Magnetic bead detection using nano-transformers

A novel scheme to detect magnetic beads using a nano-scale transformer with a femtoweber resolution is reported. We have performed a Faraday's induction experiment with the nano-transformer at room temperature. The transformer shows the linear output voltage responses to the sinusoidal input current. When magnetic beads are placed on the transformer, the output responses are increased by an amount corresponding to the added magnetic flux from the beads when compared with the case of no beads on the transformer. In this way, we could determine whether magnetic beads are on top of the transformer in a single particle level.     

Magnetic bead based immunoassay for autonomous detection of toxins

We are developing an automated system for the simultaneous, rapid detection of a group of select agents and toxins in the environment. To detect toxins, we modified and automated an antibody-based approach previously developed for manual medical diagnostics that uses fluorescent eTag reporter molecules and is suitable for highly multiplexed assays. Detection is based on two antibodies binding simultaneously to a single antigen, one of which is labeled with biotin while the other is conjugated to a fluorescent eTag through a cleavable linkage. Aqueous samples are incubated with the mixture of antibodies along with streptavidin-coated magnetic beads and a photoactive porphyrin complex. In the presence of antigen, a molecular complex is formed where the cleavable linkage is held in proximity to the photoactive group. Upon excitation at 680 nm, free radicals are generated, which diffuse and cleave the linkage, releasing the eTags. Released eTags are analyzed using capillary gel electrophoresis with laser-induced fluorescence detection. Limits of detection for ovalbumin and botulinum toxoid individually were 4 (or 80 pg) and 16 ng/mL (or 320 pg), respectively, using the manual assay. In addition, we demonstrated the use of pairs of antibodies from different sources in a single assay to decrease the rate of false positives. Automation of the assay was demonstrated in a flow-through format with higher LODs of 32 ng/mL (or 640 ng) each of a mixture of ovalbumin and botulinum toxoid. This versatile assay can be easily modified with the appropriate antibodies to detect a wide range of toxins and other proteins.     

Carbon nanocapsules as an effective sensing platform for fluorescence-enhanced nucleic acid detection

In this communication, we demonstrate the proof of concept that carbon nanocapsules (CNCs) can be used as an effective fluorescent sensing platform for nucleic acid detection with selectivity down to single-base mismatch. The detection is accomplished by two steps: (1) CNC adsorbs and quenches the fluorescence of the dye-labeled single-stranded DNA (ssDNA) probe; (2) in the presence of the target, a hybridization event occurs, which produces a double-stranded DNA (dsDNA) that detaches from the CNC surface, leading to recovery of the dye fluorescence.     

Biochemical detection for direct bead surface analysis

A continuous-flow biochemical detection system is presented which recognizes biologically active compounds immobilized to solid phases. This approach can be used to screen, for example, solid-phase combinatorial libraries for lead compounds. Biochemical detection is performed by mixing a plug of a solid-phase suspension with labeled affinity protein. During a short reaction time, the labeled affinity protein will only bind to ligands, i.e., compounds with biological activity. Hereafter, the free and bound labels are separated by means of a hollow fiber module. Quantitation of the free label is performed with a conventional flow-through fluorescence detector. Total assay time amounts to less than 3 min. Biochemical detection for direct bead surface analysis was developed for two model systems. The first model system used fluorescence-labeled avidin as affinity protein and its ligands biotin and iminobiotin immobilized to agarose as analytes. The second model system used fluorescence-labeled antisheep (Fab)(2) fragments as affinity protein and different IgGs immobilized to agarose as analytes. The feasibility of this approach for recognition of solid-phase immobilized ligands was documented by screening 50 samples with a 100% hit rate.     

Reusable electrochemical sensing platform for highly sensitive detection of small molecules based on structure-switching signaling aptamers

Aptamers are nucleic acids that have high affinity and selectivity for their target molecules. A target may induce the structure switching from a DNA/DNA duplex to a DNA/target complex. In the present study, a reusable electrochemical sensing platform based on structure-switching signaling aptamers for highly sensitive detection of small molecules is developed using adenosine as a model analyte. A gold electrode is first modified with polytyramine and gold nanoparticles. Then, thiolated capture probe is assembled onto the modified electrode surface via sulfur-gold affinity. Ferrocene (Fc)-labeled aptamer probe, which is designed to hybridize with capture DNA sequence and specifically recognize adenosine, is immobilized on the electrode surface by hybridization reaction. The introduction of adenosine triggers structure switching of the aptamer. As a result, Fc-labeled aptamer probe is forced to dissociate from the sensing interface, resulting in a decrease in redox current. The decrement of peak current is proportional to the amount of adenosine. The present sensing system could provide both a wide linear dynamic range and a low detection limit. In addition, high selectivity, good reproducibility, stability, and reusability are achieved. The recovery test demonstrates the feasibility of the designed sensing system for an adenosine assay.     

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.     

A nanochannel/nanoparticle-based filtering and sensing platform for direct detection of a cancer biomarker in blood

A rapid nanochannel-based immunoassay capable of the filtering and subsequent detection of proteins in whole blood without any sample preparation is described. This is accomplished by using a nanoporous/nanochannel membrane modified with antibodies, the conductivity of which toward a redox indicator is tuned by primary and secondary immunoreactions with proteins and gold nanoparticles. This interesting nanopore blockage by gold nanoparticles is enhanced by silver deposition that further decreases the diffusion of the signaling indicator through the nanochannel. The efficiency of the nanochannels to act as immunoreaction platforms including the use of nanoparticles is also monitored by microscopic techniques. Successful detection of immunoglobulins including a cancer biomarker is achieved in buffer as well as in whole blood. This system constitutes an efficient immunoassay capable of detecting up to 52 U mL(-1) of CA15-3. The developed nanochannel/nanoparticle-based device can be used for several other proteins and extended also to DNA detection with interest not only for diagnostics but also environmental monitoring, food analysis, safety, and security applications.     

Hybrid surface platform for the simultaneous detection of proteins and DNAs using a surface plasmon resonance imaging sensor

In this work, we present a novel surface and assay for the simultaneous detection of DNA and protein analytes on a surface plasmon resonance (SPR) imaging sensor. A mixed DNA/oligo (ethylene glycol) (OEG) self-assembled monolayer (SAM) is created using a microarrayer. Thiol-modified single-stranded DNA sequences are spotted onto a gold-coated glass substrate. Backfilling with an OEG-modified alkanethiol creates a protein-resistant surface background. Antibodies conjugated to complementary single-stranded DNA sequences are immobilized on the surface through DNA hybridization. By converting only part of the DNA array into a protein array, simultaneous detections of DNA and protein analytes are possible. A model system of two cDNA sequences and two human pregnancy hormones are used to demonstrate the assay. No cross-reactivity was observed between DNA or protein analytes and nontargeted immobilized cDNA sequence or antibodies. A response from a detection of a single analyte in a mixture of protein and DNA analytes corresponds well with that of a single-analyte solution.     

Ultrafast trace-level detection of methyl nicotinate biomarker using TiO2/SiNWs nanocomposite-based sensing platform

Journal of Materials Science: Materials in Electronics - The reported work presents an ultrafast and ultrasensitive sensing platform for the precise and reliable trace-level detection of Methyl...     

Simple bead assay for detection of live bacteria (Escherichia coli)

Bead assays are an important rapid microbial detection technology suitable for extremely low pathogen levels. We report a bead assay for rRNA extracted from Escherichia coli K12 that does not require amplification steps and has readout on an Agilent 2100 Bioanalyzer flow cytometry system. Our assay was able to detect 125 ng of RNA, which is 16 times less than reported earlier. The specificity was extremely high, with no binding to a negative control organism (Bacillus subtilis). We discuss challenges faced during optimization of the key assay components, such as varying amounts of RNA in the samples, number of beads, aggregation, and reproducibility.     

2,4,6-Tris (2-pyridyl)-1,3,5-triazine nanobelts as an effective fluorescent sensing platform for DNA detection

In the present study, we report on the use of 2,4,6-tris (2-pyridyl)-1,3,5-triazine nanobelts (TPTNBs) as an effective fluorescent sensing platform for DNA detection for the first time. The general concept used in this approach is based on adsorption of fluorescently labeled single-stranded DNA (ssDNA) probe by TPTNB, due to the strong pi-pi stacking between unpaired DNA bases and TPTNB. As a result, the fluorophor is brought into close proximity of TPTNB, leading to fluorescence quenching. Upon presence of the target ssDNA, specific hybridization with the target takes place to form a double-stranded DNA (dsDNA). The resultant dsDNA cannot be adsorbed by TPTNB due to its rigid conformation and the absence of unpaired DNA bases. Thus, the fluorophor is seperated from TPTNB accompanied by fluorescence recovery. The present system shows a detection limit as low as 3 nM and has a high selectivity down to single-base mismatch.     

Magnetic and fluorescent core-shell nanoparticles for ratiometric pH sensing

This paper describes the preparation of nanoparticles composed of a magnetic core surrounded by two successive silica shells embedding two fluorophores, showing uniform nanoparticle size (50-60 nm in diameter) and shape, which allow ratiometric pH measurements in the pH range 5-8. Uncoated iron oxide magnetic nanoparticles (～10 nm in diameter) were formed by the coprecipitation reaction of ferrous and ferric salts. Then, they were added to a water-in-oil microemulsion where the hydrophilic silica shells were obtained through hydrolysis and condensation of tetraethoxyorthosilicate together with the corresponding silylated dye derivatives-a sulforhodamine was embedded in the inner silica shell and used as the reference dye while a pH-sensitive fluorescein was incorporated in the outer shell as the pH indicator. The magnetic nanoparticles were characterized using vibrating sample magnetometry, dynamic light scattering, transmission electron microscopy, x-ray diffraction and Fourier transform infrared spectroscopy. The relationship between the analytical parameter, that is, the ratio of fluorescence between the sensing and reference dyes versus the pH was adjusted to a sigmoidal fit using a Boltzmann type equation giving an apparent pK(a) value of 6.8. The fluorescence intensity of the reference dye did not change significantly (～3.0%) on modifying the pH of the nanoparticle dispersion. Finally, the proposed method was statistically validated against a reference procedure using samples of water and physiological buffer with 2% of horse serum, indicating that there are no significant statistical differences at a 95% confidence level.     

Unimolecular beacons for the detection of DNA-binding proteins

A new methodology for detecting sequence-specific DNA-binding proteins has been recently developed (Heyduk, T.; Heyduk, E. Nat. Biotechnol. 2002, 20, 171). The core feature of this methodology is protein-dependent association of two fluorochrome-labeled DNA fragments, which allows generation of a fluorescence signal reporting the presence of the target protein. Previous kinetic experiments identified the association of the two DNA fragments as the rate-limiting step of the assay. Here we report on a variant of the assay, in which components of the assay--fluorescent DNA fragments--were covalently tethered by a non-DNA linker with the goal of increasing the rate of association of the two fragments. We investigated the effect of the tether on the performance of the assay under a variety of conditions using a model DNA-binding protein. Quantitative titrations and rapid kinetic stopped-flow experiments were conducted to validate the molecular model that describes the two linked equilibria: oscillation of the tethered construct between the open and closed states and the exclusive association of the protein with the closed state. Experiments were also performed to demonstrate the ability of these tethered constructs to signal when attached to a solid surface. The major advantage of this new assay format is the faster response time for the detection allowing the higher throughput of the analysis. Additionally, it will be possible to attach tethered beacons to other solid surfaces, thus allowing the preparation of arrays containing molecular beacons for many different DNA-binding proteins.     

Analytical performances of aptamer-based sensing for thrombin detection

Aptamer-based assays represent a modern and attractive approach in bioanalytical chemistry. The DNA thrombin aptamer has been extensively investigated, and the coupling of this aptamer to different transduction principles has demonstrated the wide applicability of aptamers as bioreceptors in bioanalytical assays. The goal of this work was to critically evaluate all the parameters that can influence the sensor performances by using the thrombin aptamer immobilized onto piezoelectric quartz crystals. The optimization of the immobilization and the binding protocol was of paramount importance, and improvements in analytical performances could be obtained by optimizing simple steps in immobilization and assay conditions. Moreover, the work demonstrated the possibility of using aptamer-based sensors in complex matrixes, opening the possibility of a real application to diagnostics or medical investigation.     

PEI-conjugated AuNPs as a sensing platform for arsenic (AS-III)

We have developed a simple method for synthesis of spherical gold nanoparticles (AuNPs) with enhanced surface properties. The polyethyleneimine (PEI) has good potential to minimise the size of the precursor. The UV–vis spectra of synthesised AuNPs with reducing agents (PEI) have been characterised with a peak at 530?nm. The size and shape measurement of AuNPs was confirmed by transmission electron microscopy (TEM) which shows that the mean diameter is 3.9?nm. The optimal concentration of reducing agents was found to be 1% for synthesis of AuNPs. PEI-conjugated AuNP shows binding with arsenic III (0.1?ppm) as confirmed by scanning electron microscope (SEM)/energy dispersive X-rays mapping. TEM revealed the particle shape and size. Zeta potential, zeta deviation, effective particle size, Z-average diameter, polydispersity index and electrophoretic mobility have been observed in order to understand the stability of AuNPs. The image of SEM confirmed that As (III) particles were eventually distributed in PEI-conjugated AuNPs matrix. Further, this study demonstrated that PEI-conjugated AuNPs is a sensing platform of As (III).     

Mid-infrared materials and devices on a Si platform for optical sensing

In this article, we review our recent work on mid-infrared (mid-IR) photonic materials and devices fabricated on silicon for on-chip sensing applications. Pedestal waveguides based on silicon are demonstrated as broadband mid-IR sensors. Our low-loss mid-IR directional couplers demonstrated in SiN_x waveguides are useful in differential sensing applications. Photonic crystal cavities and microdisk resonators based on chalcogenide glasses for high sensitivity are also demonstrated as effective mid-IR sensors. Polymer-based functionalization layers, to enhance the sensitivity and selectivity of our sensor devices, are also presented. We discuss the design of mid-IR chalcogenide waveguides integrated with polycrystalline PbTe detectors on a monolithic silicon platform for optical sensing, wherein the use of a low-index spacer layer enables the evanescent coupling of mid-IR light from the waveguides to the detector. Finally, we show the successful fabrication processing of our first prototype mid-IR waveguide-integrated detectors.     

Nanopatterned cadmium selenide Langmuir-Blodgett platform for leukemia detection

We present results of the studies relating to preparation of Langmuir-Blodgett (LB) monolayers of tri-n-octylphosphine oxide-capped cadmium selenide quantum dots (QCdSe) onto indium-tin oxide (ITO) coated glass substrate. The monolayer behavior has been studied at the air-water interface under various subphase conditions. This nanopatterned platform has been explored to fabricate an electrochemical DNA biosensor for detection of chronic myelogenous leukemia (CML) by covalently immobilizing the thiol-terminated oligonucleotide probe sequence via a displacement reaction. The results of electrochemical response studies reveal that this biosensor can detect target DNA in the range of 10(-6) to 10(-14) M within 120 s, has a shelf life of 2 months, and can be used about 8 times. Further, this nucleic acid sensor has been found to distinguish the CML-positive and the control negative clinical patient samples.     

Magnetic levitation as a platform for competitive protein-ligand binding assays

This paper describes a method based on magnetic levitation (MagLev) that is capable of indirectly measuring the binding of unlabeled ligands to unlabeled protein. We demonstrate this method by measuring the affinity of unlabeled bovine carbonic anhydrase (BCA) for a variety of ligands (most of which are benzene sulfonamide derivatives). This method utilizes porous gel beads that are functionalized with a common aryl sulfonamide ligand. The beads are incubated with BCA and allowed to reach an equilibrium state in which the majority of the immobilized ligands are bound to BCA. Since the beads are less dense than the protein, protein binding to the bead increases the overall density of the bead. This change in density can be monitored using MagLev. Transferring the beads to a solution containing no protein creates a situation where net protein efflux from the bead is thermodynamically favorable. The rate at which protein leaves the bead for the solution can be calculated from the rate at which the levitation height of the bead changes. If another small molecule ligand of BCA is dissolved in the solution, the rate of protein efflux is accelerated significantly. This paper develops a reaction-diffusion (RD) model to explain both this observation, and the physical-organic chemistry that underlies it. Using this model, we calculate the dissociation constants of several unlabeled ligands from BCA, using plots of levitation height versus time. Notably, although this method requires no electricity, and only a single piece of inexpensive equipment, it can measure accurately the binding of unlabeled proteins to small molecules over a wide range of dissociation constants (K(d) values within the range from ~10 nM to 100 μM are measured easily). Assays performed using this method generally can be completed within a relatively short time period (20 min-2 h). A deficiency of this system is that it is not, in its present form, applicable to proteins with molecular weight greater than approximately 65 kDa.