The ELF -97 phosphatase substrate provides a sensitive, photostable method for labelling cytological targets.

We compared fluorescent signals obtained with fluorescein conjugates and the ELF-97 (enzyme-labelled fluorescence) phosphatase substrate [2-(5'-chloro-2-phosphoryloxyphenyl)-6-chloro-4(3H)-quinazolinone] in labelling cytological structures requiring high spatial resolution. Enzymatic cleavage of the ELF-97 phosphatase substrate yields an extremely fine precipitate that remains well localized to the site of enzymatic activity. This precipitate fluoresces bright yellow-green, with maximal excitation at approximately 360 nm and maximal emission at approximately approximately 530 nm. The ELF substrate was used with streptavidin-alkaline phosphatase, to fluorescently label site-specific probes bound to their targets, including cell-surface sites, cytoplasmic organelles, nuclear antigens and cytoskeletal networks. All targets were labelled successfully with both the ELF substrate and fluoresceinated probes or protein conjugates. However, the ELF method was frequently more sensitive, with lower background fluorescence, allowing detection of more lysosomes, actin filaments, microtubules and nuclear targets than were visible with corresponding fluoresceinated probes. The ELF substrate was also used with antifluorescein-alkaline phosphatase to amplify fluorescein signals. We found that the ELF signal was in all cases brighter and more photostable than fluorescein signals, permitting shorter film exposures and allowing more time for examining samples. Surprisingly, relative brightness and photostability depended on the target, rather than being a general phenomenon related to the choice of dye alone.

Sensitive determination of cell number using the CyQUANT cell proliferation assay.

We describe here the development and characterization of the CyQUANT cell proliferation assay, a highly sensitive, fluorescence-based microplate assay for determining numbers of cultured cells. The assay employs CyQUANT GR dye, which produces a large fluorescence enhancement upon binding to cellular nucleic acids that can be measured using standard fluorescein excitation and emission wavelengths. The fluorescence emission of the dye-nucleic acid complexes correlated linearly with cell number over a large range using a wide variety of cell types. Under the recommended assay conditions, standard curves were linear (r(2)>0.995), detecting as few as 10-50 cells and as many as 25,000-50,000 cells with a single dye concentration, depending on cell type. Increasing the dye concentration extended the linear range of the assay to 100,000-250,000 cells. Results of cell proliferation and growth inhibition studies with the assay were similar to those obtained in published studies using other standard assays. CyQUANT assay measurements of serum-stimulated cell proliferation correlated well with measurements made using [3H]-thymidine. Also, the assay was used to analyze cellular DNA or RNA content, with the addition of a nuclease digestion step to the protocol. The assay procedure is simple and convenient, with no wash steps, and is readily amenable to automation.

Fluorescence microplate-based assay for tumor necrosis factor activity using SYTOX Green stain.

We have developed a simple, sensitive, fluorescence microplate-based assay for tumor necrosis factor (TNF) biological activity. The assay employs SYTOX Green nucleic acid stain to detect TNF-induced cell necrosis in actinomycin D sensitized cultured cell lines. SYTOX Green stain is a cationic unsymmetrical cyanine dye that is excluded from live cells but can readily penetrate cells with compromised cell membranes. Upon binding to cellular nucleic acids, the dye exhibits a large enhancement in fluorescence, which is monitored at fluorescein wavelengths. We detected 2.5 pg/mL and quantitated 25-500 pg/mL recombinant murine (rm) and recombinant human (rh) TNF-alpha, using mouse fibroblast-derived WEHI 164, WEHI 13var, and L929 cell lines. The procedure can also be used to detect agents that modulate TNF activity. We demonstrated complete inhibition of rhTNF-alpha using monoclonal anti-human TNF-alpha antibody and determined that approximately 20 ng/mL antibody was sufficient to neutralize 50% of the biological activity of 250 pg/mL rhTNF-alpha in these cell lines. Reagents are added in a single step, followed by a 6- to 8-h incubation period, during which the cytokine exhibits its effects. There are no wash steps, and the assay is readily amenable to automation and high-throughput screening procedures.

Detection of endogenous alkaline phosphatase activity in intact cells by flow cytometry using the fluorogenic ELF-97 phosphatase substrate.

BACKGROUND: The alkaline phosphatase (AP) substrate 2-(5'-chloro-2'-phosphoryloxyphenyl)-6-chloro-4-(3H)-quinazolinone (ELF((R))-97 for enzyme-labeled fluorescence) has been found useful for the histochemical detection of endogenous AP activity and AP-tagged proteins and oligonucleotide probes. In this study, we evaluated its effectiveness at detecting endogenous AP activity by flow cytometry. METHODS: The ELF-97 phosphatase substrate was used to detect endogenous AP activity in UMR-106 rat osteosarcoma cells and primary cultures of chick chondrocytes. Cells were labeled with the ELF-97 reagent and analyzed by flow cytometry using an argon ultraviolet (UV) laser. For comparison purposes, cells were also assayed for AP using a Fast Red Violet LB azo dye assay previously described for use in detecting AP activity by flow cytometry. RESULTS: The ELF-97 phosphatase substrate effectively detected endogenous AP activity in UMR-106 cells, with over 95% of the resulting fluorescent signal resulting from AP-specific activity (as determined by levamisole inhibition of AP activity). In contrast, less than 70% of the fluorescent signal from the Fast Red Violet LB (FRV) assay was AP-dependent, reflecting the high intrinsic fluorescence of the unreacted components. The ELF-97 phosphatase assay was also able to detect very low AP activity in chick chondrocytes that was undetectable by the azo dye method. CONCLUSIONS: The ELF-97 phosphatase assay was able to detect endogenous AP activity in fixed mammalian and avian cells by flow cytometry with superior sensitivity to previously described assays. This work also shows the applicability of ELF-97 to flow cytometry, supplementing its previously demonstrated histochemical applications.

A high-resolution, fluorescence-based method for localization of endogenous alkaline phosphatase activity.

We describe a high-resolution, fluorescence-based method for localizing endogenous alkaline phosphatase in tissues and cultured cells. This method utilizes ELF (Enzyme-Labeled Fluorescence)-97 phosphate, which yields an intensely fluorescent yellow-green precipitate at the site of enzymatic activity. We compared zebrafish intestine, ovary, and kidney cryosections stained for endogenous alkaline phosphatase using four histochemical techniques: ELF-97 phosphate, Gomori method, BCIP/NBT, and naphthol AS-MX phosphate coupled with Fast Blue BB (colored) and Fast Red TR (fluorescent) diazonium salts. Each method localized endogenous alkaline phosphatase to the same specific sample regions. However, we found that sections labeled using ELF-97 phosphate exhibited significantly better resolution than the other samples. The enzymatic product remained highly localized to the site of enzymatic activity, whereas signals generated using the other methods diffused. We found that the ELF-97 precipitate was more photostable than the Fast Red TR azo dye adduct. Using ELF-97 phosphate in cultured cells, we detected an intracellular activity that was only weakly labeled with the other methods, but co-localized with an antibody against alkaline phosphatase, suggesting that the ELF-97 phosphate provided greater sensitivity. Finally, we found that detecting endogenous alkaline phosphatase with ELF-97 phosphate was compatible with the use of antibodies and lectins. (J Histochem Cytochem 47:1443-1455, 1999)

Characterization of SYBR Gold nucleic acid gel stain: a dye optimized for use with 300-nm ultraviolet transilluminators.

The highest sensitivity nucleic acid gel stains developed to date are optimally excited using short-wavelength ultraviolet or visible light. This is a disadvantage for laboratories equipped only with 306- or 312-nm UV transilluminators. We have developed a new unsymmetrical cyanine dye that overcomes this problem. This new dye, SYBR Gold nucleic acid gel stain, has two fluorescence excitation maxima when bound to DNA, one centered at approximately 300 nm and one at approximately 495 nm. We found that when used with 300-nm transillumination and Polaroid black-and-white photography, SYBR Gold stain is more sensitive than ethidium bromide, SYBR Green I stain, and SYBR Green II stain for detecting double-stranded DNA, single-stranded DNA, and RNA. SYBR Gold stain's superior sensitivity is due to the high fluorescence quantum yield of the dye-nucleic acid complexes ( approximately 0.7), the dye's large fluorescence enhancement upon binding to nucleic acids ( approximately 1000-fold), and its capacity to more fully penetrate gels than do the SYBR Green gel stains. We found that SYBR Gold stain is as sensitive as silver staining for detecting DNA-with a single-step staining procedure. Finally, we found that staining nucleic acids with SYBR Gold stain does not interfere with subsequent molecular biology protocols.

Comparison of SYBR Green I nucleic acid gel stain mutagenicity and ethidium bromide mutagenicity in the Salmonella/mammalian microsome reverse mutation assay (Ames test).

SYBR Green I nucleic acid gel stain is an unsymmetrical cyanine dye developed for sensitive detection of nucleic acids in electrophoretic gels. Its mechanism of nucleic acid binding is not known, whereas the most commonly used nucleic acid gel stain, ethidium bromide, is a well-characterized intercalator. We compared the mutagenicity of SYBR Green I stain with that of ethidium bromide in Salmonella/mammalian microsome reverse mutation assays (Ames tests). As expected [J. McCann, E. Choi, E. Yamasaki, B.N. Ames, Proc. Natl. Acad. Sci. USA, 72 (1975) 5135-5139], ethidium bromide showed high revertant frequencies in several frameshift indicator strains (averaging 68-fold higher than vehicle controls in TA98, 80-fold higher in TA1538, 15-fold higher in TA1537, and 4.4-fold higher in TA97a), only in the presence of rat liver extracts (S9). Small increases in revertant frequencies were observed for ethidium bromide in the base-substitution indicator strain TA102 both in the presence and absence of S9 (averaging 2.0- and 1.8-fold higher than vehicle controls, respectively) and in base-substitution indicator strain TA100 in the presence of S9 (averaging 1.6-fold higher than vehicle controls). A small mutagenic effect was detected for SYBR Green I stain in frameshift indicator strain TA98 (averaging 2. 2-fold higher than vehicle controls) only in the absence of S9 and in base-substitution indicator strain TA102, both in the presence and absence of S9 (averaging 2.2- and 2.7-fold higher than vehicle controls, respectively). Thus, SYBR Green I stain is a weak mutagen and appears to be much less mutagenic than ethidium bromide. These results suggest that SYBR Green I stain may not intercalate, and if it does, that its presence does not give rise to point mutations at a high frequency.

RNA quantitation by fluorescence-based solution assay: RiboGreen reagent characterization.

We describe the development of a sensitive fluorescence-based solution assay for RNA using a new dye, RiboGreen RNA quantitation reagent. RiboGreen reagent exhibits >1000-fold fluorescence enhancement and high quantum yield (0.65) upon binding nucleic acids, with excitation and emission maxima near those of fluorescein. Unbound dye is essentially nonfluorescent and has a large extinction coefficient (67,000 cm-1 M-1). The RiboGreen assay allows detection of as little as 1.0 ng/ml RNA in a standard fluorometer, filter fluorometer, or fluorescence microplate reader-surpassing the sensitivity achieved with ethidium bromide by 200-fold. The linear quantitation range for RiboGreen reagent extends over three orders of magnitude in RNA concentration. Using 750 nM RiboGreen reagent, we quantitated 20 ng/ml to 1.0 microg/ml RNA. By diluting the reagent to 75 nM, we could quantitate 1.0 to 50 ng/ml RNA. Both assay ranges exhibited linear fluorescence increases versus RNA concentration (r2 = 0.999). Assay linearity was maintained in the presence of salts, protein, urea, ethanol, chloroform, agarose, and some detergents. Several different RNA types yielded similar signal intensities and detection sensitivities. The assay is easy to use, rapid, and readily adaptable for automation.

Characterization of PicoGreen reagent and development of a fluorescence-based solution assay for double-stranded DNA quantitation.

A sensitive assay for detecting double-stranded (ds) DNA in solution is described. This assay employs a new dye, PicoGreen dsDNA quantitation reagent, which becomes intensely fluorescent upon binding nucleic acids. The brightness of this reagent is due to its high quantum yield (approximately 0.5, bound to ds calf thymus DNA) and large molar extinction coefficient (approximately 70,000 cm-1 M-1). The fluorescence enhancement of this dye upon binding dsDNA is > 1000-fold, with excitation and emission maxima near those of fluorescein. Unlike Hoechst 33258, PicoGreen reagent fluorescence intensity was the same upon binding to poly(dA).poly(dT) and poly(dG).poly(dC) homopolymers. The PicoGreen assay allowed the detection of 25 pg/ml dsDNA, surpassing the sensitivity achieved with Hoechst 33258 by 400-fold. The linear concentration range for DNA quantitation extended over four orders of magnitude-25 pg/ml to 1 microgram/ml-with a single dye concentration. Assay linearity was maintained even in the presence of salts, proteins, poly(ethylene glycol), urea, chloroform, ethanol, and agarose; some ionic detergents and heparin interfered. Linear DNAs yielded slightly brighter signals than supercoiled plasmids. Finally, the assay showed greater dsDNA:RNA selectivity than Hoechst 33258 in low ionic strength buffer and better dsDNA:single-stranded DNA selectivity in 1 M NaCl.

Optimal filter combinations for photographing SYPRO orange or SYPRO red dye-stained gels.

Photography or electronic image acquisition is required to document results obtained from staining protein gels with the fluorescent SYPRO dyes. We found that, when using Polaroid type 667 or 57 instant films, the choice of optical filter combination and photographic exposure time strongly influences protein detection sensitivity limits. Ultraviolet light-blocking Kodak Wratten No. 2A and 2B gelatin filters autofluorescence when illuminated at 300 nm. The use of these filters in combination with Wratten No. 22 or 25 filters or SYPRO gel photographic filters gives rise to increased background signals, which for long photographic exposures can obscure signals due to protein bands. Surprisingly, the use of these same ultraviolet lightblocking filters enhanced the protein detection sensitivity obtained with short photographic exposures. Under the conditions tested, we found minimal differences in performance for Polaroid type 667 and 57 films.

Detection of apoptosis in live cells by MitoTracker red CMXRos and SYTO dye flow cytometry.

We characterized the ability of six SYTO nucleic acid stains and a mitochondrial stain to resolve by flow cytometry camptothecin-induced apoptotic and non-apoptotic cells. Staining live human lymphoid B-cells showed such resolution with SYTO 11, 12, 13, 14, and 16 dyes. H9, HL-60, and Jurkat cells did not show resolution with the SYTO 12 dye, but did with the others. SYTO 15 dye did not show resolution with any cell type. RNase A treatment of fixed lymphoid B-cells strongly reduced fluorescence after staining with SYTO 12 dye; the other SYTO dyes showed little or no RNase A sensitivity. Reduced SYTO 12 fluorescence may reflect RNA breakdown during apoptosis, while decreased fluorescence of the other SYTO dyes in apoptotic cells may be due to chromosomal alterations during apoptosis. In all cell types tested, clear resolution between apoptotic and non-apoptotic cells was observed with the MitoTracker Red dye CMXRos. In double-staining experiments, cells exhibiting reduced SYTO 11 fluorescence were the same as those showing decreased CMXRos fluorescence. We conclude that changes in nucleic acid stability or conformation may vary during apoptosis from one cell type to another, but mitochondrial demise may be common to all apoptotic pathways.

The ELF-97 alkaline phosphatase substrate provides a bright, photostable, fluorescent signal amplification method for FISH.

We used the ELF-97 (Enzyme-Labeled Fluorescence) phosphatase substrate, 2-(5'-chloro-2-phosphoryloxyphenyl)-6-chloro-4(3H)-quinazolinone, with alkaline phosphatase conjugates of streptavidin and appropriate antibodies to amplify signals from biotinylated and haptenylated hybridization probes. The dephosphorylated product, ELF-97 alcohol, is a bright yellow-green fluorescent precipitate optimally excited at approximately 360 nm, with emission centered at approximately 530 nm. This large Stokes shift allows ELF-97 signals to be easily distinguished from sample autofluorescence and signals arising from counterstains or other fluorophores. The ELF-97 precipitate was extremely photostable compared to fluorescein, allowing multiple photographic exposures of samples without significant signal intensity loss. For RNA in situ hybridization, labeling was specific and localized well to targets in cultured cells, tissue sections, and whole-mount zebrafish embryos. ELF-97 signals developed in seconds to minutes and were easily distinguished from pigmented tissues or cells, unlike those obtained using colorimetric substrates. We used the substrate with singly biotinylated short oligonucleotides to detect actin mRNA in MDCK cells and actin and beta-galactosidase mRNA in LacZ+ mouse fibroblasts. We also used a biotinylated cDNA, complementary to the mRNA encoded by the constant region of the T-cell receptor beta-chain, to specifically identify T-cells in mouse lymph node tissue sections. With digoxigenin-labeled probes, we detected several developmentally expressed mRNAs in whole-mount zebrafish embryos. Hybridization to centromere repeat regions in human metaphase and interphase chromosomes was also detected; ELF-97 signals were manyfold brighter than signals obtained with fluorescein conjugates. Finally, Southern blot hybridization using singly labeled oligonucleotide probes yielded a sensitivity similar to that obtained with radioactivity.

Analysis of mitochondrial morphology and function with novel fixable fluorescent stains.

Investigation of mitochondrial morphology and function has been hampered because photostable, mitochondrion-specific stains that are retained in fixed, permeabilized cells have not been available. We found that in live cell preparations, the CMXRos and H2-CMXRos dyes were more photostable than rhodamine 123. In addition, fluorescence and morphology of mitochondria stained with the CMXRos and CMXRos-H2 dyes were preserved even after formaldehyde fixation and acetone permeabilization. Using epifluorescence microscopy, we showed that CMXRos and H2-CMXRos dye fluorescence fully co-localized with antibodies to subunit I of cytochrome c oxidase, indicating that the dyes specifically stain mitochondria. Confocal microscopy of these mitochondria yielded colored banding patterns, suggesting that these dyes and the mitochondrial enzyme localize to different suborganellar regions. Therefore, these stains provide powerful tools for detailed analysis of mitochondrial fine structure. We also used poisons that decrease mitochondrial membrane potential and an inhibitor of respiration complex II to show by flow cytometry that the fluorescence intensity of CMXRos and H2-CMXRos dye staining responds to changes in mitochondrial membrane potential and function. Hence, CMXRos has the potential to monitor changes in mitochondrial function. In addition, CMXRos staining was used in conjunction with spectrally distinct fluorescent probes for the cell nucleus and the microtubule network to concomitantly evaluate multiple features of cell morphology.

SYPRO orange and SYPRO red protein gel stains: one-step fluorescent staining of denaturing gels for detection of nanogram levels of protein.

We have developed two new fluorescent dyes, SYPRO Orange protein gel stain and SYPRO Red protein gel stain, to detect proteins in electrophoretic gels. Stained protein bands can be excited by ultraviolet light at approximately 300 nm, or at visible wavelengths, with excitation maxima of 472 nm for the Orange stain and 547 nm for the Red stain. Detection can be documented with sensitivity similar to that achieved with silver stain, using standard UV transilluminators and Polaroid 667 black and white film, CCD cameras, or commercially available laser scanners. Staining with these dyes is noncovalent and is accomplished using a one-step procedure. Protein gels do not require fixation steps prior to incubation with the dyes. Staining is complete 30 to 60 min following electrophoresis, with no destaining required. Staining can also be accomplished by including dye in the running buffer; in this case a brief one-step destaining procedure follows electrophoresis. The dyes appear to bind to the detergent coat surrounding proteins in sodium dodecyl sulfate (SDS) denaturing gels; thus, staining in such gels is not strongly selective for particular polypeptides. Fluorescent signals are relatively photostable, allowing multiple photographs of gels to be taken without significant signal reduction.

Applications of SYPRO orange and SYPRO red protein gel stains.

We have further characterized the sensitivity and specificity of SYPRO Orange protein gel stain and SYPRO Red protein gel stain with native and 2-dimensional polyacrylamide gels and for staining gels prior to Western blot analysis. We found that nucleic acids are not stained by the SYPRO protein gel stains, in contrast to results obtained with commonly used silver staining techniques. Bacterial lipopolysaccharides also stain very weakly with SYPRO dyes in comparison to silver staining. Thus, gels containing whole cell lysates from either bacterial or mammalian cells can be analyzed more easily with the SYPRO stains than by silver staining. In this paper, we demonstrate that SYPRO stains can be used to monitor protein induction in bacterial overproducing strains and are effective stains for 2-dimensional gels. In addition, we developed protocols to detect proteins with these dyes in native gels. Finally, we found that staining proteins in transfer buffer prior to Western blotting does not affect the sensitivity of subsequent immunodetection.

Quantitative nonradioactive CAT assays using fluorescent BODIPY 1-deoxychloramphenicol substrates.

We report the development of fluorescent BODIPY 1-deoxychloramphenicol substrates for chloramphenicol acetyltransferase (CAT). These substrates not only simplify and improve quantitation of CAT activity but also extend the linear range of detection. Because the 1-deoxychloramphenicol derivatives have only one acetylation site, the enzyme reaction creates only one product, whereas chloramphenicol and its fluorescent derivatives produce three acetylated products, each of which accumulates at a different rate. Thus, 1-deoxychloramphenicol substrates eliminate the need to account for multiple products and provide a method in which product formation corresponds directly to enzyme activity. These nonradioactive substrates also allow researchers to streamline the standard thin-layer chromatography separation procedure: visible results can be obtained within minutes and quantitative results in a few hours. The sensitivity of CAT assays using fluorescent 1-deoxychloramphenicol substrates is comparable to that achieved using [14C]chloramphenicol--between 10(-5) and 10(-6) units of activity in a 1-h reaction--and the linear range extends through 3.6 or more orders of magnitude. We expect that CAT assays employing BODIPY 1-deoxychloramphenicol CAT substrates will be a valuable improvement over other methods currently in use.

Fluorescence-based signal amplification technology.

The ELF alkaline phosphate substrate can be used to fluorescently label a wide variety of biological targets. This substrate yields a bright, photostable yellow-green fluorescent precipitate at the site of enzymatic activity. ELF labeling can be as much as 40 times as bright and hundreds of times as photostable as labeling with conventional fluorophores and yields signals capable of very fine submicroscopic resolution. Signal development is also extremely rapid, making the signal amplification technology well suited for applications such as RNA in situ hybridization.

Telomeric associations involving Yq12 in a lymphoblastoid cell line.

A number of apparent telomeric associations/fusions (TAs) involving Yq12 were observed in a lymphoblastoid cell line (GM6892A) established from a fragile-X-negative, phenotypically normal male with the fragile X gene mutation. The TAs were seen when these cells were grown for an extended period of time in medium 199, which is deficient in thymidine and folic acid. Because the low thymidine and folic acid condition of medium 199 is known to induce chromosome and chromatid gaps and breaks at folate-sensitive fragile sites, other fragile site-induction regimes were examined to determine if the TAs seen in GM6892A were due to a fragile site in the Yq12 band. No TAs were seen with any of the other regimes that were tried.

A wide variety of DNA sequences can functionally replace a yeast TATA element for transcriptional activation.

We created a library of DNA molecules in which the required TATA element of a yeast gal-his3 promoter is replaced by random-sequence oligomers averaging 16 bp in length. Surprisingly, 1% of such random sequences functionally replace the native yeast TATA element. In many cases, sequences completely unrelated to the consensus TATA element (TATAAA) stimulate transcription with equal or increased efficiency. Transcription mediated by these synthetic elements requires GAL4 and is initiated from normal his3 initiation sites, suggesting that it occurs by a mechanism indistinguishable from that involving wild-type TATA elements. Many, but not all, of these elements act as substrates for yeast TFIID in reconstituted transcription reactions in vitro. These observations indicate that yeast TFIID can stimulate transcription from TATA elements whose sequences differ from the consensus, and they suggest the possibility of alternative factors that may provide a related function for transcriptional activation.

Characterization of heat shock in Bacillus subtilis.

We characterized the general properties of the heat shock response in Bacillus subtilis W168, B. subtilis JH642, and an spo0A mutant by using pulse-labeling of bacterial proteins and one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The transfer of cells from 37 to 50 degrees C repressed synthesis of most cellular proteins and led to the induction of at least 26 distinct heat shock proteins after about 3 min. Ethanol (4% [vol/vol]) induced a similar set of proteins, but somewhat more slowly. Synthesis of the majority of heat shock proteins at 50 degrees C returned to a steady-state level 20 to 40 min after the shock. Although no B. subtilis heat shock protein has yet been extensively characterized, three of these proteins were found to be immunologically related to the Escherichia coli heat shock proteins Dnak, Lon, and GroEL. Synthesis of both sigma 28 and sigma 43 proteins was sharply reduced during heat shock. Although a spo0A amber mutation blocks transcription from promoters used by at least two minor B. subtilis sigma factors, it did not alter the kinetics or general properties of the heat shock response.