Plasmonic properties of the multispot copper-capped nanoparticle array chip and its application to optical biosensors for pathogen detection of multiplex DNAs

A localized surface plasmon resonance (LSPR)-based optical biosensor in connection with a multispot copper-capped nanoparticle array (MC-NPA) chip was proposed and developed. The copper (Cu) films, used as a shell, formed a "cap-like" layer on the top of the silica nanoparticles, used as a core, in an orderly fashion, to form the surface called a "Cu-capped nanoparticle array chip". The plasmonic properties of this nanostructure type were initially investigated while controlling the shell thickness of the deposited Cu. Also, we quantified the sensitivity of MC-NPA chip to changes in bulk refractive index (RI). As a result of its LSPR properties, the MC-NPA chip displayed a sensitivity of 67.8 nm per RI unit, and the wavelength shift of the LSPR spectrum peak was sensitive to the RI of the surrounding bulk medium, such as the biomolecular layers. Using MC-NPA chips, multiplex sensing of target DNAs from reference bacteria and clinical samples was possible in a quantitative manner with a detection limit of 10 fM (50 zmol). The optical biosensor developed in this study represents a unique approach to performing LSPR that utilizes a simple and cost-effective optical setup with disposable chips.     

Label-free detection of peptide nucleic acid-DNA hybridization using localized surface plasmon resonance based optical biosensor

The development of label-free optical biosensors for DNA and other biomolecules has the potential to impact life sciences as well as screening in medical and environmental applications. In this report, we developed a localized surface plasmon resonance (LSPR) based label-free optical biosensor based on a gold-capped nanoparticle layer substrate immobilized with peptide nucleic acids (PNAs). PNA probe was designed to recognize the target DNA related to tumor necrosis factor. The nanoparticle layer was formed on a gold-deposited glass substrate by the surface modified silica nanoparticles using silane-coupling reagent. The optical properties of gold-capped nanoparticle layer substrate were characterized through monitoring the changes in the absorbance strength, as the thickness of the biomolecular layer increased with hybridization. The detection of PNA-DNA hybridization with target oligonucleotides and PCR-amplified real samples were performed with a limit of detection value of 0.677 pM target DNA. Selective discrimination against a single-base mismatch was also achieved. Our LSPR-based biosensor with the gold-capped nanoparticle layer substrate is applicable to the design of biosensors for monitoring of the interaction of other biomolecules, such as proteins, whole cells, or receptors with a massively parallel detection capability in a highly miniaturized package.     

A colorimetric gold nanoparticle sensor to interrogate biomolecular interactions in real time on a surface

This paper presents a new label-free optical method to study biomolecular interactions in real time at the surface of an optically transparent substrate. The method relies on the change in the absorbance spectrum of a self-assembled monolayer of colloidal gold on glass, as a function of biomolecular binding to the surface of the immobilized colloids. Using this approach, we demonstrate proof of principle of a label-free optical biosensor to quantify biomolecular interactions in real time on a surface in a commercially available UV-visible spectrophotometer and of a colorimetric end-point assay using an optical scanner. The spectrophotometric sensor shows concentration-dependent binding and a detection limit of 16 nM for streptavidin. The sensor is easy to fabricate, is reproducible in its performance, has minimal technological requirements, namely, the availability of an UV-visible spectrophotometer or an optical scanner, and will enable high-throughput screening of biomolecular interactions in real time in an array-based format.     

Quantitative acoustic microscopy of anodized and coated aluminium at frequencies up to 1 GHz

Quantitative acoustic microscopy (QAM) has been used to measure surface wave velocities on polished, anodized and coated aluminium substrates, these materials being representative of those used for adhesive bonding in the aerospace industry. Good quality acoustic measurements were obtainable at frequencies between 225 and 980 MHz, despite the inhomogeneous nature of the oxide layer produced by phosphoric acid anodization (PAA). Good agreement was obtained between the surface acoustic wave dispersion measured on aluminium coated with 0.2 and 1.0 m PMMA, and that calculated by a simple isotropic layer model. The anodized aluminium was modelled as a transversely isotropic oxide layer on an aluminium substrate. At 0.2 m, the oxide layer was too thin for the comparison between measurement and calculation to be conclusive, but the calculations suggest that a change in porosity of 10% in a 0.6 m oxide layer, as obtained with an industry standard PAA treatment, should be readily detectable. The highly dispersive nature of some of the surface acoustic wave modes makes QAM extremely sensitive to small changes in the material parameters.     

Chip-based optical detection of DNA hybridization by means of nanobead labeling

A new scheme for the detection of molecular interactions based on optical readout of nanoparticle labels has been developed. Capture DNA probes were arrayed on a glass chip and incubated with nanoparticle-labeled target DNA probes, containing a complementary sequence. Binding events were monitored by optical means, using reflected and transmitted light for the detection of surface-bound nanoparticles. Control experiments exclude significant influence of nonspecific binding on the observed contrast. Scanning force microscopy revealed the distribution of nanoparticles on the chip surface.     

Optimisation of distributed feedback laser biosensors

A new integrated optical sensor chip is proposed, based on a modified distributed- feedback (DFB) semiconductor laser. The semiconductor layers of different refractive indices that comprise a laser form the basis of a waveguide sensor, where changes in the refractive index of material at the surface are sensed via changes in the evanescent field of the lasing mode. In DFB lasers, laser oscillation occurs at the Bragg wavelength. Since this is sensitive to the effective refractive index of the optical mode, the emission wavelength is sensitive to the index of a sample on the waveguide surface. Hence, lasers are modelled as planar waveguides and the effective index of the fundamental transverse electric mode is calculated as a function of index and thickness of a thin surface layer using the beam propagation method. We find that an optimised structure has a thin upper cladding layer of ~0.15 mum, which according to this model gives detection limits on test layer index and thickness resolution of 0.1 and 1.57 nm, respectively, a figure which may be further improved using two lasers in an interferometer-type configuration.     

Nano-C(60) : a novel, effective, fluorescent sensing platform for biomolecular detection

Water-soluble nano-C(60) can serve as a novel, effective, fluorescent sensing platform for biomolecular detection with high sensitivity and selectivity. In this paper, fluorescent detection of DNA and thrombin via nano-C(60) is demonstrated for the first time. The principle of the assay lies in the fact that the adsorption of the fluorescently labeled single-stranded DNA (ssDNA) probe by nano-C(60) leads to substantial fluorescence quenching. In the presence of a target, the biomolecular mutual interaction suppresses this quenching, signaling the existence of the target. This sensing system rivals graphene oxide but is superior to other carbon-structure-based systems. The present method can also achieve multiplex DNA detection and withstand the interference from human blood serum.     

Peeling Back the Layers: Controlled Erosion and Triggered Disassembly of Multilayered Polyelectrolyte Thin Films

Methods for the layer‐by‐layer deposition of oppositely charged polymers on surfaces can be used to assemble thin multilayered films using a broad range of natural, synthetic, and biologically relevant materials. These methods also permit precise, nanometer‐scale control over the compositions and internal structures of multicomponent assemblies. Provided that the individual components of these materials are selected or designed appropriately, these methods provide tantalizing new opportunities to design thin films and coatings that provide spatial, temporal, or active control over the release of one or several different agents from surfaces. The last two years have seen a significant increase in reports describing the development of new chemical, physical, and biomolecular approaches to the controlled erosion, triggered disassembly, or general deconstruction of multilayered polymer films. In this Progress Report, we highlight recent work from our laboratory and several other groups toward the design of ultrathin multilayered assemblies that i) permit broad, tunable, and sophisticated control over film erosion, and ii) provide new opportunities for the localized release of macromolecular therapeutics, such as DNA and proteins, from surfaces.     

Internal reflection ellipsometry for real-time monitoring of polyelectrolyte multilayer growth onto tantalum pentoxide

Internal reflection ellipsometry was used for detection of the consecutive coating of two polyelectrolytes, poly(allylamine hydrochloride) (PAH) and poly(acrylic acid) (PAA), onto a tantalum pentoxide (Ta₂O₅) substrate until the 10th bilayer. The UV patterned PAH-PAA-multilayer was characterized in air via ellipsometry and atomic force microscopy. Suited optical models enabled the determination of the layer thicknesses in wet and dry states. Linear multilayer formation could be proved by Attenuated Total Reflection — Fourier Transformed Infrared Spectroscopy measurements following the increase of the ν(C=O) band depending on the adsorption of the PAA. Streaming potential measurements after each layer deposition step indicated a change in surface charge after each layer deposition due to the consecutive coating of PAH and PAA. In this article the internal reflection ellipsometry is shown to be a convenient possibility to analyze the modification of a thin transparent Ta₂O₅ substrate.     

Simple multiscale algorithm for layer detection with lidar

Lidar is a powerful active remote sensing device used in the detection of the optical properties of aerosols and clouds. However, there are difficulties in layer detection and classification. Many previous methods are too complex for large dataset analysis or limited to data with too high a signal-to-noise ratio (SNR). In this study, a mechanism of multiscale detection and overdetection rejection is proposed based on a trend index function that we define. Finally, we classify layers based on connected layers employing a quantity known as the threshold of the peak-to-base ratio. We find good consistency between retrieved results employing our method and visual analysis. The testing of synthetic signals shows that our algorithm performs well with SNRs higher than 4. The results demonstrate that our algorithm is simple, practical, and suited to large dataset applications.     

Optical waveguide biosensors constructed with subwavelength gratings

The reflection resonance spectrum of a subwavelength diffraction-grating-coupled waveguide is used to analyze biomolecular interactions in real time. By detecting this resonance wavelength shift, the optical waveguide biosensor provides the ability to identify the kinetics of the biomolecular interaction on an on-line basis without the need for extrinsic labeling of the biomolecules. A theoretical analysis of the subwavelength optical waveguide biosensor is performed. A biosensor with a narrow reflection resonance spectrum, and hence an enhanced detection resolution, is then designed and fabricated. Currently, the detection limit of the optical waveguide sensor is approximately 10(-5) refractive-index units. The biosensor is successfully applied to study of the dynamic response of an antibody interaction with protein G adsorbed on the sensing surface.     

Nanomechanical membrane-type surface stress sensor

Nanomechanical cantilever sensors have been emerging as a key device for real-time and label-free detection of various analytes ranging from gaseous to biological molecules. The major sensing principle is based on the analyte-induced surface stress, which makes a cantilever bend. In this letter, we present a membrane-type surface stress sensor (MSS), which is based on the piezoresistive read-out integrated in the sensor chip. The MSS is not a simple "cantilever," rather it consists of an "adsorbate membrane" suspended by four piezoresistive "sensing beams," composing a full Wheatstone bridge. The whole analyte-induced isotropic surface stress on the membrane is efficiently transduced to the piezoresistive beams as an amplified uniaxial stress. Evaluation of a prototype MSS used in the present experiments demonstrates a high sensitivity which is comparable with that of optical methods and a factor of more than 20 higher than that obtained with a standard piezoresistive cantilever. The finite element analyses indicate that changing dimensions of the membrane and beams can substantially increase the sensitivity further. Given the various conveniences and advantages of the integrated piezoresistive read-out, this platform is expected to open a new era of surface stress-based sensing.     

On‐Electrode Synthesis of Shape‐Controlled Hierarchical Flower‐Like Gold Nanostructures for Efficient Interfacial DNA Assembly and Sensitive Electrochemical Sensing of MicroRNA

The performance for biomolecular detection is closely associated with the interfacial structure of a biosensor, which profoundly affects both thermodynamics and kinetics of the assembly, binding and signal transduction of biomolecules. Herein, it is reported on a one‐step and template‐free on‐electrode synthesis method for making shape‐controlled gold nanostructures on indium tin oxide substrates, which provide an electrochemical sensing platform for ultrasensitive detection of nucleic acids. Thus‐prepared hierarchical flower‐like gold nanostructures (HFGNs) possess large surface area that can readily accommodate the assembly of DNA probes for subsequent hybridization detection. It is found that the sensitivity for electrochemical DNA sensing is critically dependent on the morphology of HFGNs. By using this new strategy, a highly sensitive electrochemical biosensor is developed for label‐free detection of microRNA‐21 (miRNA‐21), a biomarker for lung cancers. Importantly, it is demonstrated that this biosensor can be employed to measure the miRNA‐21 expression level from human lung cancer cell (A549) lysates and worked well in 100% serum, suggesting its potential for applications in clinical diagnosis and a wide range of bioanalysis.     

泪滴状铝纳米结构紫外-近红外宽带吸收体的制备

宽波段光吸收体在太阳能利用、光探测等领域具有重要的应用价值.本研究以带铝基的多孔氧化铝(AAO)膜为模板,采用真空电子束蒸镀技术,结合后续的高温退火、湿化学刻蚀和胶带剥离等处理过程,制备出了泪滴状铝纳米结构宽带吸收体,其吸收率在200～980 nm的波长范围内均高于93％,在紫外光谱区的吸收带宽大于文献中报道的单一金属...     

Micromachining microcarrier-based biomolecular encoding for miniaturized and multiplexed immunoassay

Micromachining techniques, which originated in the microelectronics industry, have been employed to manufacture microparticles bearing an engraved dot-type signature for biomolecular encoding. These metallic microstructures are photolithographically defined and manufactured in a highly reproducible manner. In addition, the code introduced on the particle face is a straightforward visible feature that is easily recognizable with the use of optical microscopy. The number of distinct codes theoretically could be many thousands, depending on the coding element numbers. Such microparticles are, thus, with appropriate surface organic functionalizations, ideal for encoding biomolecular libraries and serving as a platform for developing high-throughput multiplexed bioassay schemes based on suspension array technology. As proof of this statement, we demonstrated that encoded microparticles tagged with antibodies to human immunoglobulin classes are capable, using imaging detection as the interrogating approach, of high sensitivity and high specificity, as well as multiplexed detection of the respective antigens in a microliter-sample volume.     

Screening the Insecticidal Efficacy of Nano ZnO Synthesized via in-situ Polymerization of Crosslinked Polyacrylic Acid as a Template

Nano zinc oxide (ZnO) is a very useful and important material in many industrial and biological applications. In the present work, ZnO was synthesized by post thermal degradation of the precursor "zinc acetate di-hydrate" templated in crosslinked polyacrylic acid (PAA). The crosslinked PAA template was prepared through an in-situ polymerization process adopted in presence of ammonium per sulphate, as an initiator, and N, Nmethylene bis-acrylamide as the crosslinker. Variation of preparation parameters and their impact on the oxide stoichiometry, crystal structure, crystallite size and surface texture of the oxide were investigated. Energy dispersive X-ray technique (EDX), X-ray diffraction (XRD) and scanning electron microscopy (SEM) were convincingly used to reveal the oxide structural features and characteristics. The performed bioassay tests indicated the efficacy of this method of preparation to produce nano ZnO with novel insecticidal activity against the greater wax moth, Galleria mellonella.     

Electrical detection of DNA hybridization based on enzymatic accumulation confined in nanodroplets

Electrical monitoring of DNA hybridization is one way to reduce the cost and size of the DNA chip reader in comparison with the more classical optical detection. Within electrical methods, electrochemical detection shows very high performances in terms of accuracy and sensitivity, especially when an enzymatic accumulation is used to amplify the signal. However, signal multiplexing for miniaturized systems based on both enzymatic accumulation and electrochemical detection remains challenging due to the Brownian diffusion of the detected product of the enzymatic reaction. We present here a DNA chip with electrical detection based on the following sequence: (i) hybridization of nucleic acids and washing in a liquid layer as usual, (ii) formation of independent nanodroplets on each detection site, (iii) enzymatic accumulation in each droplet avoiding cross-contamination between neighboring sites, and (iv) electrochemical detection of the product accumulated during the enzymatic reaction. The simple and fast transition from the liquid layer (hybridization step) to an array of nanodroplets (enzymatic accumulation and detection steps) was performed through the filling of the hybridization chamber with a solution containing the enzymatic substrates, the drawing of this solution, and the simultaneous creation of droplets thanks to retention areas based on circular rims or hydrophilic rings. Using this approach, hybridization is achieved in a liquid layer as usual, followed by the enzymatic accumulation in nanodroplets to avoid the cross-talk between neighboring sites. Moreover, working in droplets enables a fast increase in the concentration of the product generated by the enzymatic reaction and thus an improvement of the detection limit of the system.     

A "seed-refine" algorithm for detecting protein complexes from protein interaction data

New technology advances in large-scale protein-protein interaction detection provide researchers an initial view of proteins on a global scale. These massive data sets provide a valuable source for elucidating the biomolecular mechanism in the cell. In this paper, we investigate the problem of protein complex detection from noisy protein interaction data, i.e., finding the subsets of proteins that are closely coupled via protein interactions. We identify the challenges and propose a "seed-refine" approach. We propose a novel statistically meaningful subgraph quality measure, a two-layer seeding heuristic to find good seeds, and a novel subgraph refinement method that controls the overlap between subgraphs. Experiments show the desirable properties of our subgraph quality measure and the effectiveness of our "seed-refine" algorithm     

Multi-layered plasma-polymerized chips for SPR-based detection

The surface functionalization of a noble metal is crucial in a surface plasmon resonance-based biomolecular detection system because the interfacial coating must retain the activity of immobilized biomolecules while enhancing the optimal loading. We present here a one-step, room-temperature, high-speed, gas-phase plasma polymerization process for functionalizing gold substrates using siloxane as an adhesion layer and acrylic acid as a functional layer. Siloxane- and thiol-based coatings were compared for their performance as adhesion and the interfacial layer for subsequent functionalization. An in situ sequential deposition of siloxane and acrylic acid resulted in a 7-fold increase in carboxylic functionality surfacial content compared to films deposited with thiol-containing precursors. Grading of the layer composition achieved as a consequence of ion-induced mixing on the surface coating under the application of the plasma is confirmed through secondary ion mass spectroscopic studies. DNA hybridization assays were demonstrated on gold/glass substrates using surface plasmon enhanced ellipsometry and the applicability of this coating for protein immunoassays were demonstrated with plasma functionalized gold/plastic substrates in Biacore 3000 SPR instrument.     

On the Modeling of New Tunnel Junction Magnetoresistive Biosensors

A fully integrated biochip based on a 16 $times$ 16 scalable matrix structure of aluminum oxide magnetic tunnel junctions (MTJs) and thin-film diodes (TFDs of hydrogenated amorphous silicon) was fabricated and included as the biosensor of a portable handheld microsystem developed for biomolecular recognition detection using magnetic labels [deoxyribonucleic acid (DNA) hybridization, antibody antigen interaction, etc.]. The system uses magnetic field arraying of magnetically tagged biomolecules and can potentially be used to detect single or few biomolecules. Each biosensor matrix node is the series between a TFD (p-i-n or Schottky-barrier type) and an MTJ. In this paper, this matrix basic cell biosensor element is completely characterized and modeled. Experimental measured data are provided and compared with the proposed theoretical models results. It is shown that the diode may be used both as the matrix switching device and as an in-site temperature sensor and that the MTJ may act as the magnetoresistive sensor for detecting the fringe field of immobilized magnetic markers. Therefore, the fabricated fully integrated biochip included in the developed handheld microsystem may be used for biomolecular recognition.