with two-dimensional correlation spectroscopy (2DCOS), with duration of exposure to laser as the perturbation, is applied to solve this problem.     

Optimization of the preparation of glass-coated, dye-tagged metal nanoparticles as SERS substrates

Dye-tagged metal nanoparticles are of significant interest in SERS-based sensitive detection applications. Coating these particles in glass results in an inert spectral tag that can be used in applications such as flow cytometry with significant multiplexing potential. Maximizing the SERS signal obtainable from these particles requires care in partitioning available nanoparticle surface area (binding sites) between the SERS dyes and the functionalized silanes necessary for anchoring the glass coating. In this article, we use the metal-mediated fluorescence quenching of SERS dyes to measure surface areas occupied by both dyes and silanes and thus examine SERS intensities as a function of both dye and silane loading. Notably, we find that increased surface occupation by silane increases the aggregative power of added dye but that decreasing the silane coverage allows a greater surface concentration of dye. Both effects increase the SERS intensity, but obtaining the optimum SERS intensity will require balancing aggregation against surface dye concentration.