Evaluating the compatibility of three colorimetric protein assays for two-dimensional electrophoresis experiments

To evaluate compatibility of commonly used colorimetric protein assays for 2-DE experiments, we investigated the interfering mechanisms of major 2-DE component(s) in the Lowry-based assay, the Bradford assay and the bicinchoninic acid (BCA) assay. It was found that some 2-DE components did not directly interfere with the assays' color development reaction, but possibly influenced the quantitation results by interacting with proteins. Generally, simultaneous presence of 2-DE components in the samples demonstrated a cooperative rather than additive interference. Interference by reductants in the Lowry-based assay and the BCA assay were too prominent and could not be completely eliminated by either the reported alkylation procedure or the water dilution procedure. The Bradford assay however, presented a more suitable method for quantitating 2-DE samples because it was less interfered by most 2-DE components. Furthermore, despite slightly compromising protein solubility, utilization of reductant free 2-DE sample buffers conferred application of the Lowry-based and BCA assays in the 2-DE experiments.     

Constitution and quantity of lysis buffer alters outcome of reverse phase protein microarrays

Application of novel technology to clinical samples requires optimization of procedures. Reverse phase protein lysate arrays use femtomolar quantities of tissue lysate from clinical samples with which to profile biochemical events happening in the tumor. We analyzed the effects of different tissue solubilization buffers on frozen ovarian tumor samples in order to identify the system with the best signal intensity dynamic range, reproducibility, tissue solubility, and signal consistency. A modified RIPA-like buffer supplemented with DTT and SDS was deemed optimal.     

Quantitation of adenovirus DNA and virus particles with the PicoGreen fluorescent Dye.

A microplate assay for the rapid quantitation of adenovirus DNA has been developed using the fluorescent dye PicoGreen, which selectively binds double-stranded DNA. The method was first applied to extracted adenoviral DNA and then extended to samples of intact, purified adenovirus after lysis of the viral capsid with the ionic detergent SDS. Utilizing the stoichiometric relationship between adenovirus DNA and intact particles, a physical particle count of intact virus is then derived for the sample. This PicoGreen-based assay has excellent reproducibility, linearity, and sensitivity. In its present form, this assay has a limit of quantitation of 10.3 ng/ml viral DNA, predicted to correspond to 2.6 x 10(8) virus particles/ml. This procedure was compared to a widely utilized spectroscopic method, in which samples are lysed with SDS and absorbance is read at 260 nm, and found to be 10- to 20-fold more sensitive. The dye binding assay also uses considerably less sample volume (<20%) than that needed for the spectroscopic method. Particle count values generated by the PicoGreen procedure are consistently lower (typically 1.5- to 2-fold) than this spectroscopic method. The applications and limitations of this method in the analysis of adenovirus samples are discussed.     

pH and buffering in the bicinchoninic acid (4,4'-dicarboxy-2,2'-biquinoline) protein assay

The HCO3/CO3(2-) buffer used in the bicinchoninic acid (BCA) protein assay has only weak buffering capacity at the recommended pH (11.25). Consequently the assay is rather sensitive to interference from effectively acid or alkaline samples, particularly in the micro method. Adjustment of pH in these alkaline solutions of high [Na+] is complicated by Na+ errors on the pH electrode. Hence it is recommended to prepare the buffers from known amounts of NaHCO3 and Na2CO3, and to reduce the pH to around 10.7; this offers much better buffering capacity with only a limited reduction in color development.     

Interference by Tris buffer in the estimation of protein by the Lowry procedure

Tris buffers were found to distort the measurement of protein by the Lowry method both by decreasing chromophore development with protein and by contributing blank color. Tris at an assay concentration of 0.37 mm markedly affects measured results. Similar Tris effects were observed at all wavelengths between 450 and 800 nm and with diverse protein samples. The distortion due to Tris is not correctable by simple blank correction, but it can be overcome by incorporating the same amount of Tris in the standards used. The distortion at Tris concentrations <0.15 mm appears to be within tolerable limits. No interference or distortion was observed with sodium phosphate buffer to an assay concentration of 40 mm. An automated Lowry procedure is also presented which gives excellent correlation with the manual method and an average coefficient of variation of <4%.     

A solid-phase method for the quantitation of protein in the presence of sodium dodecyl sulfate and other interfering substances

We describe a simple assay for small amounts of protein that is insensitive to sodium dodecyl sulfate (SDS) or many common interfering substances including Tris and reducing sugars. For this reason, it is particularly useful in the analysis of protein content of samples prior to SDS electrophoresis. The assay consists of the following steps: (i) absorption of protein to nitrocellulose; (ii) fixation of the bound protein with methanol; (iii) staining of the bound protein with amido black; and (iv) elution and spectrophotometric measurement of the bound dye. The assay is sensitive to as little as 0.5 microgram of protein in 1 microliter of solution. Although SDS does not interfere appreciably with measurement, Nonidet-P40 does.     

Protein measurement using bicinchoninic acid: elimination of interfering substances

Protein quantitation based on bicinchoninic acid (BCA) is simple, sensitive, and tolerant to many detergents and substances known to interfere with the Lowry method. However, certain compounds often used during protein purification do interfere with the BCA protein assay. The response of the BCA chromophore to various interfering substances has provided insight into the mechanism of protein quantitation by BCA. Certain substances (e.g., glucose, mercaptoethanol, and dithiothreitol) elicit a strong absorbance at 562 nm when combined with the BCA working reagent. The absorbance appears to be identical to the normal response elicited by protein. Other agents (e.g., ammonium sulfate and certain ampholytes) diminish the protein-induced color development and shift the wave-length of the color response. Both types of interference can be eliminated by selectively precipitating protein with deoxycholate and trichloroacetic acid (A. Bensadoun and D. Weinstein (1976) Anal. Biochem. 70,241-250) prior to reaction with bicinchoninic acid. The modifications described here permit quick, efficient removal of many interfering substances that are commonly utilized during protein purification.     

A dot-blot assay for quantitation of nanogram amounts of protein in the presence of carrier ampholytes and other possibly interfering substances

A method for protein determination in one- and two-dimensional electrophoresis sample buffer is presented. Accurate quantitation of protein in two-dimensional electrophoresis sample buffer (9.5 M urea, 2% Nonidet P-40, 2% carrier ampholytes, and 5% 2-mercaptoethanol) required removal of carrier ampholytes prior to the assay. This was made possible by taking advantage of the mutual solubility/insolubility of carrier ampholytes/proteins in saturated ammonium sulfate solution. In addition, improvement of protein determination in denaturing electrophoresis sample buffer containing the anionic detergent sodium dodecyl sulfate and the reducing agent 2-mercaptoethanol was achieved. The assay covers a range of sensitivity from 40 ng to 20 micrograms of protein. The procedure is applicable to large numbers of samples.     

Microplate quantification of plant leaf superoxide dismutases

Superoxide dismutases (SODs) catalyze the dismutation of superoxide radicals in a broad range of organisms, including plants. Quantification of SOD activity in crude plant extracts has been problematic due to the presence of compounds that interfere with the dose-response of the assay. Although strategies exist to partially purify SODs from plant extracts, the requirement for purification limits the rapidity and practical number of assays that can be conducted. In this article, we describe modification of a procedure using o-dianisidine as substrate that permits relatively rapid quantification of SOD activity in crude leaf extracts in a microplate format. The method employs the use of a commercial apparatus that permits lysis of 12 tissue samples at once and the use of Pipes buffer to reduce interference from compounds present in crude leaf extracts. The assay provided a linear response from 1 to 50 units of SOD. The utility of the assay was demonstrated using tissue extracts prepared from a group of taxonomically diverse plants. Reaction rates with tissue extracts from two grasses were linear for at least 60 min. Tissues of certain species contained interfering compounds, most of which could be removed by ultrafiltration. The presence of plant catalases, peroxidases, and ascorbate in physiological quantities did not interfere with the assay. This approach provides a means to quantify SOD activity in relatively large numbers of plant samples provided that the possibility for the presence of interfering compounds is considered. The presence of interfering compounds in certain plant tissues necessitates caution in interpreting the effects of plant stresses on SOD.     

A method for quantitating nanogram amounts of soluble protein using the principle of silver binding

A highly sensitive and quantitative assay for measuring protein in solution based on the capacity of protein to bind silver is described. In this procedure, protein samples are first treated with glutaraldehyde and then exposed to ammoniacal silver. After 10 min, the reaction is terminated by the addition of sodium thiosulfate and the optical density measured at 420 nm. The useful range of the assay for the majority of standard proteins tested lies between 15 and 2000 ng. This represents a 100-fold increase in sensitivity over the Coomassie brilliant blue dye-binding procedure. There is little or no interference from carbohydrates, nonionic detergents, or ethanol, and pretreatment of protein samples with Bio-Gel P-2 to remove salts, thiol agents, EDTA, and sodium dodecyl sulfate makes this procedure compatible with most commonly used buffers. The cost in terms of silver utilization is nominal with a typical assay involving 10 samples tested in triplicate amounting to less than $0.02 U. S.     

Microwave-enhanced ink staining for fast and sensitive protein quantification in proteomic studies

A novel microwave-enhanced ink staining method was developed for rapid and sensitive estimation of protein content in sample buffers containing chaotropes, dyes, detergents, and reducing agents. Dye-based Blue-Black ink was used to quantitatively visualize proteins spotted on a nitrocellulose membrane. The total staining time was greatly reduced to 3 min by brief exposure to microwave radiation. The stained membrane was washed with distilled water, baked in a microwave oven for complete desiccation, transparentized with mineral oil, and documented by a desktop scanner or densitometer. Only 1 microL of protein sample (protein solubilized in SDS-PAGE sample buffer or IEF rehydration buffer) was used for protein spotting. The novel solid-phase protein assay gives a 500-fold dynamic range from 19.5 to 10000 ng/microL and can be scaled up for high-throughput protein quantification analysis. The fast, sensitive and low-cost microwave-enhanced ink staining procedure is ideal for protein quantification in proteomic analysis.     

Electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels to a positively charged membrane filter

Zeta-bind, a positively charged nylon membrane, was tested as an immobilizing matrix for the electrophoretic transfer of proteins from sodium dodecyl sulfate-polyacrylamide gels. It was found that Zeta-bind has a considerably greater capacity than does nitrocellulose for protein binding. Because of this property, more efficient elution of proteins from gels can be used (by omitting methanol from transfer buffers). The procedure described is more amenable to quantitation than usual nitrocellulose-based transfer. Antibody or lectin overlay techniques are also more sensitive on Zeta-bind than on nitrocellulose.     

Development and validation of a plasma assay for acyclovir using high-performance capillary electrophoresis with sample stacking

A sensitive plasma assay for acyclovir has been developed and validated. Acyclovir was separated from plasma components using Oasis HLB columns. Separation was obtained with no plasma interference using micellar electrokinetic chromatography (175 mM SDS) and hydroxypropyl-beta-cyclodextrin (100 mM) in 90 mM borate buffer (pH 8.8) containing 0.2% NaCl. High sensitivity was achieved by large volume sample introduction and stacking. The linear range was from 20 to 10000 ng/ml with a limit of quantitation of 20 ng/ml. This method is a viable alternative to HPLC because of its high separation and sensitivity, reproducibility, and adaptability to other nucleoside analogs.     

Improving soil protein extraction for metaproteome analysis and glomalin‐related soil protein detection

Soil contains low amounts of protein but high amounts of interfering substances. Current extraction methods for soil protein cannot produce high‐quality samples suitable for proteomic analysis. To resolve the problem, we devised a sequential extraction method, through sequentially extracting soil in citrate and SDS buffers, followed by phenol extraction. The method allows for obtaining applicable 1‐D and 2‐D protein profiles with various agricultural soils and detecting glomalin‐related soil protein. The method may be a valuable tool for soil proteomics.     

Antibodies to the most tightly bound proteins in eukaryotic DNA

DNA released from eukaryotic cells by proteases/SDS or by alkali/SDS still contains distinct proteins which are not removed by these cell lysis procedures nor by subsequent phenol treatment. The proteins most tightly bound to DNA can only be isolated by degradation of DNA. In contrast to the protein-DNA complexes, the protein material isolated after degradation of DNA is sensitive to protease treatment. Moreover, the isolated protein material tends to form aggregates which are insoluble in buffers not containing detergents. They are only poorly soluble in buffers containing SDS. The partially solubilized material can be separated by SDS-polyacrylamide gel electrophoresis into two main bands. Antibodies were raised in rabbits against the polypeptides contained in these main bands. Immunofluorescence micrographs are presented of cells treated with the antibodies. The results indicate that the proteins characterized by their involvement in extremely stable protein-DNA complexes also occur independently of DNA in eukaryotic cells.     

Analytical Characterization of a Sensitive Radioassay for Tyrosine Hydroxylase Activity in Rodent Striatum

Several buffer compositions with a wide range of pH values have been reported for radiometric assay of tyrosine hydroxylase (TH) in biological samples. Assay sensitivity becomes a prime concern while analyzing TH in minute samples like tissue biopsies or discrete regions of rodent brain wherein lower enzyme levels are anticipated due to smaller sample sizes. It was therefore rationalized to evaluate relative affinities of three commonly used assay buffers (sodium phosphate, sodium acetate, and Tris-acetate) with TH enzyme activity. The impact of buffer pH and cofactor concentration on the sensitivity of TH assay was also investigated. Striata from rats or mice were homogenized, respectively, with 1.0 or 0.5 ml of the assay buffer containing 0.5% Triton X-100. The supernatants (200 microl) were incubated (20 min, 37 degrees C) with 0.8 microCi [3H] L-tyrosine, 1.5 mM DL-6-methyl-5,6,7,8-tetrahydropterine (6-MPH4), 100 U catalase, and 1.0 microM dithiothreitol in a total volume of 300 microl. The reaction was terminated by 1-ml suspension of activated charcoal in 0.1 M HCl. After centrifugation, 200-microl aliquots were mixed with 5 ml of cocktail for quantitation of [3H] H2O in supernatant. The results showed significant impact of pH rather than the buffer composition on the sensitivity of TH assay. An optimal pH range was found to be 5.5-6.0, whereas TH activity was significantly inhibited at pH 5.0 and pH 6.8 (F = 55.09, P = 0.000). A significantly high TH activity was observed with 1.5 mM 6-MPH4, whereas higher concentrations (3.0-4.5 mM) inhibited TH activity (F = 7.47, P = 0.005). Analysis of serially diluted striatal homogenates showed a significant correlation between TH activity and sample amount. The assay reaction was linear for 20- and 30-min incubation for rat and mice striata, respectively.     

The use of an amino acid analyzer for the rapid identification and quantitative determination of chitosan oligosaccharides.

The oligosaccharides of chitosan, glucosamine through chitohexaose, were separated and quantitated with the use of an amino acid analyzer. The oligosaccharides can be satisfactorilly resolved with a step gradient using two buffers, but resolution is improved with a linear buffer gradient. Using experimentally determined color factors, the method permits the rapid quantitation and identification of small amounts of chitosan oligosaccharides.     

Assay of Malondialdehyde in Biological Fluids by Gas Chromatography-Mass Spectrometry

Malondialdehyde (MDA) is assayed in femtomole quantities in biological samples by gas chromatography-mass spectrometry (GC-MS). The MDA trapped in protein as a Schiff base is released by H₂SO₄, the protein precipitated using Na₂WO₄, and the MDA derivatized with pentafluorophenylhydrazine to form the stable adduct, N-pentafluorophenylpyrazole. Negative chemical ionization (NCI) capability allows the sensitive detection of this MDA adduct in biological samples at a level of 5 nM on-column. A stable-isotope-labeled MDA, [²H₂]MDA, was used as an internal standard for quantitation. MDA recovery from plasma was 76%. This assay provides two forms of confirmation of the analyte, retention time and mass ion, thus minimizing error due to interfering compounds. The commonly used thiobarbituric acid assay for MDA overestimates the MDA levels by over 10-fold, possibly resulting from cross-reactivity with other aldehydes and artifactual oxidation due to 100°C temperature conditions. In our assay, all steps were performed at room temperature thereby suppressing artifactual oxidation of the sample. We have successfully applied this assay to biological samples including plasma, tissue homogenates, and sperm.     

Two-dimensional Separation of the Prolamins of Normal and High Lysine Barley (Hordeum vulgare L.)

The polypeptide components of the reduced prolamin fraction(hordein) of barley seed proteins have been separated, beforeand after alkylation, by polyacrylamide gel electrophoresisusing buffers containing urea and/or sodium dodecylsulphate(SDS). Alkylation of the protein with 4-vinylpyridine or acrylonitrileresults in a considerable sharpening of the protein bands andsome minor changes in the band pattern. The procedure has beenused to compare the hordeins of the normal commercial varieties,Julia and Bomi, to those of a high lysine mutant of Bomi (Rise,1508). Whereas the alkylated hordein fractions of Bomi and Julia containSDS bands of apparent molecular weights 13 000, 16 000, 20 000,30 000, 43 000, 51 000, 67 000, and 86 000, the mutant hordeinfractions contain predominantly the low molecular weight (13000, 16 000, and 20 000) and mol. wt. 51 000 bands. Further resolution of the fractions was obtained by two-dimensionalelectrophoresis using 6 M urea in glycine/acetate buffer atpH 4?6 as the first dimension and SDS in tris/borate bufferat pH 8?9 as the second. Separation of the Rise 1508 hordeinin this system demonstrated that the mol. wt. 51 000 band containsseveral closely similar components.