Fluorescence single-molecule counting assays for protein quantification using epi-fluorescence microscopy with quantum dots labeling

A single-molecule counting approach for quantifying the antibody affixed to a surface using quantum dots and epi-fluorescence microscopy is presented. Modifying the glass substrates with carboxyl groups provides a hydrophilic surface that reacts with amine groups of an antibody to allow covalent immobilization of the antibody. Nonspecific adsorption of single molecules on the modified surfaces was first investigated. Then, quantum dots were employed to form complexes with surface-immobilized antibody molecules and used as fluorescent probes for single-molecule imaging. Epi-fluorescence microscopy was chosen as the tool for single-molecule fluorescence detection here. The generated fluorescence signals were taken by an electron multiplying charge-coupled device and were found to be proportional to the sample concentrations. Under optimal conditions, a linear response range of 5.0 × 10⁻¹⁴-3.0 × 10⁻¹² mol L⁻¹ was obtained between the number of single molecules and sample concentration via a single-molecule counting approach.     

Quantitative detection of antibody based on single-molecule counting by total internal reflection fluorescence microscopy with quantum dot labeling

We presented a sensitive method to quantify antibody based on single-molecule counting by total internal reflection fluorescence microscopy with quantum dot labeling. In this method, the biotinylated monoclonal anti-human IgG molecules were immobilized on the silanized glass substrate surface. By the strong biotin-streptavidin affinity, streptavidin-coated quantum dots were labeled to the target molecules as fluorescent probe. Then, images of fluorescent spots in the evanescent wave field were obtained by a high-sensitivity electron multiplying charge-coupled device. Finally, the number of fluorescent spots corresponding to single molecules in the subframe images was counted, one by one. The linear range of 8.0 × 10⁻¹⁴ to 5.0 × 10⁻¹² mol L⁻¹ was obtained between the number of single molecules and the sample concentration.     

Quantitative analysis of human serum leptin using a nanoarray protein chip based on single-molecule sandwich immunoassay

We report a method for the quantitative analysis of human serum leptin, which is a protein hormone associated with obesity, using a nanoarray protein chip based on a single-molecule sandwich immunoassay. The nanoarray patterning of a biotin-probe with a spot diameter of 150 nm on a self-assembled monolayer functionalized by MPTMS on a glass substrate was successfully accomplished using atomic force microscopy (AFM)-based dip-pen nanolithography (DPN). Unlabeled leptin protein molecules in human serum were detected based on the sandwich fluorescence immunoassay by total internal reflection fluorescence microscopy (TIRFM). The linear regression equation for leptin in the range of 100 zM-400 aM was determined to be y = 456.35x + 80,382 (R = 0.9901). The accuracy and sensitivity of the chip assay were clinically validated by comparing the leptin level in adult serum obtained by this method with those measured using the enzyme-linked immunosorbent assay (ELISA) performed with the same leptin standards and serum samples. In contrast to conventional ELISA techniques, the proposed chip methodology exhibited the advantages of ultra-sensitivity, a smaller sample volume and faster analysis time.     

Competitive magnetic immunoassay for protein detection in thin channels

Functional magnetic nanoparticles are prepared and characterized for protein detection in a magnetic separation channel. This detection method is based on a competitive immunoassay of magnetic separation in thin channels using functional magnetic nanoparticles. We used protein A–IgG complex to demonstrate the feasibility. Free IgG and fixed number of IgG-labeled microparticles were used to compete for limited sites of protein A on the magnetic nanoparticles. Several experimental parameters were investigated for protein detection. The deposited percentages of IgG-labeled microparticles at various concentrations of free IgG were determined and used as a reference plot. The IgG concentration in a sample was deduced and determined based on the reference plot using the deposited percentage of IgG-labeled microparticles from the sample. The linear range of IgG detection was from 5.0 × 10⁻⁸ to 1.0 × 10⁻¹¹ M. The detection limit was 3.69 × 10⁻¹² M. The running time was less than 10 min. Selectivities were higher than 92% and the relative errors were less than 7%. The IgG concentration of serum was determined to be 3.6 mg ml⁻¹. This measurement differed by 8.3% from the ELISA measurement. The recoveries of IgG spiked in serum were found to be higher than 94%. This method can provide simple, fast, and selective analysis for protein detection and other immunoassay-related applications.     

Preparation and characterization of a polyclonal antibody from rabbit for detection of trinitrotoluene by a surface plasmon resonance biosensor

A polyclonal antibody against trinitrophenyl (TNP) derivatives was raised in rabbit, and the antibody was applied to detection of trinitrotoluene (TNT) using a surface plasmon resonance (SPR) biosensor. TNP-keyhole limpet hemocyanine (TNP-KLH) conjugate was injected into a rabbit, and a polyclonal anti-TNP antibody was realized after purification of the sera using protein G. Aspects of the anti-TNP antibody against various nitroaromatic compounds, such as cross-reactivities and affinities, were characterized. The temperature dependence of the affinity between the anti-TNP antibody and TNT was also evaluated. The quantification of TNT was based on the principle of indirect competitive immunoassay, in which the immunoreaction between the TNP-β-alanine-ovalbumin (TNP-β-ala-OVA) and anti-TNP antibody was inhibited in the presence of free TNT in solution. TNP-β-ala-OVA was immobilized to the dextran matrix on the Au surface by amine coupling. The addition of a mixture of free TNT to the anti-TNP antibody was found to decrease the incidence angle shift due to the inhibitory effect of TNT. The immunoassay exhibited excellent sensitivity for the detection of TNT in the concentration range of 3 × 10⁻¹¹ to 3 × 10⁻⁷ g/ml. To increase the sensitivity of the sensor, anti-rabbit IgG antibody was used. After flowing the mixture of free TNT and anti-TNP antibody, anti-rabbit IgG antibody was injected, and the incidence angle shift was measured. Amplification of the signal was observed and the detection limit was improved to 1 × 10⁻¹¹ g/ml.     

A novel immunoassay based on the dissociation of immunocomplex and fluorescence quenching by gold nanoparticles

This study reports a novel, simple and sensitive immunoassay using fluorescence quenching caused by gold nanoparticles coated with antibody. The method is based on a non-competitive heterogeneous immunoassay of human IgG conducted by the typical procedure of sandwich immunocomplex formation. Goat anti-human IgG was first adsorbed on polystyrene microwells, and human IgG analyte was captured by the primary antibody and then sandwiched by antibody labeled with gold nanoparticles. The sandwich-type immunocomplex was subsequently dissociated by the mixed solution of sodium hydroxide and trisodium citrate, the solution obtained, which contains gold nanoparticles coated with antibody, was used to quench fluorescence. The fluorescence intensity of fluorescein at 517 nm was inversely proportional to the logarithm of the concentration of human IgG in the dynamic range of 10-5000 ng mL⁻¹ with a detection limit of 4.7 ng mL⁻¹. The electrochemical experiments and the UV-vis measurements were applied to demonstrate whether the immunoglod was dissociated completely and whether the gold nanoparticles aggregated after being dissociated, respectively. The proposed system can be extended to detect target molecules such as other kinds of antigen and DNA strands, and has broad potential applications in disease diagnosis.     

Study of binding and denaturation dynamics of IgG and anti-IgG using dual color fluorescence correlation spectroscopy

In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules using fluorescence auto- and cross-correlation spectroscopy to investigate their diffusion characteristics, binding kinetics, and the effect of small organic molecule, urea on their binding. Through our analysis, we found that the diffusion coefficient for IgG and Fab fragment of anti-IgG molecules were 37 ± 2 μm² s⁻¹ and 56 ± 2 μm² s⁻¹, respectively. From the binding kinetics study, the respective forward (k_a) and backward (k_d) reaction rates were (5.25 ± 0.25) × 10⁶ M⁻¹ s⁻¹ and 0.08 ± 0.005 s⁻¹, respectively and the corresponding dissociation binding constant (K_D) was 15 ± 2 nM. We also found that urea inhibits the binding of these molecules at 4 M concentration due to denaturation.     

IgG adsorption on a new protein A adsorbent based on macroporous hydrophilic polymers. I. Adsorption equilibrium and kinetics

Experimental determination and modeling of IgG binding on a new protein A adsorbent based on a macroporous resin were performed. The new adsorbent consists of polymeric beads based on hydrophilic acrylamido and vinyl monomers with a pore structure optimized to allow favorable interactions of IgG with recombinant protein A coupled to the resin. The particles have average diameter of 57 μm and a narrow particle size distribution. The IgG adsorption equilibrium capacity is 46 mg/cm³ and the effective pore diffusivity determined from pulse response experiments for non-binding conditions is 8.0 × 10⁻⁸ cm²/s. The IgG adsorption kinetics can be described with the same effective diffusivity by taking into account a heterogeneous binding mechanism with fast binding sites, for which adsorption is completely diffusion controlled, and slow binding sites for which adsorption is controlled by the binding kinetics. As a result of this mechanism, the breakthrough curve exhibits a tailing behavior, which appears to be associated with the slow binding sites. A detailed rate model taking into account intraparticle diffusion and binding kinetics is developed and is found capable of predicting both batch adsorption and breakthrough behavior over an ample range of experimental conditions. The corresponding effective diffusivity is independent of protein concentration in solution over the range 0.2–2 mg/cm³ and of protein binding as a result of the large pore size of the support matrix. Overall, the small particle size and low diffusional hindrance allow capture of IgG with short residence times while attaining substantial dynamic binding capacities.     

Detection of single-molecule DNA hybridization by using dual-color total internal reflection fluorescence microscopy

We examined the use of prism-type simultaneous dual-color total internal reflection fluorescence microscopy (TIRFM) to probe DNA molecules at the single-molecule level. The system allowed the direct detection of the complementary interactions between single-stranded probe DNA molecules (16-mer) and various lengths of single-stranded target DNA molecules (16-mer and 55-mer) that had been labeled with different fluorescent dyes (Cy3, Cy5, and fluorescein). The polymer-modified glass substrate and the extent of DNA probe immobilization were easily characterized either with standard TIRFM or with atomic force microscopy. However, only dual-color TIRFM could provide unambiguous images of individual single-stranded target DNA molecules hybridized with the correct sequence in the range of fM–aM. Succinic anhydride showed low RMS roughness and was found to be an optimal blocking reagent against non-specific adsorption, with an efficiency of 92%. This study provides a benchmark for directly monitoring the interactions and the detection of co-localization of two different DNA molecules and can be applied to the development of a nanoarray biochip at the single-molecule level.     

Radiolabeling of HER2-specific Affibody molecule with F-18

The presence of human epidermal growth factor type 2 (HER2) on 20-30% of human breast cancer is a prognostic indicator of more rapid disease progression and a therapeutic indicator for anti-HER2 monoclonal antibodies. Because the literature has demonstrated some discordance between primary and metastatic tumors in the same patient for expression of the HER2 marker, we set out to develop an imaging agent that could be used to assess the marker concentration in vivo in an individual patient. The pharmaceutical company Affibody^® AB has optimized the specificity of Affibody^® molecules for HER2. Two Affibody^® molecules, a 7 kDa and an 8 kDa protein, were designed with a single carboxy terminal cysteine in order to provide a specific location for the purposes of labeling for various types of imaging. We have prepared [¹⁸F]FBEM utilizing a coupling reaction between [¹⁸F]fluorobenzoic acid and aminoethylmaleimide. We then optimized the conjugation of this radiolabeled maleimide to the free sulfhydryl of cysteine by incubating at pH 7.4 in phosphate buffered saline containing 0.1% sodium ascorbate. An overall uncorrected yield of radiolabeled Affibody^® molecule of approximately 10% from [¹⁸F]fluoride was achieved in a 2 h synthesis. These conjugated Affibody^® molecules were obtained with a specific activity of 2.51 ± 0.92 MBq/μg. Characterization of the product by HPLC-MS supported the conjugation of [¹⁸F]FBEM with the Affibody^® molecule. The radiolabeled Affibody^® molecule retained its binding specificity as demonstrated by successful imaging of xenografts expressing HER2.     

Spectral imaging of single molecules by transmission grating-based epi-fluorescence microscopy

A spectral imaging method of single protein molecules labeled with a single fluorophore is presented. The method is based on a transmission grating and a routine fluorescence microscope. The bovine serum alubmin (BSA) and antiBSA molecules labeled with Alexa Fluor 488 and Alexa Fluor 594, respectively, are used as the model proteins. The fluorescence of single molecules is dispersed into zeroth-order spectrum and first-order spectrum by the transmission grating. Results show that the fluorescence emission spectrum of single molecule converted from the first-order spectral imaging is in good agreement with the bulk fluorescence spectrum. The spectral resolution of 2.4 nm/pixel is obtained, which is sufficient for identifying the molecular species in a multicomponent system.     

Engineering properties of a camelid antibody affinity sorbent for Immunoglobulin G purification

An IgG-specific camelid antibody matrix (BAC, Naarden, The Netherlands), developed from an immune phage display library, was characterized regarding engineering properties including mass transfer characteristics. Uptake kinetics and equilibrium binding capacity were determined by a finite bath method. Adsorption kinetic parameters were also determined using a real time biosensor. Slightly different properties to conventional Staphylococcal protein A affinity media were shown; especially a 2–2.5 times lower maximal binding capacity with a value of 26 mg/ml polyclonal IgG was obtained. Mass transfer could be described by using a film and pore diffusion model (D_e = 5 × 10⁻⁸ cm²/s). Determined engineering parameters were used to predict breakthrough behaviour in column mode considering film and pore resistances. The dynamic binding capacity at 10% breakthrough did not change when residence time was at least 6 min.     

A composite thin film optical sensor for dissolved oxygen in contaminated aqueous environments

A robust optical composite thin film dissolved oxygen sensor was fabricated by ionically trapping the dye ruthenium(II) tris(4,7-diphenyl-1,10-phenanthroline) dichloride in a blended fluoropolymer matrix consisting of Nafion^® and Aflas^®. Strong phosphorescence, which was strongly quenched by dissolved oxygen (DO), was observed when the sensor was immersed in water. The sensor was robust, optically transparent, with good mechanical properties. Fast response, of a few seconds, coupled with sensitivity of about 0.1 mg L⁻¹ (DO) over the range 0-30 mg L⁻¹ and resistance to leaching, were also exhibited by this system. The Stern-Volmer (SV) plot exhibited slight downward turning at all oxygen concentrations. A linear plot was obtained when the SV equation was modified to account for the varying sensitivity of dye molecules in the matrix to the quencher. Good long term stability was observed.     

Understanding and improving direct UV detection of monosaccharides and disaccharides in free solution capillary electrophoresis

Direct UV detection of carbohydrates in free solution capillary electrophoresis at 270 nm is made possible by a photo-oxidation reaction. Glucose, rhamnose and xylose were shown to have unique UV absorption spectra hypothesizing different UV absorbing intermediates for their respective photo-oxidation. NMR spectroscopy of the photo-oxidation end products proved they consisted of carboxylates and not malondialdehyde as previously theorized and that oxygen thus plays a key role in the photo-oxidation pathway. Adding the photo-initiator Irgacure^® 2959 in the background electrolyte increased sensitivity by 40% at an optimum concentration of 1 × 10⁻⁴ mM and 1 × 10⁻⁸ mM for conventional 50 μm i.d. capillaries and for the corresponding extended light path capillaries, respectively.     

Double electrochemical covalent coupling method based on click chemistry and diazonium chemistry for the fabrication of sensitive amperometric immunosensor

A double electrochemical covalent coupling method based on click chemistry and diazonium chemistry for the fabrication of sensitive amperometric immunosensor was developed. As a proof-of-concept, a designed alkyne functionalized human IgG was used as a capture antibody and a HRP-labeled rabbit anti-goat IgG was used as signal antibody for the determination of the anti-human IgG using the sandwich model. The immunosensor was fabricated by electrochemically grafting a phenylazide on the surface of a glassy carbon electrode, and then, by coupling the alkyne functionalized human IgG with the phenylazide group through an electro-click chemistry in the presence of Cu(II). The amperometric measurement for the determination of the anti-human IgG was performed after the fabricated immunosensor was incubated with the target anti-human IgG and then with the HRP-labeled anti-goat IgG at −0.25 V in 0.10 M PBS (pH 7.0) containing 0.1 mM hydroquinone and 2.0 mM H₂O₂. The results showed that the increased current was linear with the logarithm of the concentration of the anti-human IgG in the range from 1.0 × 10⁻¹⁰ g mL⁻¹ to 1.0 × 10⁻⁸ g mL⁻¹ with a detection limit of 3 × 10⁻¹¹ g mL⁻¹. Furthermore, the feasibility of the double electrochemical covalent coupling method proposed in this work for fabricating the amperometric immunosensor array was explored. This work demonstrates that the double electrochemical covalent coupling method is a promising approach for the fabrication of the immunosensor and immunosensor array.     

Local factor analysis of rank-deficient reaction systems

A variety of biochemical and physical properties of proteins are regulated by calcium ion (Ca²⁺) binding with varying specificity and affinity. Calcium ion binding can adjust the phospholipid-protein interactions through changing the properties of phospholipid membrane. As an attractive detection technique, whole column imaging detection (WCID) coupled to capillary isoelectric focusing (cIEF) displays several advantages in the study of protein-ligand and protein-protein interactions, including fast and high-efficient separation, high resolution, and simple operation. In this study, a cIEF-WCID method was evaluated for studying the effect of Ca²⁺ binding on protein structural changes and phospholipid-protein interactions. Four proteins with different isoelectirc point (pI), trypsin inhibitor (pI = 4.5), β-lactoglobulin B (pI = 5.2), phosphorylase b (pI = 6.3), and trypsinogen (pI = 9.3), were used for this purpose. The targeted proteins exhibited altered cIEF profiles due to protein conformation changes resulting from the Ca²⁺ binding. The study showed that Ca²⁺ can be buried in the phospholipid membrane, modify the membrane property, and change the phospholipid-protein interactions. The utility of the cIEF-WCID technique demonstrates that the calcium binding plays a crucial role in the protein structural changes and the phospholipid-protein interactions, and elucidates the possible mechanisms involved in calcium-protein binding and calcium bound phospholipid-protein interactions.     

Comparison of an antibody and its recombinant derivative for the detection of the small molecule explosive 2,4,6-trinitrotoluene

Antibodies are commonly used as recognition elements in immunoassays because of their high specificity and affinity, and have seen extensive use in competitive assays for the detection of small molecules. However, these complex molecules require production either in animals or by mammalian cell cultures, and are not easily tailored through genetic manipulation. Single chain antibodies (scFv), recombinantly expressed molecules consisting of only the antibody's binding region joined via a linking peptide, can provide an alternative to intact antibodies. We describe the characterization of a new monoclonal antibody (mAb), 2G5B5, able to detect the small molecule explosive 2,4,6-trinitrotoluene (TNT) and the scFv derived from its variable regions. The mAb and scFv were tested by surface plasmon resonance to determine their affinity for an immobilized TNT surrogate; dissociation constants were determined to be 1.5 × 10⁻¹³ M and 4.8 × 10⁻¹⁰ M respectively. Circular dichroism was used to determine their melting temperatures. The mAb is more stable melting at ∼75 °C while the scFv melts at ∼65 °C. The recognition elements were incorporated into a competitive assay format using a bead-based multiplexing platform to examine their sensitivity and specificity. The scFv was able to detect TNT ∼10-fold more sensitively than the mAb in this assay format, allowing detection of TNT concentrations down to at least 1 μg L⁻¹. The 2G5B gave similar detection limits to a commercial anti-TNT mAb, but was less specific, recognizing 1,3,5-trinitrobenzene (TNB) equally well as TNT.     

A novel electrochemical sensing strategy for rapid and ultrasensitive detection of Salmonella by rolling circle amplification and DNA–AuNPs probe

A novel electrochemical sensing strategy was developed for ultrasensitive and rapid detection of Salmonella by combining the rolling circle amplification with DNA–AuNPs probe. The target DNA could be specifically captured by probe 1 on the sensing interface. Then the circularization mixture was added to form a typical sandwich structure. In the presence of dNTPs and phi29 DNA polymerase, the RCA was initiated to produce micrometer-long single-strand DNA. Finally, the detection probe (DNA–AuNPs) could recognize RCA product to produce enzymatic electrochemical signal. Under optimal conditions, the calibration curve of synthetic target DNA had good linearity from 10 aM to 10 pM with a detection limit of 6.76 aM (S/N = 3). The developed method had been successfully applied to detect Salmonella as low as 6 CFU mL⁻¹ in real milk sample. This proposed strategy showed great potential for clinical diagnosis, food safety and environmental monitoring.     

High performance protein microarrays based on glycidyl methacrylate-modified polyethylene terephthalate plastic substrate

There is a great challenge to immobilize high density of probe molecules for high performance protein microarrays, and this is achieved in this work by using polyethylene terephthalate (PET) plastic substrate onto which glycidyl methacrylate (GMA) photopolymer is grafted under mild conditions to introduce high density of epoxy groups for covalent immobilization of proteins. The poly(GMA)-grafted PET (PGMA-PET) surface was characterized with atomic force microscope (AFM) and attenuated total reflectance Fourier transform infra-red (ATR-FTIR) spectroscopy. For high density of protein immobilization and good quality of microspots, experiments were conducted to optimize the printing buffer, and an optimal buffer was found out to be PBS with 10% glycerol + 0.003% triton X-100. According to the studies of loading capacity and immobilization kinetics, the optimal protein probe concentration and incubation time for the efficient immobilization are 200 μg mL⁻¹ and 8 h, respectively. The performance of the PGMA-PET-based protein microarrays is evaluated with sandwich immunoassay using rat IgG and anti-rat IgG as model proteins, demonstrating a limit of detection (LOD) of 10 pg mL⁻¹ and a dynamic range of five orders of magnitude which are better than or very comparable with the reported or commercially available immunoassays, while providing a high-throughput approach. The work renders a simple and economic method to manufacture high performance protein microarrays and is expected to have great potentials in broad applications related to clinic diagnosis, drug discovery and proteomic research.     

Organic-inorganic matrix for electrochemical immunoassay: Detection of human IgG based on ZnO/chitosan composite

A new strategy to construct amperometric immunosensor for human IgG assay based on ZnO/chitosan composite as sensing platform has been described. This material, which combined the advantages of inorganic species, ZnO and organic polymer, chitosan, can maintain biological activity well. A sequential sandwich immunoassay format was performed on the ZnO/chitosan composite supported by glass carbon electrode (GCE) using goat-anti-human IgG antibody (IgG Ab) and human IgG as a model system. Amperometry was used to determine the amount of horse-radish peroxidase (HRP) fixed on the sensor surface, which was related to the content of the desired human IgG. Assay conditions that were optimized included the amount of labeled antibody, the incubation time and temperature, the pH of the substrate solution, etc. Using hydroquinone as a mediator, amperometric detection at −150 mV (versus SCE) resulted in a detection range 2.5-500 ng mL⁻¹, with a detection limit of 1.2 ng mL⁻¹. The simple manipulations of the construction of ZnO/chitosan composite, as well as low-cost and broad linear range, are the main features of the proposed immunosensing method.