Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles

A Nuclear-Targeted AIE Photosensitizer for Enzyme Inhibition and Photosensitization in Cancer Cell Ablation

The nucleus is considered the ideal target for anti-tumor therapy because DNA and some enzymes in the nucleus are the main causes of cell canceration and malignant proliferation. However, nuclear target drugs with good biosafety and high efficiency in cancer treatment are rare. Herein, a nuclear-targeted material MeTPAE with aggregation-induced emission (AIE) characteristics was developed based on a triphenylamine structure skeleton. MeTPAE can not only interact with histone deacetylases (HDACs) to inhibit cell proliferation but also damage telomere and nucleic acids precisely through photodynamic treatment (PDT). The cocktail strategy of MeTPAE caused obvious cell cycle arrest and showed excellent PDT anti-tumor activity, which offered new opportunities for the effective treatment of malignant tumors.

Nanomaterial-Based Fluorescence Resonance Energy Transfer (FRET) and Metal-Enhanced Fluorescence (MEF) to Detect Nucleic Acid in Cancer Diagnosis

Nucleic acids, including DNA and RNA, have received prodigious attention as potential biomarkers for precise and early diagnosis of cancers. However, due to their small quantity and instability in body fluids, precise and sensitive detection is highly important. Taking advantage of the ease-to-functionality and plasmonic effect of nanomaterials, fluorescence resonance energy transfer (FRET) and metal-enhanced fluorescence (MEF)-based biosensors have been developed for accurate and sensitive quantitation of cancer-related nucleic acids. This review summarizes the recent strategies and advances in recently developed nanomaterial-based FRET and MEF for biosensors for the detection of nucleic acids in cancer diagnosis. Challenges and opportunities in this field are also discussed. We anticipate that the FRET and MEF-based biosensors discussed in this review will provide valuable information for the sensitive detection of nucleic acids and early diagnosis of cancers.

Rapid and sensitive multiplex molecular diagnosis of respiratory pathogens using plasmonic isothermal RPA array chip

The current clinically available multiplex molecular diagnostic technologies are difficult to apply to onsite diagnostic platforms due to their large and sophisticated instrumentation, long amplification times and limited number of simultaneous detections. We developed a plasmonic isothermal recombinase polymerase amplification (RPA) array chip for rapid and sensitive multiplex molecular detection. The 3D plasmonic substrate composed of Au nanoparticles (NPs) on dense Au nanopillars (NPOP) showed highly enhanced plasmon-enhanced fluorescence (PEF) of RPA products with long DNA amplicons (~200 bp). The plasmonic 4-plex RPA array chip successfully detected bacterial DNA within 30 min and viral RNA within 40 min; the sensitivity of the plasmonic RPA array chip was comparable to or 10-fold higher than that of the 4-pelx liquid-phase RPA and 4-plex liquid-phase PCR techniques. Additionally, no cross-reactivity was observed. The 4-plex plasmonic RPA array chip was preliminary evaluated using clinical respiratory viral-positive nasopharyngeal swab samples. This approach enables rapid, sensitive and high-multiplex molecular detection and can be used in the realization of a simplified and miniaturized platform for onsite multiplex molecular diagnostics.

Analyte Co-localization at Electromagnetic Gap Hot-Spots for Highly Sensitive (Bio)molecular Detection by Plasmon Enhanced Spectroscopies

Electromagnetic hot-spots at ultranarrow plasmonic nanogaps carry immense potential to drive detection limits down to few molecules in sensors based on surface-enhanced Raman or fluorescence spectroscopies. However, leveraging the EM hot-spots requires access to the gaps, which in turn depends on the size of the analyte in relation to gap distances. Herein, we leverage a well-calibrated process based on self-assembly of block copolymer colloids on a full-wafer level to produce high-density plasmonic nanopillar arrays exhibiting a large number (>10¹⁰ cm^-2) of uniform interpillar EM hot-spots. The approach allows convenient handles to systematically vary the interpillar gap distances down to a sub-10 nm regime. The results show compelling trends of the impact of analyte dimensions in relation to the gap distances toward their leverage over interpillar hot-spots and the resulting sensitivity in SERS-based molecular assays. Comparing the detection of labeled proteins in surface-enhanced Raman and metal-enhanced fluorescence configurations further reveal the relative advantage of fluorescence over Raman detection while encountering the spatial limitations imposed by the gaps. Quantitative assays with limits of detection down to picomolar concentrations are realized for both small organic molecules and proteins. The well-defined geometries delivered by a nanofabrication approach are critical to arriving at realistic geometric models to establish meaningful correlation between the structure, optical properties, and sensitivity of nanopillar arrays in plasmonic assays. The findings emphasize the need for the rational design of EM hot-spots that takes into account the analyte dimensions to drive ultrahigh sensitivity in plasmon-enhanced spectroscopies.

A smartphone imaging-based label-free and dual-wavelength fluorescent biosensor with high sensitivity and accuracy

The accuracy of a bioassay based on smartphone-integrated fluorescent biosensors has been limited due to the occurrence of false signals from non-specific reactions as well as a high background and low signal-to-noise ratios for complementary metal oxide semiconductor image sensors. To overcome this problem, we demonstrate dual-wavelength fluorescent detection of biomolecules with high accuracy. Fluorescent intensity can be quantified using dual wavelengths simultaneously, where one decreases and the other increases, as the target analytes bind to the split capture and detection aptamer probes. To do this, we performed smartphone imaging-based fluorescence microscopy using a microarray platform on a substrate with metal-enhanced fluorescence (MEF) using Ag film and Al₂O₃ nano-spacer. The results showed that the sensitivity and specificity of the dual-wavelength fluorescent quantitative assay for the target biomolecule 17-β-estradiol in water were significantly increased through the elimination of false signals. The detection limit was 1pg/mL and the area under the receiver operating characteristic curve of the proposed assay (0.922) was comparable to that of an enzyme-linked immunosorbent assay (0.956) from statistical accuracy tests using spiked wastewater samples. This novel method has great potential as an accurate point-of-care testing technology based on mobile platforms for clinical diagnostics and environmental monitoring.

Recent Advances in Biosensing With Photonic Crystal Surfaces: A Review

Photonic crystal surfaces that are designed to function as wavelength-selective optical resonators have become a widely adopted platform for label-free biosensing, and for enhancement of the output of photon-emitting tags used throughout life science research and in vitro diagnostics. While some applications, such as analysis of drug-protein interactions, require extremely high resolution and the ability to accurately correct for measurement artifacts, others require sensitivity that is high enough for detection of disease biomarkers in serum with concentrations less than 1 pg/ml. As the analysis of cells becomes increasingly important for studying the behavior of stem cells, cancer cells, and biofilms under a variety of conditions, approaches that enable high resolution imaging of live cells without cytotoxic stains or photobleachable fluorescent dyes are providing new tools to biologists who seek to observe individual cells over extended time periods. This paper will review several recent advances in photonic crystal biosensor detection instrumentation and device structures that are being applied towards direct detection of small molecules in the context of high throughput drug screening, photonic crystal fluorescence enhancement as utilized for high sensitivity multiplexed cancer biomarker detection, and label-free high resolution imaging of cells and individual nanoparticles as a new tool for life science research and single-molecule diagnostics.

Robust nanoplasmonic substrates for aptamer macroarrays with single-step detection of PDGF-BB

An aptamer macroarray on a robust nanoplasmonic substrate with fluorescence enhancement is developed for a single-step sensitive detection of human platelet-derived growth factor-BB (PDGF-BB), a predominant cancer biomarker in cancer angiogenesis. A hybrid Au-nanoparticles-poly (dimethylsiloxane) (PDMS) as nanoplasmonic substrate is prepared via the in-situ reduction of AuCl4(-) ions in PDMS matrixes onto 96 or 384 well plates. In the absence of target molecules, unfolded PDGF-BB aptamer conjugated with dye TAMRA is electrostatically bound to a positively charged poly-L-lysine (PLL)-coated Au nanocomposites film surface, and the fluorescence enhancement effects can be optimized by varying the distance between TAMRA and the Au nanocomposites film, which is easily adjusted by varying the thickness of the biocompatible poly-(acrylic acid) (PAA/PLL) multilayers, and thus metal-enhanced fluorescence of dye TAMRA conjugated with the aptamer is generated up to 15.2-fold. The interaction of the aptamer to its target induces the reversible conformation change of the aptamer, and consequently, the electrostatic potential is overcome by binding force. As a result, the target-binding interaction of the aptamer causes the irreversible detachment of the aptamer from the nanostructured Au film surface to decrease fluorescence of TAMRA. The aptamer macroarray provides not only the appropriate sensitivity for clinical diagnostics with a wide range of linear detection from 10pg/mL to 10μg/mL, high specificity for PDGF-BB against VEGF-165, VEGF-121, NaCl and IgG, and temporal biological stability, but also a single-step detection. We envision that the efficient and robust aptamer macroarray can be extended to the detection of other biomarkers.

Photonic crystal micropost as a microarray platform

This study demonstrates a photonic crystal micropost (PCMP) substrate for microarray applications. The substrate comprises an array of circular MPs with a PC on top of these MPs. This substrate enables biomolecule-containing droplets to form a composite contact upon deposition, thus allowing biomolecules to be attached on only the MPs, forming spots. When the device (PC) is excited on resonance, the electric field intensity is enhanced on only the top surface of the MPs. This enables the fluorescence intensities to be enhanced up to 5.50x; principally, this enhancement does not engender an increase in the background (intensity outside MP or spots) and noise intensities. The PCMP substrate enhances the spot intensity and minimizes the background intensity, enabling the detection of lower concentration analytes.

Aptamers-based sandwich assay for silver-enhanced fluorescence multiplex detection

In this work, aptamers-modified silver nanoparticles (AgNPs) were prepared as capture substrate, and fluorescent dyes-modified aptamers were synthesized as detection probes. The sandwich assay was based on dual aptamers, which was aimed to accomplish the highly sensitive detection of single protein and multiplex detection of proteins on one-spot. We found that aptamers-modified AgNPs based microarray was much superior to the aptamer based microarray in fluorescence detection of proteins. The result shows that the detection limit of the sandwich assay using AgNPs probes for thrombin or platelet-derived growth factor-BB (PDGF-BB) is 80 or 8 times lower than that of aptamers used directly. For multiplex detection of proteins, the detection limit was 625 pM for PDGF-BB and 21 pM for thrombin respectively. The sandwich assay based on dual aptamers and AgNPs was sensitive and specific.

Enhanced light collection in fluorescence microscopy using self-assembled micro-reflectors

In fluorescence microscopy, the signal-to-noise ratio (SNR) of the optical system is directly linked to the numerical aperture (NA) of the microscope objective, which creates detection challenges for low-NA, wide-field and high-throughput imaging systems. Here we demonstrate a method to increase the light collection efficiency from micron-scale fluorescent objects using self-assembled vapor-condensed polyethylene glycol droplets, which act as micro-reflectors for fluorescent light. Around each fluorescent particle, a liquid meniscus is formed that increases the excitation efficiency and redirects part of the laterally-emitted fluorescent light towards the detector due to internal reflections at the liquid-air interface of the meniscus. The three-dimensional shape of this micro-reflector can be tuned as a function of time, vapor temperature, and substrate contact angle, providing us optimized SNR performance for fluorescent detection. Based on these self-assembled micro-reflectors, we experimentally demonstrate ~2.5-3 fold enhancement of the fluorescent signal from 2-10 μm sized particles. A theoretical explanation of the formation rate and shapes of these micro-reflectors is presented, along with a ray tracing model of their optical performance. This method can be used as a sample preparation technique for consumer electronics-based microscopy and sensing tools, thus increasing the sensitivity of low-NA systems that image fluorescent micro-objects.

Tip-enhanced fluorescence with radially polarized illumination for monitoring loop-mediated isothermal amplification on hepatitis C virus cDNA

A tip nanobiosensor for monitoring DNA replication was presented. The effects of excitation power and polarization on tip-enhanced fluorescence (TEF) were assessed with the tip immersed in fluorescein isothiocyanate solution first. The photon count rose on average fivefold with radially polarized illumination at 50 mW. We then used polymerase-functionalized tips for monitoring loop-mediated isothermal amplification on Hepatitis C virus cDNA. The amplicon-SYBR® Green I complex was detected and compared to real-time loop-mediated isothermal amplification. The signals of the reaction using 4 and 0.004 ng∕μl templates were detected 10 and 30 min earlier, respectively. The results showed the potential of TEF in developing a nanobiosensor for real-time DNA amplification.

A fluorescent aptasensor for H5N1 influenza virus detection based-on the core-shell nanoparticles metal-enhanced fluorescence (MEF)

A fluorescent aptasensor system has been designed for the sensitive detection of recombinant hemagglutinin (rHA) protein of the H5N1 influenza virus in human serum. Guanine-richen anti-rHA aptamers by SELEX were immobilized on the surface of the Ag@SiO2 nanoparticles which performed as a metal-enhanced fluorescence (MEF) sensing platform. Thiazole orange (TO) was used as fluorescent tag which reported to the G-quadruplex secondary structural induced by aptamer-rHA binding event. In the absence of rHA protein, TO was free in the solution with almost no fluorescence emission. When rHA protein was added to the solution, the aptamer strand bound rHA protein to form a stable G-quadruplex complex, which can bind TO and excite the fluorescence emission of TO. Moreover, the excited-state TO captured by the G-quadruplex complex was forced to the surface of the Ag@SiO2 nanoparticles and could experience a surface plasmon resonance enhancement which can be transformed into more efficient fluorescence emission signals, therefore, the fluorescence signal of TO can be amplified largely. This system does not require covalent labeling with fluorophores to the aptamer and the background noise is very low. The detection of rHA protein of the H5N1 influenza virus could be operated both in aqueous buffer and human serum with the detection limit of 2 and 3.5ng/mL respectively. More important, the whole detection process can be finished in a PE tube within 30min, which makes it suitable as a self-contained diagnostic kit for H5N1 influenza virus point-of-care (POC) diagnostic.

Shrink-induced silica multiscale structures for enhanced fluorescence from DNA microarrays

We describe a manufacturable and scalable method for fabrication of multiscale wrinkled silica (SiO2) structures on shrink-wrap film to enhance fluorescence signals in DNA fluorescence microarrays. We are able to enhance the fluorescence signal of hybridized DNA by more than 120 fold relative to a planar glass slide. Notably, our substrate has improved detection sensitivity (280 pM) relative to planar glass slide (11 nM). Furthermore, this is accompanied by a 30-45 times improvement in the signal-to-noise ratio (SNR). Unlike metal enhanced fluorescence (MEF) based enhancements, this is a far-field and uniform effect based on surface concentration and photophysical effects from the nano- to microscale SiO2 structures. Notably, the photophysical effects contribute an almost 2.5 fold enhancement over the concentration effects alone. Therefore, this simple and robust method offers an efficient technique to enhance the detection capabilities of fluorescence based DNA microarrays.

Photonic crystal enhancement of a homogeneous fluorescent assay using submicron fluid channels fabricated by E-jet patterning

We demonstrate the enhancement of a liquid-based homogenous fluorescence assay using the resonant electric fields from a photonic crystal (PC) surface. Because evanescent fields are confined to the liquid volume nearest to the photonic crystal, we developed a simple approach for integrating a PC fabricated on a silicon substrate within a fluid channel with submicron height, using electrohydrodynamic jet (e-jet) printing of a light-curable epoxy adhesive to define the fluid channel pattern. The PC is excited by a custom-designed compact instrument that illuminates the PC with collimated light that precisely matches the resonant coupling condition when the PC is covered with aqueous media. Using a molecular beacon nucleic acid fluorescence resonant energy transfer (FRET) probe for a specific miRNA sequence, we demonstrate an 8× enhancement of the fluorescence emission signal, compared to performing the same assay without exciting resonance in the PC detecting a miRNA sequence at a concentration of 62 nM from a liquid volume of only ∼20 nL. The approach may be utilized for any liquid-based fluorescence assay for applications in point-of-care diagnostics, environmental monitoring, or pathogen detection.

Hybrid silver nanoparticle/conjugated polyelectrolyte nanocomposites exhibiting controllable metal-enhanced fluorescence

Metal-enhanced fluorescence of conjugated polyelectrolytes (CPs) is realized using a simple, green hybrid Ag nanocomposite film. Ag nanoparticles (Ag NPs) are pre-prepared by sodium citrate reduction and incorporated into agarose by mixing to form an Ag-containing agarose film (Ag@agarose). Through variation of the amount of Ag NPs in the Ag@agarose film as well as the thickness of the interlayer between CPs and the Ag@agarose film prepared of layer-by-layer assembly of chitosan and sodium alginate, a maximum 8.5-fold increase in the fluorescence of CPs is obtained. After introducing tyrosinase, this system also can be used to detect phenolic compounds with high sensitivity and good visualization under ultraviolet light.

Metal-enhanced fluorescence platforms based on plasmonic ordered copper arrays: wavelength dependence of quenching and enhancement effects

Ordered arrays of copper nanostructures were fabricated and modified with porphyrin molecules in order to evaluate fluorescence enhancement due to the localized surface plasmon resonance. The nanostructures were prepared by thermally depositing copper on the upper hemispheres of two-dimensional silica colloidal crystals. The wavelength at which the surface plasmon resonance of the nanostructures was generated was tuned to a longer wavelength than the interband transition region of copper (>590 nm) by controlling the diameter of the underlying silica particles. Immobilization of porphyrin monolayers onto the nanostructures was achieved via self-assembly of 16-mercaptohexadecanoic acid, which also suppressed the oxidation of the copper surface. The maximum fluorescence enhancement of porphyrin by a factor of 89.2 was achieved as compared with that on a planar Cu plate (CuP) due to the generation of the surface plasmon resonance. Furthermore, it was found that while the fluorescence from the porphyrin was quenched within the interband transition region, it was efficiently enhanced at longer wavelengths. It was demonstrated that the enhancement induced by the proximity of the fluorophore to the nanostructures was enough to overcome the highly efficient quenching effects of the metal. From these results, it is speculated that the surface plasmon resonance of copper has tremendous potential for practical use as high functional plasmonic sensor and devices.

Metal-enhanced fluorescence of nano-core-shell structure used for sensitive detection of prion protein with a dual-aptamer strategy

Metal-enhanced fluorescence (MEF) as a newly recognized technology is widespread throughout biological research. The use of fluorophore-metal interactions is recognized to be able to alleviate some of fluorophore photophysical constraints, favorably increase both the fluorophore emission intensity and photostability. In this contribution, we developed a novel metal-enhanced fluorescence (MEF) and dual-aptamer-based strategy to achieve the prion detection in solution and intracellular protein imaging simultaneously, which shows high promise for nanostructure-based biosensing. In the presence of prion protein, core-shell Ag@SiO2, which are functionalized covalently by single stranded aptamer (Apt1) of prions and Cyanine 3 (Cy3) decorated the other aptamer (Apt2) were coupled together by the specific interaction between prions and the anti-prion aptamers in solution. By adjusting shell thickness of the pariticles, a dual-aptamer strategy combined MEF can be realized by the excitation and/or emission rates of Cy3. It was found that the enhanced fluorescence intensities followed a linear relationship in the range of 0.05-0.30 nM, which is successfully applied to the detection of PrP in mice brain homogenates.

Polyethylenimine-capped Ag nanoparticle film as a platform for detecting charged dye molecules by surface-enhanced Raman scattering and metal-enhanced fluorescence

Many drugs are charged molecules and are weak bases or acids having counterions. Their binding to biological surfaces is generally difficult to assess by vibrational spectroscopy. In this work, we demonstrated the potential of surface-enhanced Raman scattering (SERS) conducted using a polyethylenimine (PEI)-capped Ag nanoparticle film for the quantification of an electrostatic adsorption process of charged drug molecules, by using charged dye molecules such as sulforhodamine B (SRB) and rhodamine-123 (R123) as model drugs. It was possible to detect small-sized anions such as SCN(-) at 1 × 10(-9) M by SERS because of the cationic property of PEI. We were subsequently able to detect a prototype anionic dye molecule, SRB, by SERS at a subnanomolar concentration. On the other hand, it was difficult to detect cationic dyes such as R123 because of the electrostatically repulsive interaction with PEI. Nonetheless, we found that even R123 could be detected at subnanomolar concentrations by SERS by depositing an anionic polyelectrolyte such as poly(sodium 4-styrenesulfonate) (PSS) and poly(acrylic acid) (PAA) onto the PEI-capped Ag nanoparticles. Another noteworthy point is that a subnanomolar detection limit can also be achieved by carefully monitoring the fluorescence background in the measured SERS spectra. This was possible because charged dyes were not in contact with Ag but formed ion pairs with either PEI or PSS (PAA), allowing metal-enhanced fluorescence (MEF). The PEI-capped Ag nanoparticle film can thus serve as a useful indicator to detect charged drug molecules by SERS and MEF.

Highly sensitive fluorescence detection of avidin/streptavidin with an optical interference mirror slide

This paper presents highly sensitive fluorescence detections of avidin and streptavidin using an optical interference mirror (OIM) slide consisting of a plane mirror covered with an optical interference layer. Compared with a common glass slide, the OIM slide can enhance the fluorescence from a dye by more than 100-fold. We fabricated an OIM slide by depositing an optical interference layer of Al(2)O(3) on an Ag mirror. To enhance the fluorescence maximally, the optimal thickness of the Al(2)O(3) layer was estimated from optical interference theory. For detections of protein, avidin/streptavidin labeled with fluorescein, Cy3, and Cy5 were detected with biotin immobilized on an OIM slide with the optimal Al(2)O(3) thickness. We achieved a sensitivity improvement of more than 50-fold, comparing with a glass slide. Such a high degree of improvement would be a significant contribution to further progress in biomedical research and medical diagnostics.

Highly sensitive detection of proteins based on metal-enhanced fluorescence with novel silver nanostructures

We present a highly sensitive metal enhanced fluorescence (MEF) method based on a novel silver nanostructure fabricated with Cy5-functionalized silver nanoparticles (AgNPs) and AgNO(3). The analytical performance has been demonstrated by microarray detection of streptavidin (SA) and human IgE. The fluorescence intensity can be enhanced substantially with the combined use of AgNPs and fluorescence enhanced solution (FES). Aptamers have been used for the preparation of Tag-C, which demonstrate IgE detection from 0.5 ng/mL to 16 ng/mL, and the limit of detection is determined to be 0.25 ng/mL. SEM images show nanogaps exist in the aggregated silver nanoparticles and the nanogaps allow for the trap of fluorophores in the nanostructures that emit brighter light upon excitation. The silver nanostructures formed by Tags and FES proved to be an excellent platform for MEF of fluorophores whose excitation and emission occurred between 436 nm and 1000 nm. Finite-difference time-domain (FDTD) simulation has been carried out to confirm the enhanced electromagnetic field inside silver nanostructures, leading to strong overlap/resonance coupling and eventual fluorescence enhancement.

Metal-enhanced fluorescent probes based on silver nanoparticles and its application in IgE detection

In this paper, a novel metal plasmon coupled with an aptamer-nucleotide hybridized probe was fabricated and applied for protein detection. The specific aptamer and single-strand oligonucleotide were chemically bound to silver nanoparticles (AgNPs), and Cy5-labeled, complementary single-strand oligonucleotides were hybridized with the particle-bound oligonucleotides. The hybridized DNA duplexes were regarded as rigid rods that separated the fluorophore Cy5 and the surface of AgNPs to reduce the competitive quenching. Using a model system comprising human immunoglobulin E (IgE) as the analyte and goat antihuman IgE as immobilized capture antibody on glass slides, we demonstrate that the detection performance of the synthetic probe was superior to the aptamer-based fluorescent probes. The results showed a good linear correlation for human IgE in the range from 10 ng/ml to 6.25 μg/ml. The detection limit obtained was 1 ng/ml, which was 50 times lower than that using Cy5 oligonucleotide/aptamer hybrid duplex (Probe2) due to the metal-enhanced fluorescence effect. This new strategy opens the possibility for the preparation of high-sensitivity detection probes based on metal nanoparticles.

Spatially selective photonic crystal enhanced fluorescence and application to background reduction for biomolecule detection assays

By combining photonic crystal label-free biosensor imaging with photonic crystal enhanced fluorescence, it is possible to selectively enhance the fluorescence emission from regions of the PC surface based upon the density of immobilized capture molecules. A label-free image of the capture molecules enables determination of optimal coupling conditions of the laser used for fluorescence imaging of the photonic crystal surface on a pixel-by-pixel basis, allowing maximization of fluorescence enhancement factor from regions incorporating a biomolecule capture spot and minimization of background autofluorescence from areas between capture spots. This capability significantly improves the contrast of enhanced fluorescent images, and when applied to an antibody protein microarray, provides a substantial advantage over conventional fluorescence microscopy. Using the new approach, we demonstrate detection limits as low as 0.97 pg/ml for a representative protein biomarker in buffer.

Plasmonic substrates for multiplexed protein microarrays with femtomolar sensitivity and broad dynamic range

Protein chips are widely used for high-throughput proteomic analysis, but to date, the low sensitivity and narrow dynamic range have limited their capabilities in diagnostics and proteomics. Here we present protein microarrays on a novel nanostructured, plasmonic gold film with near-infrared fluorescence enhancement of up to 100-fold, extending the dynamic range of protein detection by three orders of magnitude towards the fM regime. We employ plasmonic protein microarrays for the early detection of a cancer biomarker, carcinoembryonic antigen, in the sera of mice bearing a xenograft tumour model. Further, we demonstrate a multiplexed autoantigen array for human autoantibodies implicated in a range of autoimmune diseases with superior signal-to-noise ratios and broader dynamic range compared with commercial nitrocellulose and glass substrates. The high sensitivity, broad dynamic range and easy adaptability of plasmonic protein chips presents new opportunities in proteomic research and diagnostics applications.

The fabrication of highly ordered silver nanodot patterns by platinum assisted nanoimprint lithography

Silver has been widely used for optical sensing and imaging applications which benefit from localized surface plasmon resonance (LSPR) in a nanoscale configuration. Many attempts have been made to fabricate and control silver nanostructures in order to improve the high performance in sensing and other applications. However, a fatal mechanical weakness of silver and a lack of durability in oxygen-rich conditions have disrupted the manufacturing of reproducible nanostructures by the top-down lithography approach. In this study, we suggest a steady fabrication strategy to obtain highly ordered silver nanopatterns that are able to provide tunable LSPR characteristics. By using a protecting layer of platinum on a silver surface in the lithography process, we successfully obtained large-area (2.7 × 2.7 mm(2)) silver nanopatterns with high reproducibility. This large-area silver nanopattern was capable of enhancing the low concentration of a Cy3 fluorescence signal (∼10(-10) M) which was labeled with DNA oligomers.

Improved sensitivity of DNA microarrays using photonic crystal enhanced fluorescence

DNA microarrays are used to profile changes in gene expression between samples in a high-throughput manner, but measurements of genes with low expression levels can be problematic with standard microarray substrates. In this work, we expand the detection capabilities of a standard microarray experiment using a photonic crystal (PC) surface that enhances fluorescence observed from microarray spots. This PC is inexpensively and uniformly fabricated using a nanoreplica molding technique, with very little variation in its optical properties within- and between-devices. By using standard protocols to process glass microarray substrates in parallel with PCs, we evaluated the impact of this substrate on a one-color microarray experiment comparing gene expression in two developmental stages of Glycine max. The PCs enhanced the signal-to-noise ratio observed from microarray spots by 1 order of magnitude, significantly increasing the number of genes detected above substrate fluorescence noise. PC substrates more than double the number of genes classified as differentially expressed, detecting changes in expression even for low expression genes. This approach increases the dynamic range of a surface-bound fluorescence-based assay to reliably quantify small quantities of DNA that would be impossible with standard substrates.

Recent advancements in optical DNA biosensors: exploiting the plasmonic effects of metal nanoparticles

The emerging field of plasmonics, the study of electromagnetic responses of metal nanostructures, has revealed many novel signal enhancing phenomena. As applied to the development of label-free optical DNA biosensors, it is now well established that plasmon-based surface enhanced spectroscopies on nanostructured metal surfaces or metal nanoparticles can markedly improve the sensitivity of optical biosensors, with some showing great promise for single molecule detection. In this review, we first summarize the basic concepts of plasmonics in metal nanostructures, as well as the characteristic optical phenomena to which plasmons give rise. We will then describe recent advances in optical DNA biosensing systems enabled by metal nanoparticle-derived plasmonic effects, including the use of surface enhanced Raman scattering (SERS), colorimetric methods, "scanometric" processes, and metal-enhanced fluorescence (MEF).

Surface plasmon enhanced fluorescence of cationic conjugated polymer on periodic nanoarrays

The fluorescence from conjugated polymer assembled onto lithographically fabricated gold nanoarrays using genetically engineered peptides as molecular linkers is studied. A 16-fold increase in the photoluminescence of the conjugated polymer is observed when assembled on the optimized nanostructures due to surface plasmon enhanced fluorescence. This is achieved using a water-soluble cationic conjugated polymer, poly[(9,9-bis(6'-((N,N,N-trimethylammonium)hexyl)-2,7-fluorene)-co-4,7-di-2-thienyl-2,1,3-benzothiadiazole] dibromide (PFDBT-N(+)), systematically tuning the vertical distance of PFDBT-N(+) from the gold nanopillar surface using solid-specific peptide linkers and horizontally optimizing the localized surface plasmon resonance by varying the geometric arrangements of the patterned metal nanoarrays. The diameter and tip-to-tip spacing of the nanopillars along with vertically tuning the distance of PFDBT-N(+) from the nanopillar affected the observed fluorescence enhancements. The collective optical properties of conjugated polymers combined with the photonic properties of nanoparticles provide a new means in the development of metal enhanced hybrid nanomaterials for biotechnology.

Fluorescence enhancement and reflection of the excitation light observed with a multilayered substrate

Fluorescence enhancement from a multilayered substrate fabricated with Ag and Al(2)O(3) was investigated using fluorescein, rhodamine B, Cy3, and Cy5 as fluorophores. The change in the fluorescence enhancement with Al(2)O(3) had two peaks and one valley in the range from 0 to 300 nm of Al(2)O(3) thickness, and such peaks and valley were found to appear periodically. Moreover, the reflection of the excitation light from the multilayered substrate was investigated. The reflection of the excitation light periodically changed depending on the Al(2)O(3) thickness as well, and the maximum reflection was observed near the Al(2)O(3) thickness of the peak fluorescence enhancement. It was found that the periodic changes of the fluorescence enhancement and the reflection of the excitation light could be explained, for the most part, with the integral multiples of the lambda/4 derived by a simple interference theory.

Silver-coated silica beads applicable as core materials of dual-tagging sensors operating via SERS and MEF

We have developed dual-tagging sensors, operating via both surface-enhanced Raman scattering (SERS) and metal-enhanced fluorescence (MEF), composed of silver-coated silica beads onto which were deposited SERS markers and dye-grafted polyelectrolytes, for multiplex immunoassays. Initially, a very simple electroless-plating method was applied to prepare Ag-coated silica beads. The Raman markers were then assembled onto the Ag-coated silica beads, after which they were brought to stabilization by the layer-by-layer deposition of anionic and cationic polyelectrolytes including a dye-grafted polyelectrolyte. In the final stage, the dual-tagging sensors were assembled onto them with specific antibodies (antihuman-IgG or antirabbit-IgG) to detect target antigens (human-IgG or rabbit-IgG). The MEF signal was used as an immediate indicator of molecular recognition, while the SERS signals were subsequently used as the signature of specific molecular interactions. For this reason, these materials should find wide application, especially in the areas of biological sensing and recognition that rely heavily on optical and spectroscopic properties.

Hydrogel-based protein and oligonucleotide microchips on metal-coated surfaces: enhancement of fluorescence and optimization of immunoassay

Manufacturing of hydrogel-based microchips on metal-coated substrates significantly enhances fluorescent signals upon binding of labeled target molecules. This observation holds true for both oligonucleotide and protein microchips. When Cy5 is used as fluorophore, this enhancement is 8-10-fold in hemispherical gel elements and 4-5-fold in flattened gel pads, as compared with similar microchips manufactured on uncoated glass slides. The effect also depends on the hydrophobicity of metal-coated substrate and on the presence of a layer of liquid over the gel pads. The extent of enhancement is insensitive to the nature of formed complexes and immobilized probes and remains linear within a wide range of fluorescence intensities. Manufacturing of gel-based protein microarrays on metal-coated substrates improves their sensitivity using the same incubation time for immunoassay. Sandwich immunoassay using these microchips allows shortening the incubation time without loss of sensitivity. Unlike microchips with probes immobilized directly on a surface, for which the plasmon mechanism is considered responsible for metal-enhanced fluorescence, the enhancement effect observed using hydrogel-based microchips on metal-coated substrates might be explained within the framework of geometric optics.

Nanomaterial-assisted signal enhancement of hybridization for DNA biosensors: a review

Detection of DNA sequences has received broad attention due to its potential applications in a variety of fields. As sensitivity of DNA biosensors is determined by signal variation of hybridization events, the signal enhancement is of great significance for improving the sensitivity in DNA detection, which still remains a great challenge. Nanomaterials, which possess some unique chemical and physical properties caused by nanoscale effects, provide a new opportunity for developing novel nanomaterial-based signal-enhancers for DNA biosensors. In this review, recent progress concerning this field, including some newly-developed signal enhancement approaches using quantum-dots, carbon nanotubes and their composites reported by our group and other researchers are comprehensively summarized. Reports on signal enhancement of DNA biosensors by non-nanomaterials, such as enzymes and polymer reagents, are also reviewed for comparison. Furthermore, the prospects for developing DNA biosensors using nanomaterials as signal-enhancers in future are also indicated.

Label-free DNA detection on nanostructured Ag surfaces

The dramatic local electric-field enhancement property of Ag nanoparticles was used as the basis to significantly increase the signal output of a novel label-free (or "self-labeled") fluorescence-based DNA detection system. In response to identical amounts of analyte, nanostructured Ag substrates provided a posthybridization fluorescent sensor response over 10-fold larger than the response from planar Au substrates. Detection performance strongly depended upon the Ag substrate roughness. Consistent with work by others on metal-enhanced fluorescence, fluorescence intensity also depended strongly on the distance between the fluorophore and the Ag substrate surface. Adjusting the surface roughness, amount of the Ag deposited on the surface, and the DNA probe length allowed for production of an optimized response. In addition to constituting a novel label-free DNA sensor, we anticipate that these structures will provide a unique platform for testing concepts in plasmonics.

Metal-Enhanced Fluorescence (MEF): Physical Characterization of Siver-Island Films and Exploring Sample Geometries

In this study we have analyzed metal-enhanced fluorescence (MEF) effects from different density silver island films (SiFs) and the effects of sample geometry on the observed enhancement of fluorescence (EF). It is shown that silver islands grow exponentially with SiF deposition time (DT<7min), optical density of SiFs almost linearly depends on DT; electrical conductivity is zero. At DT>7 min, silver islands merge, exhibiting a sharp increase in electrical conductivity. It has been shown that the newly proposed SiF-Glass sample geometry exhibits higher EF values than the commonly used in MEF studies SiF-SiF sample geometry. The SiF-Glass geometry demonstrates high sensitivity for surface immunoassays, a growing application of metal-enhanced fluorescence.

A detection instrument for enhanced-fluorescence and label-free imaging on photonic crystal surfaces

We report on the design and demonstration of an optical imaging system capable of exciting surface-bound fluorophores within the resonant evanescent electric field of a photonic crystal surface and gathering fluorescence emission that is directed toward the imaging objective by the photonic crystal. The system also has the ability to quantify shifts in the local resonance angle induced by the adsorption of biomolecules on the photonic crystal surface for label-free biomolecular imaging. With these two capabilities combined within a single detection system, we demonstrate label-free images self-registered to enhanced fluorescence images with 328x more sensitive fluorescence detection relative to a glass surface. This technique is applied to a DNA microarray where label-free quantification of immobilized capture DNA enables improved quality control and subsequent enhanced fluorescence detection of dye-tagged hybridized DNA yields 3x more genes to be detected versus commercially available microarray substrates.

Design of fluorescent assays for cyanide and hydrogen peroxide based on the inner filter effect of metal nanoparticles

We have demonstrated the design of a new type fluorescent assay based on the inner filter effect (IFE) of metal nanoparticles (NPs), which is conceptually different from the previously reported metal NPs-based fluorescent assays. With a high extinction coefficient and tunable plasmon absorption feature, metal NPs are expected to be capable of functioning as a powerful absorber to tune the emission of the fluorophore in the IFE-based fluorescent assays. In this work, we presented two proof-of-concept examples based on the IFE of Au NPs by choosing MDMO-PPV as a model fluorophore, whose fluorescence could be tuned by the absorbance of Au NPs with a much higher sensitivity than the corresponding absorbance approach. While the first assay worked in a turn-on mode upon the etching of Au NPs by the analyte, CN(-), the second one functioned in a turn-off mode upon the catalytic growth of Au NPs by the analyte, H(2)O(2). As a result, the present IFE-based approach can detect cyanide ranging from 1.0 x 10(-6) to 6.0 x 10(-4) M with a detection limit of 6.0 x 10(-7) M and H(2)O(2) ranging from 1.5 x 10(-7) to 2.2 x 10(-5) M with a detection limit of 8.5 x 10(-8) M, respectively. Notably, the present IFE-based approach allows the design of fluorescent assays in a more simple, time-saving, and economical approach when compared with conventional metal NPs-based fluorescent assays, since no modification step of the fluorophore was needed any more.