Gold-nanorod-enhanced Raman spectroscopy encoded micro-quartz pieces for the multiplex detection of biomolecules

Analytical and Bioanalytical Chemistry - The rapid analysis and detection of biomolecules has become increasingly important in biological research. Hence, here we propose a novel suspension array...     

Fluorescence-based nucleic acid detection and microarrays

Recent analytical innovations for nucleic acid detection have revolutionized the biological sciences. Single nucleic acid sequence detection methods have been expanded to incorporate multiplexed detection strategies. A variety of nucleic acid detection formats are now available that can address high throughput genomic interrogation. Many of these parallel detection platforms or arrays, employ fluorescence as the signaling method. Fluorescence-based assays offer many advantages, including increased sensitivity, safety and multiplexing capabilities, as well as the ability to measure multiple fluorescence properties. Multiplexed microarray platforms provide parallel detection capabilities capable of measuring thousands of simultaneous responses. This review will discuss both single target detection and microarray applications with a focus on gene expression and pathogenic microorganism (PM) detection.     

Preparation of polydiacetylene immobilized optically encoded beads

Polydiacetylene (PDA), which can change the chromic and fluorescence properties by inducing environmental perturbations, is immobilized on planar solid supports for many biological applications. In this work, we immobilize PDA onto optically encoded spherical beads (PDA-SERS beads). The prepared PDA immobilized beads (36 μm) exhibit a blue color without fluorescence. By inducing stress, their color and fluorescence properties are changed to red with fluorescence. The SERS spectra of the PDA-SERS beads can be recognized over the PDA background. Moreover, our PDA immobilization methods are successfully applied to silica-surface SERS-encoded beads (5 μm) and proven to also be useful in fluorescence encoding systems.     

High-performance fluorescence-encoded magnetic microbeads as microfluidic protein chip supports for AFP detection

Fluorescence-encoded magnetic microbeads (FEMMs), with the fluorescence encoding ability of quantum dots (QDs) and magnetic enrichment and separation functions of Fe₃O₄ nanoparticles, have been widely used for multiple biomolecular detection as microfluidic protein chip supports. However, the preparation of FEMMs with long-term fluorescent encoding and immunodetection stability is still a challenge. In this work, we designed a novel high-temperature chemical swelling strategy. The QDs and Fe₃O₄ nanoparticles were effectively packaged into microbeads via the thermal motion of the polymer chains and the hydrophobic interaction between the nanoparticles and microbeads. The FEMMs obtained a highly uniform fluorescent property and long-term encoding and immunodetection stability and could be quickly magnetically separated and enriched. Then, the QD-encoded magnetic microbeads were applied to alpha fetoprotein (AFP) detection via sandwich immunoreaction. The properties of the encoded microspheres were characterized using a self-designed detecting apparatus, and the target molecular concentration in the sample was also quantified. The results suggested that the high-performance FEMMs have great potential in the field of biomolecular detection.     

Fluorescence-based nitric oxide detection by ruthenium porphyrin fluorophore complexes

The ruthenium(II) porphyrin fluorophore complexes [Ru(TPP)(CO)(Ds-R)] (TPP = tetraphenylporphinato dianion; Ds = dansyl; R = imidazole (im), 1, or thiomorpholine (tm), 2) were synthesized and investigated for their ability to detect nitric oxide (NO) based on fluorescence. The X-ray crystal structures of 1 and 2 were determined. The Ds-im or Ds-tm ligand coordinates to an axial site of the ruthenium(II) center through a nitrogen or sulfur atom, respectively. Both exhibit quenched fluorescence when excited at 368 or 345 nm. Displacement of the metal-coordinated fluorophore by NO restores fluorescence within minutes. These observations demonstrate fluorescence-based NO detection using ruthenium porphyrin fluorophore conjugates.     

Development of an integrated microsystem for injection, transport and manipulation of encoded microbeads

An integrated microsystem for injection, transport and manipulation of encoded microbeads on a single microchip is presented. The device also incorporates a customized reaction chamber to process individual, optically encoded microbeads. This research illustrates how microfabrication technologies enable convenient integration of multiple capabilities of microbeads, controlled microfluidic injection, integration of heater elements and temperature sensors and detection of microbeads in a single microfluidic chip. A practical application for the integrated microsystem is confirmed by the ability to select a specific DNA sequence of interest from a 4 x 4 cDNA library. This application emphasizes the advantages of component integration for rapid bio-assay development in a complete microsystem.     

Fluorescence-based detection of nitric oxide in aqueous and methanol media using a copper(II) complex

The quenched fluorescent intensity of a copper(II) complex, 1, of a fluorescent ligand, in degassed methanol or aqueous (buffered at pH 7.2) solution, was found to reappear on exposure to nitric oxide. Thus, it can function as a fluorescence based nitric oxide sensor. It has been found that the present complex can be used to sense nanomolar quantities of nitric oxide in both methanol and pH 7.2 buffered-water medium.     

Stimuli-responsive 2D polyelectrolyte photonic crystals for optically encoded pH sensing

A versatile photonic crystal sensing motif based on a two-dimensional (2D) inverse opal monolayer of stimuli-responsive polyelectrolyte gel with tunable optical properties is reported. The photonic membrane shows prompt response to pH and can be readily read out from either its optical spectra or interference colours.     

Multiplexed assay for proteins based on sequestration electrochemistry using the protein binding electroactive magnetic microbeads

The paramagnetic microbead-based electrochemical binding assay was demonstrated for detecting two kinds of protein simultaneously. The principle of this assay is based on the sequestration electrochemistry. The protein binding electroactive magnetic microbeads which are conjugated with an electroactive compound and a ligand to bind specifically with a target protein were prepared. The avidin-biotin and soybean agglutinin (SBA)-galactosamine were chosen as model protein-ligand systems. The avidin binding electroactive magnetic microbead (ABEMMb) and SBA binding electroactive magnetic microbead (SBEMMb) are constructed by biotin/thionine and galactosamine/ferrocene modified on paramagnetic microbeads. The voltammetric response for these functionalized microbeads was measured by the Nd-Fe-B magnet-incorporating carbon paste rotating disk electrode. The measurements were performed in a microliter droplet using a rotating disk electrode system. Avidin and SBA were simultaneously detected by the decrease in the current responses from the reduction of ABEMMb and SBEMMb that was caused by the binding with target proteins. The limits of detection for avidin and SBA were 4 × 10(-10) and 2 × 10(-10) M, respectively.     

DNA hybridization at microbeads with cathodic stripping voltammetric detection

In electrochemical DNA hybridization sensors generally a single-stranded probe DNA was immobilized at the electrode followed by hybridization with the target DNA and electrochemical detection of the hybridization event at the same electrode. In this type of experiments nonspecific adsorption of DNA at the electrode caused serious difficulties especially in the case of the analysis of long target DNAs. We propose a new technology in which DNA is hybridized at a surface H and the hybridization is detected at the detection electrode (DE). This technology significantly extends the choice of hybridization surfaces and DEs. Here we use paramagnetic Dynabeads Oligo(dT)(25) (DBT) as a transportable reactive surface H and a hanging mercury drop electrode as DE. We describe a label-free detection of DNA and RNA (selectively captured at DBT) based on the determination of adenines (at ppb levels, by cathodic stripping voltammetry) released from the nucleic acids by acid treatment. The DNA and RNA nonspecific adsorption at DBT is negligible, making thus possible to detect the hybridization event with a great specificity and sensitivity. Specific detection of the hybridization of polyribonucleotides, mRNA, oligodeoxynucleotides, and a DNA PCR product (226 base pairs) is demonstrated. New possibilities in the development of the DNA hybridization sensors opened by the proposed technology, including utilization of catalytic signals in nucleic acid determination at mercury (e.g. signals of osmium complexes covalently bound to DNA) and solid DEs (e.g. using enzyme-labeled antibodies against chemically modified DNAs) are discussed.     

Fluorescence-based aluminum ion sensing using a surface-functionalized microstructured optical fiber

The first microstructured optical fiber-based sensor platform for aluminum ions using a surface-attached derivative of lumogallion (3), a known fluorescence-based indicator, has been fabricated. These fibers allow for strong evanescent field interactions with the surrounding media because of the small core size while also providing the potential for real-time and distributed measurements. The fluorescence response to aluminum ions was first demonstrated by applying the procedure to glass slides. This was achieved through the covalent attachment of the fluorophore to a polyelectrolyte-coated glass surface and then to the internal holes of a suspended-core microstructured optical fiber to give an effective aluminum sensor. Whereas the sensor platform reported is fabricated for aluminum, the approach is versatile, with applicability to the detection of other ions.     

Fluorescence-based detection of single nucleotide permutation in DNA via catalytically templated reaction

Templated reduction of low fluorescence azidocoumarin-PNA conjugate to high fluorescence aminocoumarin was achieved using a catalytic amount of DNA with single nucleotide resolution.     

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.     

Sequential capillary electrophoresis analysis using optically gated sample injection and UV/vis detection

We present sequential CE analysis of amino acids and l ‐asparaginase‐catalyzed enzyme reaction, by combing the on‐line derivatization, optically gated (OG) injection and commercial‐available UV‐Vis detection. Various experimental conditions for sequential OG‐UV/vis CE analysis were investigated and optimized by analyzing a standard mixture of amino acids. High reproducibility of the sequential CE analysis was demonstrated with RSD values (n = 20) of 2.23, 2.57, and 0.70% for peak heights, peak areas, and migration times, respectively, and the LOD of 5.0 μM (for asparagine) and 2.0 μM (for aspartic acid) were obtained. With the application of the OG‐UV/vis CE analysis, sequential online CE enzyme assay of l ‐asparaginase‐catalyzed enzyme reaction was carried out by automatically and continuously monitoring the substrate consumption and the product formation every 12 s from the beginning to the end of the reaction. The Michaelis constants for the reaction were obtained and were found to be in good agreement with the results of traditional off‐line enzyme assays. The study demonstrated the feasibility and reliability of integrating the OG injection with UV/vis detection for sequential online CE analysis, which could be of potential value for online monitoring various chemical reaction and bioprocesses.     

Single-step multiplex detection of toxic metal ions by Au nanowires-on-chip sensor using reporter elimination

We have developed a Au nanowires (NWs)-on-chip surface-enhanced Raman scattering (SERS) multiplex sensor that can sensitively detect multiple toxic metal ions. Most importantly, the reporter elimination method simplified the detection procedure to a single step, which has been much desired for remote environmental monitoring. This sensor has several notable features. First, it shows high reproducibility based on well-defined single-crystalline Au NWs. Second, single-NW-sensors that can detect a specific metal ion are combined for multiplex sensing of metal ions. Third, when a sample solution is put onto the NWs-on-chip sensor, a decrease in the SERS signal of a specific NW-sensor identifies the target metal ion. Simple, rapid, sensitive and quantitative detection of metal ions becomes possible through the measurement of the SERS signals. We successfully detected ions of mercury (Hg(2+)), silver (Ag(+)), and lead (Pb(2+)) coexisting in the same solution by using this sensor.     

Chemiluminescence sequential injection immunoassay for vitellogenin using magnetic microbeads

A rapid and sensitive immunoassay for the determination of carp vitellogenin (Vg) is described. The method involves a sequential injection analysis (SIA) system equipped with a chemiluminescence detector and a samarium-cobalt magnet. An anti-Vg monoclonal antibody, immobilized on magnetic beads, was used as a solid support for the immunoassay. The introduction, trapping and release of the magnetic beads in the flow cell were controlled by a samarium-cobalt magnet and the flow of the carrier solution. The immunoassay was based on a sandwich immunoreaction of anti-Vg monoclonal antibody (primary antibody) on the magnetic beads, Vg, and the anti-Vg antibody labeled with horseradish peroxidase (HRP) (secondary antibody), and was based on a subsequent chemiluminescence reaction of HRP with hydrogen peroxide and p-iodophenol, in a luminol solution. The magnetic beads to which the primary antibody was immobilized were prepared by coupling the primary antibody with the magnetic beads after an agarose-layer on the surface of the magnetic beads was epoxidized. The primary antibody-immobilized magnetic beads were introduced, and trapped in the flow cell equipped with the samarium-cobalt magnet, a Vg sample solution, an HRP-labeled secondary antibody solution and the luminol solution were sequentially introduced into the flow cell based on an SIA programmed sequence. Chemiluminescence emission was monitored by means of a photomultiplier located at the upper side of the flow cell. The optimal incubation times both for the first and second immunoreactions were determined to be 20 min. A concave calibration curve was obtained between Vg concentration and chemiluminescence intensity when various concentrations of standard Vg samples (2–100 ng mL⁻¹) were applied to the SIA system under optimal conditions. In spite of a narrow working range, the lower detection limit of the immunoassay was about 2 ng mL⁻¹.     

Microfluidic nanoplasmonic-enabled device for multiplex DNA detection

We describe a rapid, quantitative, multiplex, self-labelled, and real-time DNA biosensor employing Ag nanoparticle-bound DNA hairpin probes immobilized in a microfluidic channel. Capture of complementary target DNAs by the microarrayed DNA hairpin probes results in a positive fluorescence signal via a conformational change of the probe molecules, signalling the presence of target DNAs. The device's capability for quantitative analyses was evaluated and a detection time as low as 6 min (with a target flow rate of 0.5 μl min(-1)) was sufficient to generate significant detection signals. This detection time translates to merely 3 μl of target solution consumption. An unoptimized sensitivity of 500 pM was demonstrated for this device.     

Circular dichroism detection of optically active compounds in gas chromatography using vacuum ultraviolet synchrotron radiation

Circular dichroism has been employed as a detection technique in gas chromatography for specific monitoring of optically active compounds which absorb in the vacuum ultraviolet region. The synchrotron radiation from U9A beamline of National Synchrotron Light Source, Brookhaven National Laboratory, was used as the light source. The detection limit established using this system is at the nanogram level for a selected group of hydrocarbons.     

Multiplex quantitative foodborne pathogen detection using high resolution CE-SSCP coupled stuffer-free multiplex ligation-dependent probe amplification

Sensitive multiplex detection methods for foodborne pathogens are important in controlling food safety, and detection of genetic markers is accepted to be one of the best tools for sensitive detection. Although CE technology offers great potential in terms of sensitive multiplex detection, the necessary amplification is confined to markers sharing common primers such as the 16S rRNA gene. For precise and sensitive detection, pathogen-specific genes are optimal markers. Although multiplex ligation-dependent probe amplification (MLPA) is appropriate for amplification of specific markers, the requirement for stuffers, to ensure length-dependent separation on CE, is a major obstacle in detection of foodborne pathogens. In the present study, we developed stuffer-free MLPA using high-resolution CE-SSCP to sensitively detect ten foodborne pathogens. The probe set for MLPA prior to CE-SSCP analysis was designed for species-specific detection. After careful optimization of each MLPA step, to ensure that CE-SSCP analysis was informative, we found that all ten pathogens could be reliably identified; the limits of detection were 0.5-5 pg of genomic DNA, and more than 100-fold increase could be quantitatively determined. Thus, MLPA-CE-SSCP is a sensitive and reliable technique for pathogen detection.