Multiplexed liquid arrays for simultaneous detection of simulants of biological warfare agents

Liquid array-based multiplexed immunoassays designed for rapid, sensitive, specific, and simultaneous detection of multiple simulants of biological warfare agents have been developed. In both blind and standard laboratory trials, we demonstrate the simultaneous detection of four simulant agents from a single sample. The challenge agents comprise broad classes of pathogens (virus, protein toxins, bacterial spores, vegetative cells). Assay performance of each analyte was optimized, and dose-response curves and the limits of detection (LODs) for individual analytes are presented. Assay performance, including dynamic range, sensitivity, and LODs for liquid arrays and enzyme-linked immunosorbant assay were compared and are shown to be similar. Maximum assay sensitivity is obtained in approximately 1 h, and good sensitivity is achieved in as little as 30 min. Although the sample matrixes are very complex, even for highly multiplexed assays the samples do not exhibit evidence of nonspecific binding, demonstrating that the assays also have high specificity.     

Single Quantum Dot Analysis Enables Multiplexed Point Mutation Detection by Gap Ligase Chain Reaction

Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap‐LCR), the high sensitivity of single‐molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant‐specific ligation products are generated by Gap‐LCR and subsequently captured by QDs to form DNA–QD nanocomplexes that are detected by single‐molecule spectroscopy (SMS) through multi‐color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation‐free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre‐amplification.     

Fluorescent resonance energy transfer based detection of biological contaminants through hybrid quantum dot-quencher interactions

A nanoscale sensor employing fluorescent resonance energy transfer interactions between fluorescent quantum dots (QDs) and organic quencher molecules can be used for the multiplexed detection of biological antigens in solution. Detection occurs when the antigens to be detected displace quencher-labelled inactivated (or dead) antigens of the same type attached to QD-antibody complexes through equilibrium reactions. This unquenches the QDs, allowing detection to take place through the observation of photoluminescence in solution or through the fluorescence imaging of unquenched QD complexes trapped on filter surfaces. Multiplexing can be accomplished by using several different sizes of QDs, with each size QD labelled with an antibody for a different antigen, providing the ability to detect several types of antigens or biological contaminants simultaneously in near real-time with high specificity and sensitivity.     

Intermolecular and intramolecular quencher based quantum dot nanoprobes for multiplexed detection of endonuclease activity and inhibition

DNA cleavage by endonucleases plays an important role in many biological events such as DNA replication, recombination, and repair and is used as a powerful tool in medicinal chemistry. However, conventional methods for assaying endonuclease activity and inhibition by gel electrophoresis and chromatography techniques are time-consuming, laborious, not sensitive, or costly. Herein, we combine the high specificity of DNA cleavage reactions with the benefits of quantum dots (QDs) and ultrahigh quenching abilities of inter- and intramolecular quenchers to develop highly sensitive and specific nanoprobes for multiplexed detection of endonucleases. The nanoprobe was prepared by conjugating two sets of DNA substrates carrying quenchers onto the surface of aminated QDs through direct assembly and DNA hybridization. With this new design, the background fluorescence was significantly suppressed by introducing inter- and intramolecular quenchers. When these nanoprobes are exposed to the targeted endonucleases, specific DNA cleavages occur and pieces of DNA fragments are released from the QD surface along with the quenchers, resulting in fluorescence recovery. The endonuclease activity was quantified by monitoring the change in the fluorescence intensity. The detection was accomplished with a single excitation light. Multiplexed detection was demonstrated by simultaneously assaying EcoRI and BamHI (as model analytes) using two different emissions of QDs. The limits of detection were 4.0 × 10(-4) U/mL for EcoRI and 8.0 × 10(-4) U/mL for BamHI, which were at least 100 times more sensitive than traditional gel electrophoresis and chromatography assays. Moreover, the potential application of the proposed method for screening endonuclease inhibitors has also been demonstrated. The assay protocol presented here proved to be simple, sensitive, effective, and easy to carry out.     

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.     

Rapid simultaneous ultrasensitive immunodetection of five bacterial toxins

Rapid ultrasensitive detection of gastrointestinal pathogens presents a great interest for medical diagnostics and epidemiologic services. Though conventional immunochemical and polymerase chain reaction (PCR)-based methods are sensitive enough for many applications, they usually require several hours for assay, whereas as sensitive but more rapid methods are needed in many practical cases. Here, we report a new microarray-based analytical technique for simultaneous detection of five bacterial toxins: the cholera toxin, the E. coli heat-labile toxin, and three S. aureus toxins (the enterotoxins A and B and the toxic shock syndrome toxin). The assay involves three major steps: electrophoretic collection of toxins on an antibody microarray, labeling of captured antigens with secondary biotinylated antibodies, and detection of biotin labels by scanning the microarray surface with streptavidin-coated magnetic beads in a shear-flow. All the stages are performed in a single flow cell allowing application of electric and magnetic fields as well as optical detection of microarray-bound beads. Replacement of diffusion with a forced transport at all the recognition steps allows one to dramatically decrease both the limit of detection (LOD) and the assay time. We demonstrate here that application of this "active" assay technique to the detection of bacterial toxins in water samples from natural sources and in food samples (milk and meat extracts) allowed one to perform the assay in less than 10 min and to decrease the LOD to 0.1-1 pg/mL for water and to 1 pg/mL for food samples.     

Amplified multiplexed analysis of DNA by the exonuclease III-catalyzed regeneration of the target DNA in the presence of functionalized semiconductor quantum dots

Quantum dots (QDs) functionalized with a black-hole quencher are used as optical tracer for the detection of DNA using exonuclease as a biocatalyst. The binding of the target DNA or of a target/open hairpin complex to the functionalized QDs leads to the exonuclease-stimulated recycling of the target DNA or the target/hairpin complex. This results in the triggering of the luminescence of the QDs that provides a readout signal for the amplified sensing process. By using different-sized QDs, the multiplexed detection of DNAs is demonstrated.     

NIR‐Emitting Quantum Dot‐Encoded Microbeads through Membrane Emulsification for Multiplexed Immunoassays

NIR‐emitting CdSeTe/CdS/ZnS core/shell/shell QD‐encoded microbeads are combined with common flow cytometry with one laser for multiplexed detection of hepatitis B virus (HBV). A facile one‐pot synthetic route is developed to prepare CdSeTe/CdS/ZnS core/shell/shell QDs with high photoluminescence quantum yield and excellent stability in liquid paraffin, and a Shirasu porous glass (SPG) membrane emulsification technique is applied to incorporate the QDs into polystyrene–maleic anhydride (PSMA) microbeads to obtain highly fluorescent QD‐encoded microbeads. The relatively wide NIR photoluminescence full width half maximum of the CdSeTe/CdS/ZnS QDs is used to develop a ‘single wavelength’ encoding method to obtain different optical codes by changing the wavelengh and emission intensity of the QDs incorporated into the microbeads. Moreover, a detection platform combining NIR‐emitting CdSeTe/CdS/ZnS QD‐encoded microbeads and Beckman Coulter FC 500 flow cytometry with one laser of 488 nm is successfully used to conduct a 2‐plex hybridization assay for hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), and a 3‐plex hybridization assay for hepatitis B surface antibody (HBsAb), hepatitis B e antibody (HBeAb), and hepatitis B core antibody (HBcAb), which suggests the promising application of NIR QD‐encoded microbeads for multiplex immunoassays.     

Development of xMAP Assay for Detection of Six Protein Toxins

xMAP technology was used for simultaneous identification of six protein toxins (staphylococcal enterotoxins A and B, cholera toxin, ricin, botulinum toxin A, and heat labile toxin of E. coli). Monoclonal antibody-conjugated xMAP microspheres and biotinilated monoclonal antibodies were used to detect the toxins in a sandwich immunoassay format. The detection limits were found to be 0.01 ng/mL for staphylococcal enterotoxin A, cholera toxin, botulinum toxin A, and ricin in model buffer (PBS-BSA) and 0.1 ng/mL for staphylococcal enterotoxin B and LT. In a complex matrix, such as cow milk, the limits of detection for staphylococcal enterotoxins A and B, cholera toxin, botulinum toxin A, and ricin increased 2- to 5-fold, while for LT the detection limit increased 30-fold in comparison with the same analysis in PBS-BSA. In the both PBS-BSA and milk samples, the xMAP test system was 3-200 times (depending on the toxin) more sensitive than ELISA systems with the same pairs of monoclonal antibodies used. The time required for a simultaneous analysis of six toxins using the xMAP system did not exceed the time required for ELISA to analyze one toxin. In the future, the assay may be used in clinical diagnostics and for food and environmental monitoring.     

Minimizing nonspecific cellular binding of quantum dots with hydroxyl-derivatized surface coatings

Quantum-dot (QD) nanocrystals are promising fluorescent probes for multiplexed staining assays in biological applications. However, nonspecific QD binding to cellular membranes and proteins remains a limiting factor in detection sensitivity and specificity. Here we report a new class of hydroxyl (-OH)-coated QDs for minimizing nonspecific cellular binding and for overcoming the bulky size problems encountered with previous surface coatings. The hydroxylated QDs are prepared from carboxylated (-COOH) dots via a hydroxylation and cross-linking process. With a compact hydrodynamic size of 13-14 nm (diameter), they are highly fluorescent (>60% quantum yields) and stable under both basic and acidic conditions. By using human cancer cells, we have evaluated their superior nonspecific binding properties against that of carboxylated, protein-coated, and poly(ethylene glycol) (PEG)-coated QDs. Quantitative cellular staining data indicate that the hydroxylated QDs result in a dramatic 140-fold reduction in nonspecific binding relative to that of carboxylated dots and a still significant 10-20-fold reduction relative to that of PEG- and protein-coated dots.     

Conjugation of luminescent quantum dots with antibodies using an engineered adaptor protein to provide new reagents for fluoroimmunoassays

We describe the preparation and characterization of bioinorganic conjugates made with highly luminescent semiconductor CdSe-ZnS core-shell quantum dots (QDs) and antibodies for use in fluoroimmunoassays. The conjugation strategy employs an engineered molecular adaptor protein, attached to the QDs via electrostatic/hydrophobic self-assembly, to link the inorganic fluorophore with antibodies. In this method, the number of antibodies conjugated to a single QD can be varied. In addition, we have developed a simple purification strategy based on mixed-composition conjugates of the molecular adaptor and a second two-domain protein that allows the use of affinity chromatography. QD-antibody conjugates were successfully used in fluoroimmunoassays for detection of both a protein toxin (staphylococcal enterotoxin B) and a small molecule (2,4,6-trinitrotoluene).     

Quantum dot probes for monitoring dynamic cellular response: reporters of T cell activation

Antibody-conjugated quantum dots (QDs) have been used to map the expression dynamics of the cytokine receptor interleukin-2 receptor-alpha (IL-2Ralpha) following Jurkat T cell activation. Maximal receptor expression was observed 48 h after activation, followed by a sharp decrease consistent with IL-2R internalization subsequent to IL-2 engagement. Verification of T cell activation and specificity of QD labeling were demonstrated using fluorescence microscopy, ELISA, and FACS analyses. These antibody conjugates provide a versatile means to rapidly determine cell state and interrogate membrane associated proteins involved in cell signaling pathways. Ultimately, incorporation with a microfluidic platform capable of simultaneously monitoring several cell signaling pathways will aid in toxin detection and discrimination     

From the mouse to the mass spectrometer: detection and differentiation of the endoproteinase activities of botulinum neurotoxins A-G by mass spectrometry

We have developed an assay (Endopep-MS) that detects the specific endoproteinase activities of all seven BoNT types by mass spectrometry (MS). Each BoNT type cleaves a unique site on proteins involved in neuronal transmission. Target peptide substrates based on these proteins identify a BoNT type by its enzymatic action on the substrate and the production of two peptide products, which are then detected by matrix-assisted laser desorption/ionization time-of-flight MS or liquid chromatography electrospray ionization MS/MS. We showed the ability to detect all seven toxin types in a multiplexed assay format. The detection limits achieved range from 0.039 to 0.625 mouse LD(50)/mL for toxin types A, B, E, and F in a buffer system. The Endopep-MS assay is the first to differentiate all seven BoNT types, is sensitive, specific, and has the potential to quantify toxin activity.     

Comparison and optimization of multiplexed quantum dot-based immunohistofluorescence

Nanoparticle quantum dots (QDs) are ideal materials for multiplexed biomarker detection, localization, and quantification. Both direct and indirect methods are available for QD-based immunohistofluorescence (QD-IHF) staining; the direct method, however, has been considered laborious and costly. In this study, we optimized and compared the indirect QD-IHF single staining procedure using QD-secondary antibody conjugates and QD-streptavidin conjugates. Problems associated with sequential multiplex staining were identified quantitatively. A method using a QD cocktail solution was developed allowing simultaneous staining with three antibodies against E-cadherin, epidermal growth factor receptor and β-catenin in formalin-fixed and paraffin-embedded (FFPE) tissues. The expression of each biomarker was quantified by using the cocktail and the sequential methods. Comparison of the two methods demonstrated that the cocktail method provided more consistent and stable QD signals for each multiplexed biomarker than the sequential method, and provides a convenient tool for multiplexing biomarkers in both research and clinical applications.      

Capillary electrophoresis method for the characterization and separation of CdSe quantum dots

This paper presents a simple and rapid methodology to separate and characterize free CdSe quantum dots (QDs) in aqueous medium by capillary electrophoresis (CE). First, we describe a controlled derivatization procedure to obtain water-soluble QDs through noncovalent interactions. This derivatization methodology was based on the formation of a complex between the QDs and several types of surfactants to enhance the hydrophilicity and stability of the CdSe QDs. The surfactants used to achieve the surface functionalization were trioctylphosphine oxide/trioctylphosphine (TOPO/TOP) and sodium dodecyl sulfate (SDS). Different CdSe QDs core sizes were synthesized as function of the nanocrystals growing time and then subjected to controlled coating. These free QDs were separated by capillary zone electrophoresis (CZE) based on the differences in the charge-to-mass ratio of the QDs-TOPO/TOP-SDS complexes, and the detection was carried out with UV-vis and laser-induced fluorescence (LIF) techniques obtaining detection limits 5 times lower with CE-LIF. Under the optimal working conditions, four different-sized QDs were successfully separated whose average sizes were 3.1, 3.6, 4.3, and 4.9 nm, and the size distribution was less than 7% for all of them [calculated from the full width at half-maximum (fwhm) of the fluorescence spectra and confirmed by high-resolution transmission electron microscopy (HTEM)]. Therefore, we were able to separate QDs that differ in only 0.5 nm in diameter and 19 nm in fluorescence emission maximum. This corresponds to the better resolution achieved in the analysis of these kinds of nanoparticles. Finally, a correlation between the migration times plus or minus peak width and the core sizes plus or minus size distribution was established.     

Coherence-multiplexed fiber-optic sensor systems for measurements of pressure and temperature changes

A digital demodulation method for read-out of phase changes induced in coherence-multiplexed sensors based on highly birefringent fibers is described. The method employs the fringe counting principle and enables registration of the phase shifts simultaneously induced in two multiplexed sensors with a maximum frequency of 10 kHz and resolution of 1/4 of the interference fringe. The performance of three multiplexed systems interrogated using the proposed detection method is investigated. The first system is composed of two serial multiplexed sensors serving for measurements of pressure and temperature changes in the same location, while the two other systems are composed of two parallel or serial multiplexed temperature-compensated sensors serving for pressure measurements at different locations.     

TNT detection using multiplexed liquid array displacement immunoassays

The presence of trace contamination of soil and groundwater with explosives is an ongoing concern, for which improved methods are required to facilitate their detection and quantification. This is true both for the monitoring of remediation and for site characterization. Immunosensors have been found effective for solution-phase detection of environmental contaminants. Our work utilized the Luminex100 (flow cytometer) to detect TNT in a multiplexed displacement immunoassay format. The Luminex100 can perform a multiplexed assay by discriminating between up to 100 different bead sets. We used this capability to evaluate four different TNT monoclonal antibodies, two recombinant TNT antibodies, and a control antibody simultaneously for the rapid detection of TNT and other nitroaromatics. TNT could be detected at 0.1 ppb and quantified over the range of 1.0 ppb to 10 ppm. In addition, the assay was shown to be effective in various matrixes such as lake water, seawater, and acetone extracts of soil. Seawater required dilution with two parts buffer to avoid loss of microspheres, while the acetone extracts were diluted 100-fold or more to minimize solvent affects.     

Multiplexed immunohistochemical detection of tumor markers in breast cancer tissue using laser ablation inductively coupled plasma mass spectrometry

We optimized multiplexed immunohistochemistry (IHC) on breast cancer tissue. Up to 20 tumor markers are routinely evaluated for one patient, and thus, a common analysis results in a series of time consuming staining procedures. As an alternative, we used lanthanides for labeling of primary antibodies, which are applied in IHC. Laser ablation (LA) ICPMS was elaborated as a detection tool for multiplexed IHC of tissue sections. In this study, we optimized sample preparation steps and LA ICPMS parameters to achieve a sufficient signal-to-background ratio. The results prove the high selectivity of applied antibodies, which was sustained after labeling. Up to three tumor markers (Her 2, CK 7, and MUC 1) were detected simultaneously in a single multiplex analysis of a 5 μm thin breast cancer tissue at a laser spot size of 200 μm. Furthermore, the LA ICPMS results indicate a significantly higher expression level of MUC 1 compared to Her 2 and CK 7, which was not obvious from the conventionally stained tissue sections.     

Multi-wavelength intermittent photoluminescence of single CdSe quantum dots

A single chromophore detection using video-microscopy is one of the latest methodologies to reveal unique characteristics, which could not be obtained from ensemble measurements. Among many kinds of subjects, dynamic optical properties observed in colloidal semiconductor nanoparticles are attractive and important not only for the basis of photo-physics but also for application studies, e.g. biological labeling, electronic devices. In this study, fluorescence video-microscopy was performed on cadmium selenide (CdSe) quantum dots (QDs) spin-coated on a glass substrate. From single CdSe QDs detection, emissions at wavelengths separated over 60 nm were observed for the first time. This spectral feature was attributed to the existence of double-emissive relaxation processes in CdSe QDs. Photoluminescence intermittency was also observed both from relaxation processes. Fluorescence video-microscopy, which was advanced in biology, can be applicable for the real-time monitoring of dynamic properties in semiconductor photo-physics.