Protein microarrays with carbon nanotubes as multicolor Raman labels

The current sensitivity of standard fluorescence-based protein detection limits the use of protein arrays in research and clinical diagnosis. Here, we use functionalized, macromolecular single-walled carbon nanotubes (SWNTs) as multicolor Raman labels for highly sensitive, multiplexed protein detection in an arrayed format. Unlike fluorescence methods, Raman detection benefits from the sharp scattering peaks of SWNTs with minimal background interference, affording a high signal-to-noise ratio needed for ultra-sensitive detection. When combined with surface-enhanced Raman scattering substrates, the strong Raman intensity of SWNT tags affords protein detection sensitivity in sandwich assays down to 1 fM--a three-order-of-magnitude improvement over most reports of fluorescence-based detection. We use SWNT Raman tags to detect human autoantibodies against proteinase 3, a biomarker for the autoimmune disease Wegener's granulomatosis, diluted up to 10(7)-fold in 1% human serum. SWNT Raman tags are not subject to photobleaching or quenching. By conjugating different antibodies to pure (12)C and (13)C SWNT isotopes, we demonstrate multiplexed two-color SWNT Raman-based protein detection.     

Ag-Cu Nanoparticles Encaptured by Graphene with Magnetron Sputtering and CVD for Surface-Enhanced Raman Scattering

An efficient surface-enhanced Raman scattering (SERS) substrate has been developed based on Ag-Cu nanoparticle-decorated graphene. The Ag-Cu-graphene (Ag-Cu@G) hybrid structure was prepared by magnetron sputtering for Ag and Cu film and chemical vapor deposition (CVD) for graphene, which avoided defects produced by graphene transferring process. The hybrid materials were confirmed by scanning electron microscopy (SEM), atomic force microscopy (AFM), energy dispersive spectroscopy (EDS), and Raman spectroscopy. With R6G as analyst molecule, the enhancement factor (EF) of the order of 10⁶ for Ag-Cu@G sample was obtained. Meanwhile, the substrates had stable enhanced SERS signals after 78-day exposure in air, which could be explained by the fact that the graphene is efficient at maintaining chemical and optical stability. The formation of graphene can contribute a stabilization and fluorescence quenching effect. Moreover, the electromagnetic distribution based on AFM images was simulated by finite difference time domain (FDTD) method.     

An accurate proteomic quantification method: Fluorescence labeling absolute quantification (FLAQ) using multidimensional liquid chromatography and tandem mass spectrometry

A facile proteomic quantification method, fluorescent labeling absolute quantification (FLAQ), was developed. Instead of using MS for quantification, the FLAQ method is a chromatography-based quantification in combination with MS for identification. Multidimensional liquid chromatography (MDLC) with laser-induced fluorescence (LIF) detection with high accuracy and tandem MS system were employed for FLAQ. Several requirements should be met for fluorescent labeling in MS identification: Labeling completeness, minimum side-reactions, simple MS spectra, and no extra tandem MS fragmentations for structure elucidations. A fluorescence dye, 5-iodoacetamidofluorescein, was finally chosen to label proteins on all cysteine residues. The fluorescent dye was compatible with the process of the trypsin digestion and MALDI MS identification. Quantitative labeling was achieved with optimization of reacting conditions. A synthesized peptide and model proteins, BSA (35 cysteines), OVA (five cysteines), were used for verifying the completeness of labeling. Proteins were separated through MDLC and quantified based on fluorescent intensities, followed by MS identification. High accuracy (RSD% < 1.58) and wide linearity of quantification (1-10(5) ) were achieved by LIF detection. The limit of quantitation for the model protein was as low as 0.34 amol. Parts of proteins in human liver proteome were quantified and demonstrated using FLAQ.     

Selective quantitative bioanalysis of proteins in biological fluids by on-line immunoaffinity chromatography-protein digestion-liquid chromatography-mass spectrometry

A quantitative method for the determination of proteins in complex biological matrices has been developed based on the selectivity of antibodies for sample purification followed by proteolytic digestion and quantitative mass spectrometry. An immunosorbent of polyclonal anti-bovine serum albumin (BSA) antibodies immobilized on CNBR agarose is used in the on-line mode for selective sample pretreatment. Next, the purified sample is trypsin digested to obtain protein specific peptide markers. Subsequent analysis of the peptide mixture using a desalination procedure and a separation step coupled, on-line to an ion-trap mass spectrometer, reveals that this method enables selective determination of proteins in biological matrices like diluted human plasma. This approach enhances substantially the selectivity compared to common quantitative analysis executed with immunoassays and colorimetry, fluorimetry or luminescence detection. Hyphenation of the immunoaffinity chromatography with on-line digestion and chromatography-mass spectrometry is performed and a completely on-line quantification of the model protein BSA in bovine and human urine was established. A detection limit of 170 nmol/l and a quantification limit of 280 nmol/l is obtained using 50 microl of either standard or spiked biological matrix. The model system allows fully automated absolute quantitative mass spectrometric analysis of intact proteins in biological matrices without time-consuming labeling procedures.     

Plasmonic Interaction Between Silver Nano-Cubes and a Silver Ground Plane Studied by Surface-Enhanced Raman Scattering

The plasmonic interaction between silver nano-cubes and a silver ground plane with and without a dielectric spacer is studied for surface-enhanced Raman scattering (SERS) for rhodamine 6G (R6G) molecules absorbed onto the silver nano-cubes. Experimental results show that the composite substrates made from silver nano-cubes and the silver ground plane produce a stronger SERS signal than by the cubes alone, due to the plasmonic interaction between the cubes and the film. Numerical simulation is used to verify the plasmonic enhancement of the composite substrate and is consistent with the experimental results. The lowest concentration of R6G molecules which can be detected with the composite substrate is about 10⁻¹¹ M with our setup.     

Ag/SiO2 core-shell nanoparticle-based surface-enhanced Raman probes for immunoassay of cancer marker using silica-coated magnetic nanoparticles as separation tools

A simple, sensitive and highly specific immunoassay has been developed based on surface-enhanced Raman scattering for human alpha-fetoprotein (AFP), a tumor marker for the diagnosis of hepatocellular carcinoma. This strategy combines the Ag/SiO2 core-shell nanoparticles embedded with rhodamine B isothiocyanate dye molecules as Raman tags and the amino group modified silica-coated magnetic nanoparticle as immobilization matrix and separation tool. In the proposed system, a sandwich-type immunoassay was performed between polyclonal antibody functionalized Ag/SiO2 nanoparticle-based Raman tags and monoclonal antibody modified silica-coated magnetic nanoparticles. The presence of the analyte and the reaction between the antigen and antibody can be monitored by the Raman spectra of the Ag/SiO2 tags. Compared to the previous surface-enhanced Raman immunoassays, the main advantage of this strategy lies in two aspects. One is the high stability of Raman tags derived from the silica shell-coated silver core-shell nanostructure. The other is the use of silica-coated magnetic nanoparticles as immobilization matrix and separation tool, thus avoiding complicated pretreatment and washing steps. We have studied in detail the experimental parameters such as the effects of the antibody concentration modified on the Raman tags and on the magnetic particles, and the immunoreaction time. Using this strategy, concentration of human AFP up to 0.12 microg/ml was detected with a detection limit of 11.5 pg/ml.     

Aip1p Dynamics Are Altered by the R256H Mutation in Actin

Mutations in actin cause a range of human diseases due to specific molecular changes that often alter cytoskeletal function. In this study, imaging of fluorescently tagged proteins using total internal fluorescence (TIRF) microscopy is used to visualize and quantify changes in cytoskeletal dynamics. TIRF microscopy and the use of fluorescent tags also allows for quantification of the changes in cytoskeletal dynamics caused by mutations in actin. Using this technique, quantification of cytoskeletal function in live cells valuably complements in vitro studies of protein function. As an example, missense mutations affecting the actin residue R256 have been identified in three human actin isoforms suggesting this amino acid plays an important role in regulatory interactions. The effects of the actin mutation R256H on cytoskeletal movements were studied using the yeast model. The protein, Aip1, which is known to assist cofilin in actin depolymerization, was tagged with green fluorescent protein (GFP) at the N-terminus and tracked in vivo using TIRF microscopy. The rate of Aip1p movement in both wild type and mutant strains was quantified. In cells expressing R256H mutant actin, Aip1p motion is restricted and the rate of movement is nearly half the speed measured in wild type cells (0.88 ± 0.30 μm/sec in R256H cells compared to 1.60 ± 0.42 μm/sec in wild type cells, p < 0.005).     

Practical applications of high-affinity, albumin-binding proteins from a group G streptococcal isolate

Binding proteins that have high affinities for mammalian plasma proteins that are expressed on the surface of bacteria have proven valuable for the purification and detection of several biologically important molecules from human and animal plasma or serum. In this study, we have isolated a high affinity albumin-binding molecule from a group G streptococcal isolate of bovine origin and have demonstrated that the isolated protein can be biotinylated without loss of binding activity and can be used as a tracer for quantification of human serum albumin (HSA). The binding protein can be immobilized and used as a selective capture reagent in a competitive ELISA format using a biotinylated HSA tracer. In this assay format, the sensitivity of detection for 50% inhibition of binding of HSA was less than 1 μg/ml. When attached to the bacterial surface, this binding protein can be used to deplete albumin from human plasma, as analyzed by surface-enhanced laser desorption ionization time of flight mass spectrometry.     

Elemental and molecular detection for Quantum Dots-based immunoassays: a critical appraisal

A critical comparison between Elemental Mass Spectrometry (ICP-MS) and molecular fluorescence, as detection techniques for CdSe/ZnS Quantum Dots (QDs)-based immunoassays is presented here. Using a QDs-based progesterone immunoassay as "model" analytical system the features of both detection modes has been investigated. Minimal changes, compared to the previously developed fluorescent approach, were necessary to build the corresponding inhibition curve for the progesterone immunoassay using ICP-MS detection of cadmium (contained in the QDs core). Adequate agreement between results obtained using both elemental and molecular techniques for the determination of progesterone in cow milk has been obtained. Moreover, results from the comparison showed that fluorescence detection of the QDs is simpler, less time consuming and less expensive, but ICP-MS detection affords alternative and useful information unattainable using luminescence detection. First of all, ICP-MS allowed mass balances to be carried out (all along the sample preparation) providing an internal validation of the immunoassay procedure. Secondly, matrix-independent quantification as provided by ICP-MS enabled a direct determination of progesterone in raw milk without any further sample preparation (dilution) step. As a matter of fact, ICP-MS results showed that the quenching matrix effect suffered on bioconjugated QDs fluorescence emission (e.g. when the immunoassay was carried out directly in whole milk without any dilution) could be unequivocally attributed to nonspecific interactions between the matrix of the whole milk and the QDs surface. Finally, better sensitivity could be obtained with ICP-MS detection, IC(10)=0.028 ng/mL, versus 0.11 ng/mL using conventional fluorimetric detection, just by using lower reagents concentrations.     

Comparison of DNA and RNA quantification methods suitable for parameter estimation in metabolic modeling of microorganisms

Recent developments in cellular and molecular biology require the accurate quantification of DNA and RNA in large numbers of samples at a sensitivity that enables determination on small quantities. In this study, five current methods for nucleic acid quantification were compared: (i) UV absorbance spectroscopy at 260 nm, (ii) colorimetric reaction with orcinol reagent, (iii) colorimetric reaction based on diphenylamine, (iv) fluorescence detection with Hoechst 33258 reagent, and (v) fluorescence detection with thiazole orange reagent. Genomic DNA of three different microbial species (with widely different G+C content) was used, as were two different types of yeast RNA and a mixture of equal quantities of DNA and RNA. We can conclude that for nucleic acid quantification, a standard curve with DNA of the microbial strain under study is the best reference. Fluorescence detection with Hoechst 33258 reagent is a sensitive and precise method for DNA quantification if the G+C content is less than 50%. In addition, this method allows quantification of very low levels of DNA (nanogram scale). Moreover, the samples can be crude cell extracts. Also, UV absorbance at 260 nm and fluorescence detection with thiazole orange reagent are sensitive methods for nucleic acid detection, but only if purified nucleic acids need to be measured.     

Raman spectroscopy and chemical imaging for quantification of filtered waterborne bacteria

Rapid and reliable assessment of pathogenic microbial contamination in water is critically important. In the present work we evaluated the suitability of Raman Spectroscopy and Chemical Imaging as enumeration techniques for waterborne pathogens. The prominent C-H stretching band observed between 2800-3000 cm(-1) of the spectrum is used for quantification purposes. This band provides the highest intensity of the bacterial-spectrum bands facilitating the detection of low number of microorganisms. The intensity of the Raman response correlates with number of cells present in drops of sample water on aluminum-coated slides. However, concentration of pathogens in drinking and recreational water is low, requiring a concentration step, i.e., filtering. Subsequent evaluation of filtering approaches for water sampling for Raman detection showed significant background signal from alumina and silver membranes that reduces method sensitivity. Samples concentrated by filtration show good correlation between Raman spectroscopy and other quantification methods including turbidity (R(2)=0.92), plate counts (R(2)=0.87) and dry weight (R(2)=0.97). Background interferences did not allow for evaluation of this relationship at low cell concentrations.     

Development and validation of a method for the quantitative determination of aflatoxin contaminants in Maytenus ilicifolia by HPLC with fluorescence detection

A method for the quantification of aflatoxins B1, G1, B2 and G2 in the medicinal herb Maytenus ilicifolia was developed and validated. The method used immunoaffinity columns for sample clean-up and HPLC with fluorescence detection without any derivatisation step. The method showed good inter-day accuracy (bias values in the range 4.5-10.7%) and precision (5-16% RSD) when applied to the determination of levels of aflatoxins ranging from 7 to 20 ppb in the plant material. The detection limits for samples of the plant material spiked with aflatoxins were 3.5 ng/g for B1 and G1 and 0.1 ng/g for B2 and G2. The method was successfully applied to commercial samples of Maytenus ilicifolia for the screening of aflatoxin contaminants.     

Fluorescence quenching competitive immunoassay in micro droplets

A fluorescence quenching competitive immunoassay in micro droplets was applied to the sensitive detection of the pyrethroid insecticide, esfenvalerate. Laser induced fluorescence from rhodamine dye was used as a marker. The competitive immunoreaction was performed in micro droplets generated by a vibrating orifice aerosol generator system with a 10-microm diameter orifice. Fluorescence that was emitted from the droplets was detected by a 1/8 m imaging spectrograph with a 512 x 512 thermoelectrically cooled, charged-coupled device camera. The conjugate of esfenvalerate with rhodamine exhibited similar fluorescence to that of pure rhodamine 6G. When anti-esfenvalerate antibodies were added to the droplets, the fluorescence decreased. The reduction in emission was due to a strong quenching effect that arises from the interaction between the protein and rhodamine molecules following the antigen-antibody reaction. When a sample of esfenvalerate was added to the droplets, the release of the conjugated rhodamine from the antigen-antibody complex allowed the fluorescence signal to recover. An assay in a picoliter droplet sample was shown to enable detection down to approximately 0.1 nM. A very small mass of analyte could be detected with this method. A sample of river water was used to gauge the impact of matrix effects and was shown to give rise to negligible interference with the immunoassay.     

Spectroscopic investigations to reveal the nature of interactions between the haem protein myoglobin and the dye rhodamine 6G

In the present investigation, steady‐state and time‐resolved fluorescence with the combination of circular dichroism (CD) spectroscopic techniques were applied to study the interactions of the well‐known dye rhodamine 6 G (R6G) with the haem protein human myoglobin (Mb). From the analysis of the results it appears that the static type of fluorescence quenching mechanism is primarily involved, due to ground‐state interactions. Although considerable overlapping of fluorescence emission of the dye R6G with the absorption of Mb in the Q‐band region exists, the possibility of occurrences of the excitational singlet–singlet non‐radiative energy transfer process from R6G to Mb appears to be unlikely, according to time‐resolved fluorescence measurements. From the determinations of the thermodynamic parameters, it was apparent that the combined effect of van der Waals' interactions and hydrogen bonding plays a vital role in Mb–R6G interactions. Induced circular dichroism (ICD) studies demonstrate the possibility of interactions between R6G and Mb. The binding constants, number of binding sites and thermodynamic parameters have been computed. From CD measurements it is apparent that the binding of the dye R6G with the haem protein Mb induces negligible conformational changes in the protein and Mb retains its secondary structure and helicity when it interacts with R6G. The present detailed studies on the interactions with Mb should be helpful in further advancement of medical diagnostics and biotechnology. Copyright © 2011 John Wiley & Sons, Ltd.     

Characterization and Quantification of Intact 26S Proteasome Proteins by Real-Time Measurement of Intrinsic Fluorescence Prior to Top-down Mass Spectrometry

Quantification of gas-phase intact protein ions by mass spectrometry (MS) is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF). UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1) and β7 (PBG1) subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.     

Tapered Fiber Probe Modified by Ag Nanoparticles for SERS Detection

A tapered optical fiber fabricated by a simple chemical etching method and modified with Ag nanoparticles (AgNPs) by chemical deposition was evaluated for surface-enhanced Raman scattering (SERS). The fiber probe was used for SERS measurements in both direct and remote scattering modes, yielding desired performance in both scattering configurations. The state of the obtained AgNPs made a significant contribution to the high sensitivity of SERS to Rhodamine 6G (R6G) molecules (down to a concentration of 10^?7 M), and the substrate had an analyst enhancement factor (AEF) on the order of ～10⁸. Meanwhile, the SERS intensity during the evaporation process was investigated, showing a good stability at the later stage of the evaporation process. The fiber SERS probes demonstrated good reproducibility with the average relative standard deviation (RSD) values being less than 0.2 for the major Raman peaks.     

Functionalized fluorescent core-shell nanoparticles used as a fluorescent labels in fluoroimmunoassay for IL-6

Nanoparticle labels conjugated with biomolecules are used in a variety of different assay applications. In this paper, a sensitive fluoroimmunoassay for recombinant human interleukin-6 (IL-6) with the functionalized Rubpy-encapsulated fluorescent core-shell silica nanoparticles labeling technique has been proposed. IL-6 was measured based on the specific interaction between captured IL-6 antigen and functionalized fluorescent core-shell nanoparticles-labeled anti-IL-6 monoclonal antibody. The calibration graph for IL-6 was linear over the range 20-1250 pg ml(-1) with a detection limit of 7 pg ml(-1) (3 sigma). The regression equation of the working curve is I(F)=7.665+32.499[IL-6] (ng ml(-1)) (r=0.9980). The relative standard deviation (R.S.D.) for 11 parallel measurements of 78 pg ml(-1) IL-6 was 3.2%. Furthermore, the application of fluorescence microscopy imaging in the study of the antibody labeling and sandwich fluoroimmunoassay with the functionalized fluorescent core-shell silica nanoparticles was also explored. This proposed method has the advantage of showing the specificity of immunoassay and sensitivity of fluorescent nanoparticle labels technology. The results demonstrate that the method offers potential advantages of sensitivity, simplicity and reproducibility for the determination of IL-6, and is applicable to the determination of IL-6 in serum samples and enabling fluorescence microscopy imaging for the determination of IL-6.     

Simple, sensitive and rapid LC-MS method for the quantitation of indapamide in human plasma--application to pharmacokinetic studies

A sensitive and specific method using liquid chromatography with electrospray ionization mass spectrometry (LC-ESI-MS) has been developed and validated for the identification and quantification of indapamide in human plasma. A simple liquid-liquid extraction procedure was followed by injection of the extracts on to a C18 column with gradient elution and detection using a single quadrupole mass spectrometer in selected ion monitoring (SIM) mode. The method was tested using six different plasma batches. Linearity was established for the concentration range 0.5-100.0 ng/ml, with a coefficient of determination (r) of 0.9998 and good back-calculated accuracy and precision. The intra- and inter-day precision (RSD%) was lower than 10%, and accuracy ranged from 85 to 115%. The lower limit of quantification was reproducible at 0.2 ng/ml with 0.2 ml plasma. The proposed method enables the unambiguous identification and quantification of indapamide for pre-clinical and clinical studies.     

Highly reproducible immunoassay of cancer markers on a gold-patterned microarray chip using surface-enhanced Raman scattering imaging

This paper reports a highly reproducible immunoassay of cancer markers using surface-enhanced Raman scattering (SERS) imaging. SERS is a highly sensitive detection method but it is limited in its ability to achieve reproducible signal enhancement because of the difficulty with precisely controlling the uniform distribution of hot junctions. Consequently, inconsistent enhancement prevents the wide exploitation of SERS detection as a bio-detection tool for quantitative analysis. To resolve this problem, we explored the use of a SERS imaging-based immunoassay. For this purpose, Raman reporter-labeled hollow gold nanospheres (HGNs), were manufactured and antibodies were immobilized onto their surfaces for targeting specific antigens. After the formation of sandwich immunocomplexes using these functional HGNs on the surfaces of gold patterned wells, the SERS mapping images were measured. For target protein markers, 12×9 pixels were imaged using a Raman mapping technique in the 0-10(-4) g/mL concentration range, and the SERS signals for 66 pixels were averaged. Here, the SERS imaging-based assay shows much better correlations between concentration and intensity than does the conventional point-based assay. The limits of detection were determined to be 0.1 pg/mL and 1.0 pg/mL for angiogenin (ANG) and alpha-fetoprotein (AFP), respectively. This detection sensitivity is increased by three or four orders of magnitude over that of conventional ELISA method. The detectable dynamic range for SERS imaging (10(-4)-10(-12) g/mL) is also much wider than that for ELISA (10(-6)-10(-9) g/mL).     

A novel 1,8-naphthalimide-based fluorescent chemosensor for the detection of HSA in living cells

Human serum albumin (HSA) is an essential protein for maintaining human health. Accurate detection and quantification of HSA are of great significance for disease diagnosis and biochemical research. Here, a new HSA fluorescent probe BNPE based on the 1,8-naphthalimide fluorophore was designed and synthesized. The probe could recognize HSA through a twisted intramolecular charge transfer mechanism, effectively avoid the interference of most substances, and realize HSA fluorescence imaging in living cells.