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Alexa fluor 488

Alexa Fluor 488 is a fluorescent dye commonly used in biomedical research for labeling and detecting biomolecules.
It absorbs light at 488 nm and emits green fluorescence, making it a popular choice for fluorescence microscopy, flow cytometry, and other imaging applications.
Alexa Fluor 488 offers excellent photostability, brightness, and resistance to photobleaching, allowing for high-quality visualization of target analytes.
Researchers can leverage the power of PubCompare.ai to optimize their Alexa Fluor 488 protocols, accessing the best procedures and products from the literature, preprints, and patents, thereby enhancing reproducibility and accuracy in their experiments.

Most cited protocols related to «Alexa fluor 488»

Cells were cultured on glass coverslips (Matsunami) pre-coated with 10 µg/ml fibronectin (Sigma) and fixed with 4% (w/v) paraformaldehyde in PBS or BRB80 [80 mM Pipes (pH 6.8), 1 mM MgCl2, and 1 mM EGTA] for 10 min at room temperature. Fixed cells were stained with the respective antibodies, phalloidin conjugated with either Alexa Fluor 488 or rhodamine (Invitrogen), along with DAPI (Sigma) as described previously2 (link), 54 (link). In situ proximity ligation assay (PLA) was performed using Duolink kit (Olink Bioscience) according to the manufacturer’s instructions. After completion of the PLA reaction, samples were refixed with 4% (w/v) paraformaldehyde and incubated with Alexa Fluor-conjugated secondary antibodies (Life Technologies) to detect the individual proteins. Fluorescence images were obtained using a laser scanning confocal imaging system (LSM700, Carl Zeiss) and processed using the ImageJ software. Number of Golgi fragments was quantified by using the ImageJ particle analysis tool. Colocalization was examined using the ImageJ JACoP plugin64 (link) or Metamorph (Molecular Devices).
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Publication 2017
alexa fluor 488 Antibodies Biological Assay Cells DAPI Egtazic Acid Fluorescence FN1 protein, human Golgi Apparatus Ligation Magnesium Chloride Medical Devices paraform Phalloidine piperazine-N,N'-bis(2-ethanesulfonic acid) Proteins Rhodamine
Genes were introduced into HEK 293T or COS-7 cells either through transient transfection with Lipofectamine 2000 or lentiviral infection. For lipofection, 100 ng of the APEX-fusion plasmid and 0.7 μL Lipofectamine 2000 in MEM (without serum) was used per well of a 48-well plate (0.95 cm2) of cells at 60-80% confluence. 3-6 hours later, the cell culture medium was changed back to fresh growth media. After 24 hours, biotin-phenol labeling was initiated by changing the medium to 200 μL of fresh growth media containing 500 μM biotin-phenol. This was incubated at 37°C under 5% CO2 for 30 minutes according to previously published protocols 1 (link). Afterwards, 2 μL of 100 mM H2O2 was added to each well, for a final concentration of 1 mM H2O2, and the plate gently agitated for 1 minute. The reaction was then quenched by addition of 200 μL of 10 mM Trolox and 20 mM sodium ascorbate in DPBS (for a final concentration of 5 mM Trolox and 10 mM sodium ascorbate). Cells were washed with DPBS containing 5 mM Trolox and 10 mM sodium ascorbate three times and fixed with 3.7% paraformaldehyde in DPBS at room temperature for 10 min. Cells were then washed with DPBS three times and permeabilized with cold methanol at -20°C for 5 min. Cells were washed again three times with DPBS and blocked for 1 hour with 3% BSA in DPBS (“blocking buffer”) at 4°C. To detect APEX-fusion expression, cells were incubated with either mouse-α-FLAG antibody (Agilent, 1:500 dilution) or mouse-α-V5 antibody (Invitrogen, 1:500 dilution) for 1 hour to overnight at 4°C. After washing three times with 0.2% Tween in DPBS, cells were simultaneously incubated with secondary Alexa Fluor 488 goat anti-mouse IgG (Life Technologies, 1:750 dilution) and homemade streptavidin-Alexa Fluor 568 conjugates for 1 hour at 4°C. Cells were then washed three times with 0.2% Tween in DPBS and maintained in DPBS on ice for imaging.
Confocal imaging was performed using a Zeiss Axio Observer. Z1 microscope equipped with a Yokogawa spinning disk confocal head and a Cascade II: 512 camera. The confocal head contained a Quad-band notch dichroic mirror (405/488/568/647 nm). Samples were excited by solid state 491 nm (∼20 mW) or 561 nm (∼20 mW) lasers. Images were acquired using Slidebook 5.0 software (Intelligent Imaging Innovations), through a 48 × oil-immersion objective for YFP/AF488 (528/38 emission filter), AF568 (617/73 emission filter), and differential interference contrast (DIC) channels. Acquisition times ranged from 10 to 1000 milliseconds. Imaging conditions and intensity scales were matched for each dataset presented together unless otherwise noted.
Publication 2014

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Publication 2015
alexa fluor 488 Alexa Fluor 647 DAPI Immunoglobulins Stains
Animals were perfused with 4% paraformaldehyde in 0.1 M PB. Brains were fixed for an additional 18 hr at 4°C. Brains were then cryoprotected in 20% (w/v) sucrose in PBS at 4°C overnight. Brains were embedded in OCT and 25-μm cryosections were cut using the tape transfer method. For direct imaging of XFP, sections were DAPI stained and coverslipped as above. For single-label immunofluorescence, sections were incubated for 30 min at room temperature in PBS containing 0.3% Triton X-100 and 5% normal goat serum (NGS). Sections were incubated with anti- GFP (Abcam; 1:1000 dilution) overnight at 4°C. Sections were rinsed for 30 min in PBS containing 1% NGS, incubated in goat anti-rabbit IgG-Alexa Fluor 488 (Invitrogen; 1:400 dilution) for 2 hr at room temperature, rinsed for 10 min in PBS containing 1% NGS, and rinsed for 30 min in PBS. Sections were then DAPI stained and coverslipped as above. XFP or IHC imaging was identical to the DFISH automated fluorescence microscopy method.
Publication 2009
alexa fluor 488 Animals anti-IgG Brain Cryoultramicrotomy DAPI Fluorescent Antibody Technique Goat Microscopy, Fluorescence paraform Rabbits Serum Sucrose Technique, Dilution Triton X-100
1×105 human fibroblasts were plated in DMEM with 10%FBS on a gelatin-coated 35mm plastic tissue culture dish. The next day polybrene was added to the media (5 ug/mL) and the cells were infected with hSTEMCCA-loxP lentiviruses at a multiplicity of infection (MOI)=0.1, 1, or 10 where indicated in the text. On day 2, the media was changed to serum-free ‘iPSC media’ (see below), and on day 6 the entire well was trypsinized and passed at a 1:16 split by plating onto two 10cm gelatin-coated culture dishes which had been pre-seeded the day before with mitomycin C-inactivated mouse embryonic fibroblast (MEF) feeder cells. iPSC colonies were mechanically isolated 30 days post-infection with the 4 factor hSTEMCCA-loxP or 45 days post-infection with the 3 factor hSTEMCCA-RedLight-loxP based on morphology and expanded on MEF feeders in iPSC media. For 3 factor reprogramming, where indicated, GSK3 inhibitor (Bio) (EMD Biosciences, 361550; 10μM) was added to the culture media on days 7–30 of reprogramming. Reprogramming efficiency was calculated by dividing the number of total colonies obtained on day 30 by the number of starting input fibroblasts. To avoid miscalculating efficiency as can occur when counting the progeny of passaged cells, efficiency was determined from separate experiments in which the input fibroblasts were not passaged onto feeders prior to colony counting.
Candidate iPSC clones were characterized based on staining for expression of alkaline phosphatase (Alkaline Phophatase Substrate Kit I, Vector Laboratories, SK – 5100) or immunostaining of 4% paraformaldehyde-fixed cell colonies with antibodies against SSEA-4, TRA1-60, and TRA1-81 (ES Cell Characterization Kit, Millipore, SCR001). Primary antibodies were detected with secondary Alexa Fluor 488-conjugated, goat anti-mouse IgG or IgM (Invitrogen, A10680). In addition, the number of hSTEMCCA lentiviral integrations was determined by Southern blot of gDNA digested with BamHI and probed for the WPRE element as previously published21 (link). RT-PCR was performed as previously described21 (link).
In order to evaluate the degree of DNA methylation of the human NANOG promoter, gDNA extracts of each indicated sample underwent bisulfite conversion using the EpiTect Bisulfite Kit (Qiagen). Quantitative methylation analyses of 6 CpG islands in the proximal NANOG promoter were performed via pyrosequencing by EpigenDx Inc (Worcester, MA) using the ADS502/Human NANOG promoter assay, spanning positions −565 to −431 relative to the NANOG ATG start site.
For teratoma formation assays, 6 wells of a 6 well plate of iPSC colonies were harvested with Collagenase IV and resuspended in 140μl of DMEM/F12. Immediately prior to injection, 60μl of Matrigel (BD Biosciences) was added to the cell suspension at 4°C, and the resulting mixture was injected sub-dermally between the scapulae of each anesthetized SCID–Beige mouse (Charles River, strain 250). Resulting tumors were harvested at 6–8 weeks after injection, fixed in 4% paraformaldehyde, and paraffin tissue sections were prepared and stained with hematoxylin and eosin according to standard methods.
Publication 2010

Most recents protocols related to «Alexa fluor 488»

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We first performed linear regression correlation using the Alexa Fluor 488 and Alexa Fluor 647 intensities from the uninfected samples, similar to calculating the Pearson's correlation 𝑟. This enabled us to identify the background correlation in the intensities. We obtained the b coefficient from the linear regression model and corrected the Alexa Fluor 647 intensities (𝑦 #$%&'()$ or adjusted 𝑟) for the infected and ACV-treated correlations as follows:
where 𝑦 &*#$%&'()$ were the unadjusted Alexa Fluor 647 intensities in the infected and ACV-treated data and 𝑥 were the Alexa Fluor 488 intensities in the infected and ACV-treated data.
To evaluate if the normalized Alexa Fluor 647 intensity distributions were lower in the uninfected versus infected cells within the same infected/ACV-treated sample, we calculated 1tailed Wilcoxon ranked sum tests (the P-values in the boxen plots).
Publication 2024

Example 10

Preparation of 70 kD amino dextran AF488 scaffold: 10 mg of amino dextran (70,000 μMW, 20 amino groups; Thermo Fisher Scientific, Cat. No. D1862) was dissolved in 1.2 ml of dry DMSO containing 1.0 μl of DIEA. 0.9 mg of ALEXA FLUOR™ 488 succinimidyl ester lithium salt (643 MF; Thermo Fisher Scientific, Cat. No. A20000) was added to solution and the mixture was stirred for 3.5 hours at ambient temperature. The solution was diluted with 12 mL of ethyl acetate and the resulting suspension was centrifuged. The supernatant was discarded and the solid material was shaken with 10 mL of fresh ethyl acetate and centrifuged. This washing was repeated 3 more times with 10 mL of fresh ethyl acetate and the resulting precipitate was dried in vacuum. The solid was re-dissolved in 0.5 ml of water and solution put in 10 cm Spectra/Por Dialysis membrane (Spectrum Labs, MWCO 12-14,000 flat width 10 mm) clipped from both side. The dialysis membrane was slowly stirred in 1 L of water for 1 week. The water was replaced twice per day. The dialysis membrane was open from one end and solution was lyophilized to give amino dextran ALEXA FLUOR™ scaffold. The measured DOL is 9.7 and relative QY is 0.6 (referenced to QY of ALEXA FLUOR™ 488).

Attaching thiol linker to 70 kD amino dextran AF488 scaffold: Amino dextran AF488 scaffold (4.5 mg) was dissolved in 0.5 mL of DMSO containing 0.055 μL of N,N-Diisopropylethylamine (DIEA). Succinimidyl 3-(2-pyridyldithio)propionate (SPDP) (20 μg) was added to solution and the mixture was kept at ambient temperature overnight and then capped with acetic acid succimidyl ester (1.0 mg, 3 hrs). The solution was diluted with 10 mL of ethyl acetate. The resulting suspension was centrifuged and supernatant discarded. The solid was shaken with 10 mL of fresh ethyl acetate and centrifuged. The washing was repeated 5 more times. The resulting solid was dried in vacuum. The measured DOL is 0.74. This material was re-dissolved in 2 mL of water and 16 mg of DT was added to solution. The mixture was stirred for 5 min and loaded on G15 SEPHADEX™) column, the product was eluted with DE water as green fluorescent solution which was used for conjugation to SMCC modified streptavidin. The determined concentration was 48 μM (by dye adsorption).

Conjugation of amino dextran AF488 scaffold modified with thiol linker to SMCC modified streptavidin: SMCC modified streptavidin (35 μL solution in water) was treated with 1, 2, 3 and 4 equivalents of thiol modified amino dextran AF488 scaffold (48 μM solution in water). The reaction was carried out at ambient temperature for 3 hours and after that reaction mixture was kept overnight at 4° C. overnight. The conjugates are purified on P100 size exclusion column with 10 nM PBS buffer.

TABLE 26
Streptavidin Labeled with 70 kD Amino dextran AF488 Scaffold
(average of 9.7 molecules of dye per scaffold)
DOL by ScaffoldDOL by Dye
(Avg.)(Avg.)QYBrightness
0.99.20.524.8
1.110.20.505.1
1.8180.539.5
2.625.50.5413.7

TABLE 27
Streptavidin labeled with AF488 dye per scaffold
DOL (Avg.)QYBrightness
1.50.701.0
3.00.601.8
4.00.552.1
4.50.401.8
5.00.341.7

Results: As shown in Tables 26 and 27, conjugates made from the scaffold are brighter as compared to conjugates made from single AF488 dye. Also, QY of AF488 fluorophore drops from 0.70 to 0.34 for single dye conjugation in contrast to almost constant QY for labeling with the amino dextran scaffold.

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Patent 2024

Example 10

Preparation of 70 kD amino dextran AF488 scaffold: 10 mg of amino dextran (70,000 MW, 20 amino groups; Thermo Fisher Scientific, Cat. No. D1862) was dissolved in 1.2 ml of dry DMSO containing 1.0 μl of DIEA. 0.9 mg of ALEXA FLUOR® 488 succinimidyl ester lithium salt (643 MF; Thermo Fisher Scientific, Cat. No. A20000) was added to solution and the mixture was stirred for 3.5 hours at ambient temperature. The solution was diluted with 12 mL of ethyl acetate and the resulting suspension was centrifuged. The supernatant was discarded and the solid material was shaken with 10 mL of fresh ethyl acetate and centrifuged. This washing was repeated 3 more times with 10 mL of fresh ethyl acetate and the resulting precipitate was dried in vacuum. The solid was re-dissolved in 0.5 ml of water and solution put in 10 cm Spectra/Por Dialysis membrane (Spectrum Labs, MWCO 12-14,000 flat width 10 mm) clipped from both side. The dialysis membrane was slowly stirred in 1 L of water for 1 week. The water was replaced twice per day. The dialysis membrane was open from one end and solution was lyophilized to give amino dextran ALEXA FLUOR® scaffold. The measured DOL is 9.7 and relative QY is 0.6 (referenced to QY of ALEXA FLUOR® 488).

Attaching thiol linker to 70 kD amino dextran AF488 scaffold: Amino dextran AF488 scaffold (4.5 mg) was dissolved in 0.5 mL of DMSO containing 0.055 μL of N,N-Diisopropylethylamine (DIEA). Succinimidyl 3-(2-pyridyldithio)propionate (SPDP) (20 μg) was added to solution and the mixture was kept at ambient temperature overnight and then capped with acetic acid succimidyl ester (1.0 mg, 3 hrs). The solution was diluted with 10 mL of ethyl acetate. The resulting suspension was centrifuged and supernatant discarded. The solid was shaken with 10 mL of fresh ethyl acetate and centrifuged. The washing was repeated 5 more times. The resulting solid was dried in vacuum. The measured DOL is 0.74. This material was re-dissolved in 2 mL of water and 16 mg of DTT was added to solution. The mixture was stirred for 5 min and loaded on G15 SEPHADEX® column, the product was eluted with DE water as green fluorescent solution which was used for conjugation to SMCC modified streptavidin. The determined concentration was 48 μM (by dye adsorption).

Conjugation of amino dextran AF488 scaffold modified with thiol linker to SMCC modified streptavidin: SMCC modified streptavidin (35 μL solution in water) was treated with 1, 2, 3 and 4 equivalents of thiol modified amino dextran AF488 scaffold (48 μM solution in water). The reaction was carried out at ambient temperature for 3 hours and after that reaction mixture was kept overnight at 4° C. overnight. The conjugates are purified on P100 size exclusion column with 10 nM PBS buffer.

TABLE 26
Streptavidin Labeled with 70 kD Amino dextran AF488
Scaffold (average of 9.7 molecules of dye per scaffold)
DOL by ScaffoldDOL by Dye
(Avg.)(Avg.)QYBrightness
0.99.20.524.8
1.110.20.505.1
1.8180.539.5
2.625.50.5413.7 

TABLE 27
Streptavidin labeled with AF488 dye
DOL (Avg.)QYBrightness
1.50.701.0
3.00.601.8
4.00.552.1
4.50.401.8
5.00.341.7

Results: As shown in Tables 26 and 27, conjugates made from the scaffold are brighter as compared to conjugates made from single AF488 dye. Also, QY of AF488 fluorophore drops from 0.70 to 0.34 for single dye conjugation in contrast to almost constant QY for labeling with the amino dextran scaffold.

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Patent 2024
Secondary antibodies used were: Donkey αMouse, Alexa Fluor 594 (Dianova, 711585150); Donkey αRabbit, Alexa Fluor 488 (Invitrogen, A21206); Goat αMouse, Alexa Fluor 488 (Invitrogen, A11001); Donkey αGoat, Alexa Fluor 488 (Invitrogen, A11055); Donkey αGoat, Alexa Fluor 555 (Invitrogen, A21432).
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Publication 2024
To determine the fluorescence intensity of a single Alexa Fluor 488 fluorophore on actin, we monitored filaments sparsely labeled with Alexa Fluor 488. Mother filaments were polymerized using 0.8 μM labeled G-actin (containing 10% Alexa Fluor 568–actin and 0.1% Alexa Fluor 488–actin). Then, by testing different laser powers and acquisition times, we determined a set of illumination conditions (100% laser power, 1000 ms acquisition time) that ensure the clear detection of a single Alexa Fluor 488 fluorophore in our setup.
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Publication 2024

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Alexa Fluor 488 is a fluorescent dye used in various biotechnological applications. It has an excitation maximum at 495 nm and an emission maximum at 519 nm, producing a green fluorescent signal. Alexa Fluor 488 is known for its brightness, photostability, and pH-insensitivity, making it a popular choice for labeling biomolecules in biological research.
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DAPI is a fluorescent dye used in microscopy and flow cytometry to stain cell nuclei. It binds strongly to the minor groove of double-stranded DNA, emitting blue fluorescence when excited by ultraviolet light.
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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
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Triton X-100 is a non-ionic surfactant commonly used in various laboratory applications. It functions as a detergent and solubilizing agent, facilitating the solubilization and extraction of proteins and other biomolecules from biological samples.
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Alexa Fluor 488 phalloidin is a fluorescent dye that selectively binds to F-actin, a component of the cytoskeleton. It is used in microscopy and flow cytometry applications to visualize and study the distribution and organization of actin filaments within cells.
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Bovine serum albumin (BSA) is a common laboratory reagent derived from bovine blood plasma. It is a protein that serves as a stabilizer and blocking agent in various biochemical and immunological applications. BSA is widely used to maintain the activity and solubility of enzymes, proteins, and other biomolecules in experimental settings.
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Hoechst 33342 is a fluorescent dye that binds to DNA. It is commonly used in various applications, such as cell staining and flow cytometry, to identify and analyze cell populations.
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Alexa Fluor 594 is a fluorescent dye developed by Thermo Fisher Scientific. It is designed to emit light in the red-orange region of the visible spectrum when excited with appropriate wavelengths of light. The dye can be used in various biological and biochemical applications that require a fluorescent label.
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Alexa Fluor 488 goat anti-rabbit IgG is a fluorescent-labeled secondary antibody. It is used for the detection and visualization of rabbit primary antibodies in various immunochemical applications, such as immunofluorescence, flow cytometry, and Western blotting.
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Alexa Fluor 488 goat anti-mouse IgG is a secondary antibody conjugate used for the detection and visualization of mouse immunoglobulin G (IgG) in various immunoassays. The Alexa Fluor 488 dye is covalently attached to the goat anti-mouse IgG antibody, providing a bright fluorescent signal for identification and localization of the target protein.

More about "Alexa fluor 488"

Alexa Fluor 488 is a widely used fluorescent dye in biomedical research, known for its exceptional photostability, brightness, and resistance to photobleaching.
This green-fluorescent dye is commonly employed in various applications, such as fluorescence microscopy, flow cytometry, and imaging studies, allowing for high-quality visualization of target biomolecules.
One of the key advantages of Alexa Fluor 488 is its ability to absorb light at 488 nm and emit a vibrant green fluorescence, making it a popular choice among researchers.
This property aligns well with the excitation and emission spectra of commonly used lasers and filter sets, ensuring efficient and reliable detection.
Alongside Alexa Fluor 488, other fluorescent dyes like DAPI (4',6-diamidino-2-phenylindole) and Alexa Fluor 594 are also widely utilized in biomedical research.
DAPI is a blue-fluorescent dye that binds to DNA, while Alexa Fluor 594 is a red-fluorescent dye with different excitation and emission characteristics.
The combination of these fluorescent probes allows for multiplexed labeling and simultaneous detection of various cellular structures or biomolecules.
To enhance the performance of Alexa Fluor 488-based experiments, researchers can leverage detergents like Triton X-100 to facilitate permeabilization and improve antibody or probe accessibility.
Additionally, blocking agents such as Bovine Serum Albumin (BSA) can be used to minimize non-specific binding and improve signal-to-noise ratios.
Fluorescent-conjugated secondary antibodies, such as Alexa Fluor 488 goat anti-rabbit IgG and Alexa Fluor 488 goat anti-mouse IgG, can be employed to amplify the fluorescent signal and enable the detection of target proteins or other biomolecules.
To optimize Alexa Fluor 488 protocols and enhance the reproducibility and accuracy of their experiments, researchers can utilize the power of PubCompare.ai.
This AI-driven platform helps researchers access the best procedures and products from the literature, preprints, and patents, ensuring they have the most up-to-date and effective methods at their fingertips.
By incorporating these insights and leveraging the versatility of Alexa Fluor 488, researchers can unlock new possibilities in their biomedical investigations, from cellular imaging to flow cytometry and beyond.
PubCompare.ai can be a valuable tool in this endeavor, guiding researchers towards the most efficient and reliable Alexa Fluor 488 protocols and contributing to the advancement of their research.