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BODIPY

BODIPY (4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene) is a family of fluorescent dye molecules widely used in biological research.
These dyes offer excellent photostability, high quantum yields, and tunable spectral properties, making them valuable tools for labeling, imaging, and sensing applications.
PubCompare.ai's AI-driven platform helps researchers optimize BODIPY experiments by locating the best protocols and products from literature, preprints, and patents.
Its intelligent comparisons enhance reproducibility and accuaracy, ensuring reliable results.
Experience the power of AI-driven research optimization for your BODIPY studies today.

Most cited protocols related to «BODIPY»

1
ABCG2 Transfection in HEK-293 Cells
Cited 58 times
HEK-293 cells were transfected with either empty pcDNA3 vector (Invitrogen, Carlsbad, CA, USA) or pcDNA3 vector containing full-length ABCG2 coding either an arginine, threonine or glycine for amino-acid 482. Expression of ABCG2 in the transfectants was enforced by selection in G418 (Invitrogen, Carlsbad, CA, USA). Stable transfectants were maintained in Eagle's minimum essential medium (ATCC, Manassas, VA, USA) supplemented with 10% FCS, penicillin, and streptomycin with G418 at a concentration of 2 mg ml−1. Clones were preliminarily screened for ABCG2 expression by examining the ability of the cells to efflux BODIPY-prazosin in a flow cytometry-based assay. The ABCG2 sequence was subsequently verified in the clones examined here.
Robey R.W., Honjo Y., Morisaki K., Nadjem T.A., Runge S., Risbood M., Poruchynsky M.S, & Bates S.E. (2003). Mutations at amino-acid 482 in the ABCG2 gene affect substrate and antagonist specificity. British Journal of Cancer, 89(10), 1971-1978.
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Publication 2003
Amino Acids antibiotic G 418 Arginine Biological Assay BODIPY Clone Cells Cloning Vectors Flow Cytometry Glycine HEK293 Cells Penicillins Prazosin Streptomycin Threonine
2
Lipid Staining and Quantification in C. elegans
Cited 44 times

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Publication 2009
Animals Bacteria BODIPY Escherichia coli Eye Fatty Acids Freezing Isopropyl Alcohol Lipids Microscopy, Confocal paraform solvent red 27 Stains Sulfoxide, Dimethyl
3
Oxidative Stress Assessment in Cell Lines
Cited 43 times

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Publication 2012
2',7'-dichlorodihydrofluorescein diacetate BODIPY Cells Hanks Balanced Salt Solution Hemoglobin, Sickle Hyperostosis, Diffuse Idiopathic Skeletal MitoSOX Molecular Probes Tissues
4
3D Culture Lipid Droplet Analysis
Cited 24 times
To analyze their lipid droplet formation for the 3D culture, the organoids were transferred to 6 super-low attachment well dishes, incubated in 0.2% BODIPY (# D3922, Thermo Fisher Scientific) in PBS for 1 hr, and then fixed in 4% paraformaldehyde (PFA) in PBS for 10 min at room temperature. Fluorescence intensity of the BODIPY-stained lipid droplets was measured using a Nikon A1 confocal microscope (Tokyo, Japan) and quantified using Image J software version 2.0.0 (NIH, Bethesda, MD).
For immunostaining of the 3D culture, organoids prepared as above were fixed in 4% PFA/PBS overnight. After blocking in 3% BSA/0.1% PBS for 3 hrs at room temperature, organoids were washed 3 times for 30 min with PBS. Samples were incubated with a primary antibody including a rabbit anti-collagen monoclonal antibody (collagen 1; # 600-401-103-0.1, collagen 4; # 600-401-106-0.1, or collagen 6; # 600-401-108-0.1, Rockland Immuno-chemicals Inc.) or mouse anti-FN monoclonal antibody (# G0717, Santa Cruz Biotechnology) at 1:200 dilutions overnight at 4 °C. After a subsequent wash in PBS, the organoids were incubated with goat Alexa Fluor 488 anti-rabbit IgG (# A-11070, Thermo Fischer Scientific) or goat Alexa Fluor 594 anti-mouse IgG (# A-11020, Thermo Fischer Scientific) at 1:500 dilutions for 3 hrs at room temperature. Subsequently, for F-actin and nuclear staining, slides were incubated with Alexa Fluor 594 phalloidin (# 20553, Funakoshi) and DAPI (# D523, Dojindo) at 1:1000 dilutions for 3 hrs at room temperature. Slides were then mounted in Prolong Gold before observation by confocal microscope.
Ida Y., Hikage F., Itoh K., Ida H, & Ohguro H. (2020). Prostaglandin F2α agonist-induced suppression of 3T3-L1 cell adipogenesis affects spatial formation of extra-cellular matrix. Scientific Reports, 10, 7958.
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Publication 2020
Alexa594 alexa fluor 488 anti-IgG Antibodies, Anti-Idiotypic BODIPY Collagen Collagen Type I DAPI F-Actin Fluorescence Goat Gold Hyperostosis, Diffuse Idiopathic Skeletal Immunoglobulins Lipid Droplet Lipogenesis Mice, House Microscopy, Confocal Monoclonal Antibodies Organoids paraform Phalloidine Rabbits Technique, Dilution
5
Optimizing Cholesterol Efflux Capacity Assay
Cited 20 times
Blood collected from all the participants at baseline by means of venipuncture was placed into EDTA tubes, stored at 4°C for less than 4 hours, and centrifuged, and plasma was removed and stored at −70°C. Plasma lipids, including HDL cholesterol, were measured as described previously.11 (link) HDL particle concentration and size were measured by means of nuclear magnetic resonance spectroscopy (LipoScience).
Cholesterol efflux capacity was assessed by measuring the efflux of fluorescence-labeled cholesterol from J774 macrophages to apolipoprotein B–depleted plasma in study participants with the use of a previously described method.12 (link) This assay primarily evaluates cholesterol efflux as mediated by ATP-binding cassette transporter A1 (ABCA1). The fluorescence-labeled reagent, termed boron dipyrromethene difluoride (BODIPY) cholesterol, was used because it is more amenable to use in a large number of samples than radiolabeled cholesterol (details of the assay protocol are provided in the Supplementary Appendix). For comparison, we performed a parallel assessment of efflux capacity with the use of radiolabeled cholesterol in a limited number of plasma samples.9 (link)Cholesterol efflux capacity measured with the use of fluorescence-labeled cholesterol was moderately correlated with measurements performed with radiolabeled cholesterol (correlation coefficient for normalized cholesterol efflux, 0.54) (Fig. S1 in the Supplementary Appendix). The cholesterol efflux capacity did not change significantly when it was measured in samples obtained throughout a single day or 7 days apart (Fig. S2 in the Supplementary Appendix) or when samples underwent a freeze–thaw cycle (Fig. S3A and S3B in the Supplementary Appendix). However, as compared with 3-to-12-month storage at −70°C, parallel storage of plasma at −20°C reduced cholesterol efflux capacity measured with the use of either fluorescence-labeled cholesterol or radiolabeled cholesterol (Fig. S3C and S3D in the Supplementary Appendix). Measurements of cholesterol efflux capacity in this study were therefore performed with the use of the fluorescence-labeled cholesterol assay on plasma samples stored at −70°C.
Rohatgi A., Khera A., Berry J.D., Givens E.G., Ayers C.R., Wedin K.E., Neeland I.J., Yuhanna I.S., Rader D.R., de Lemos J.A, & Shaul P.W. (2014). HDL Cholesterol Efflux Capacity and Incident Cardiovascular Events. The New England journal of medicine, 371(25), 2383-2393.
Publication 2014
ABCA1 protein, human Apolipoproteins B Biological Assay BLOOD BODIPY boron difluoride Cholesterol dipyrromethene Edetic Acid Fluorescence Freezing High Density Lipoprotein Cholesterol Lipids Macrophage Plasma Spectroscopy, Nuclear Magnetic Resonance Venipuncture

Most recents protocols related to «BODIPY»

1
Synthesis of a BODIPY-based pH Sensor
Not available on PMC !

Example 117

[Figure (not displayed)]

BODIPY pH-sensor 163. To a solution of aldehyde 159 (0.336 g, 1 mmol) in CH2Cl2 (50 mL) 2,4-dimethylpyrrole (0.25 mL, 2.4 mmol) was added, followed by TFA (0.09 mL, 1.2 mmol). The reaction was stirred for 16 h, diluted with CHCl3 (200 mL) and washed successively with 1% Me4NOH (2×50 mL), water (50 mL), brine (50 mL), filtered through paper filter, evaporated and co-evaporated with toluene (2×30 mL). The residue was dissolved in toluene (25 mL), stirred with chloranil (0.295 g, 1.2 mmol) for 2 h, then DIEA (1.74 mmol, 10 mmol) was added, followed by Et2OBF3 (1.0 mL, 8 mmol). The mixture was stirred for 4 h, evaporated, and the residue was purified on a silica gel column (3×45 cm bed, packed with 5% MeOH and 1% AcOH in CHCl3), eluant: 5% MeOH and 1% AcOH in CHCl3. The fractions containing the compound were evaporated, and chromatographed again on the second silica gel column (4×50 cm bed, packed in EtOAc/hexanes (1:1), eluant: EtOAc/hexanes (1:1) to get compound 163 (0.180 g, 32%) as an orange oil.

US11867698B2. Fluorogenic pH sensitive dyes and their method of use (2024-01-09). Life Technologies Corporation [US]. Inventors: Jeffrey Dzubay [US], Kyle Gee [US], Vladimir Martin [US], Aleksey Rukavishnikov [US], Daniel Beacham [US].
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Patent 2024
Aldehydes Anabolism BODIPY brine Chloranil Chloroform Hexanes N,N-diisopropylethylamine orange oil PH 163 Silica Gel Toluene
2
Synthesis of BODIPY pH-sensor 158
Not available on PMC !

Example 114

[Figure (not displayed)]

BODIPY pH-sensor 158. To a solution of aldehyde 153 (0.323 g, 1 mmol) in CH2Cl2 (50 mL) 2,4-dimethylpyrrole (0.25 mL, 2.4 mmol) was added, followed by TFA (0.09 mL, 1.2 mmol). The reaction was stirred for 16 h, diluted with CHCl3 (200 mL), washed successively with 1% Me4NOH (2×50 mL), water (50 mL), brine (50 mL), filtered through paper filter, evaporated and co-evaporated with toluene (2×30 mL). The residue was dissolved in toluene (25 mL) and stirred with chloranil (0.295 g, 1.2 mmol) for 2 h, then DIEA (1.74 mmol, 10 mmol) was added, followed by Et2OBF3 (1.0 mL, 8 mmol). The mixture was stirred for 4 h, evaporated, and the residue was purified on a silica gel column (4×50 cm bed, packed with 3% MeOH and 1% AcOH in CHCl3), eluant: 3% MeOH and 1% AcOH in CHCl3. The fractions containing the compound were evaporated, and co-evaporated with toluene (3×20 mL). The residue was dissolved in CHCl3 (200 mL), allowed to stand for 2 h, filtered from precipitating silicates and evaporated to get compound 158 (0.210 g, 39%) as an orange oil.

US11867698B2. Fluorogenic pH sensitive dyes and their method of use (2024-01-09). Life Technologies Corporation [US]. Inventors: Jeffrey Dzubay [US], Kyle Gee [US], Vladimir Martin [US], Aleksey Rukavishnikov [US], Daniel Beacham [US].
Full text: Click here
Patent 2024
Aldehydes Anabolism BODIPY brine Chloranil Chloroform N,N-diisopropylethylamine orange oil Silica Gel Silicates Toluene
3
Preparation of NI-BODIPY-GO Nanocarriers
Commercial GO was used for the preparation
of NI-BODIPY-GO nanocarriers
according to the modified method previously reported elsewhere.1 (link) Briefly, 20 mg of GO was dispersed in 60 mL of
distilled water by ultrasonication (1.5 h) to obtain a homogeneous
suspension of GO. Afterward, 20 mg of NI-BODIPY derivative (10–12) was added and magnetically stirred
at room temperature for several minutes. Then, the mixture was stirred
for 40 h for dye adsorption on GO at room temperature. The resulting
mixture was filtered through a polycarbonate membrane with 0.2 mm
pores, and the obtained solid material was washed with water several
times to remove the excess of compounds 10–12 then dried in a vacuum oven for 48 h at 45 °C.
Öztürk Gündüz E., Tasasız B., Gedik M.E., Günaydın G, & Okutan E. (2023). NI-BODIPY-GO Nanocomposites for Targeted PDT. ACS Omega, 8(9), 8320-8331.
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Publication 2023
Adsorption BODIPY polycarbonate Tissue, Membrane Vacuum
4
Synthesis of BODIPY Derivatives
In a three-necked
100 mL round-bottom flask, BODIPY derivatives
(4–6) (1 eqv.) and compound 1 (2.4 eqv.) were dissolved in 40 mL of benzene. Piperidine
(0.3 mL) and glacial acetic acid (0.3 mL) were added. The solution
was refluxed using a Dean–Stark apparatus. When the solution
was concentrated, the reaction was followed by TLC until the starting
compound (4–6) was consumed. The
reaction mixture was extracted with dichloromethane/water (200 mL,
three times), and the organic layer was dried over anhydrous Na2SO4 and concentrated on a rotary evaporator until
the solvent was removed. Compounds 7–9 were isolated by column chromatography on silica gel (230–400
mesh).
Öztürk Gündüz E., Tasasız B., Gedik M.E., Günaydın G, & Okutan E. (2023). NI-BODIPY-GO Nanocomposites for Targeted PDT. ACS Omega, 8(9), 8320-8331.
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Publication 2023
Acetic Acid Benzene BODIPY Chromatography derivatives Methylene Chloride piperidine Silica Gel Solvents
5
Singlet Oxygen Generation by Photosensitizers
The 1O2 generating ability of compounds 10–12 and nanocarriers [(GO-10-12)] was
employed in both dichloromethane and PBS. 1O2 trap molecules DPBF and ABDA were used. MB was studied as a reference
triplet PS. 1O2 formation can be traced using
photobleaching and subsequent decrease in absorbance of DPBF (414
nm) and ADBA (360, 380, and 400 nm). 630 nm (4.0 mW/cm2) for DCM and 660 nm (25 mW/cm2) for PBS LED bulbs were
used as light sources. The light sources were exposed from a 5 cm
cell distance, and absorbances were taken at intervals for each solution
of PSs. Equation 2 was
used to calculate the 1O2 quantum yields where
dyad and ref refer to “NI-BODIPY and NI-BODIPY-GO” and
“MB”, respectively. k is the slope
of difference in change in absorbance of DPBF (414 nm) with irradiation
time. F is the absorption correction factor, which
is given by F = 1–10–OD (OD
is the absorption at the irradiation wavelength), and PF is light
intensity (energy flux, mW/ cm2), which was used to calculate 1O2 quantum yields.
Öztürk Gündüz E., Tasasız B., Gedik M.E., Günaydın G, & Okutan E. (2023). NI-BODIPY-GO Nanocomposites for Targeted PDT. ACS Omega, 8(9), 8320-8331.
Full text: Click here
Publication 2023
BODIPY Light Methylene Chloride Plant Bulb Radiotherapy

Top products related to «BODIPY»

1
Bodipy 581 591 c11 by Thermo Fisher Scientific
Sourced in United States, Germany, China, Italy, Japan
BODIPY 581/591 C11 is a fluorescent lipid probe used for the detection and quantification of lipid peroxidation in biological samples. It exhibits a shift in fluorescence emission from red to green upon oxidation, allowing for the monitoring of oxidative processes.
2
Bodipy by Thermo Fisher Scientific
Sourced in United States, Germany, Japan, Canada, United Kingdom
BODIPY is a fluorescent dye used for labeling and detection in various biological applications. It has a core structure consisting of a boron-dipyrromethene (BODIPY) group, which provides intense fluorescence and photostability. BODIPY dyes can be conjugated to a wide range of molecules, enabling the visualization and tracking of biological processes.
3
Bodipy 493 503 by Thermo Fisher Scientific
Sourced in United States, Germany, Italy, China, United Kingdom, Japan, France, Switzerland, Belgium
BODIPY 493/503 is a fluorescent dye that can be used to stain neutral lipids and lipid droplets. It has an excitation maximum at 493 nm and an emission maximum at 503 nm.
4
C11 bodipy by Thermo Fisher Scientific
Sourced in United States, Germany, China
C11-BODIPY is a fluorescent lipid probe designed for visualization and quantification of lipid dynamics in live cells. It consists of a BODIPY fluorescent dye attached to an eleven-carbon alkyl chain. This probe can be used to monitor lipid-related cellular processes.
5
Aldefluor kit by STEMCELL
Sourced in Canada, United States, France, China, United Kingdom, Germany, Japan, Italy
The ALDEFLUOR kit is a laboratory tool used for the identification and isolation of cells with high aldehyde dehydrogenase (ALDH) activity. It provides a standardized method for the analysis and sorting of ALDH-bright cells from cell samples.
6
C11 bodipy581 591 by Thermo Fisher Scientific
Sourced in United States, China, Spain, Morocco
C11-BODIPY581/591 is a fluorescent lipid probe used for the detection and measurement of lipid peroxidation in biological samples. It exhibits a shift in fluorescence emission from red to green upon oxidation, allowing for the monitoring of this process.
7
Hoechst 33342 by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, Japan, China, France, Canada, Spain, Belgium, Italy, Australia, Austria, Denmark, Netherlands, Switzerland, Ireland, New Zealand, Portugal, Brazil, Argentina, Singapore, Poland, Ukraine, Macao, Thailand, Finland, Lithuania, Sweden
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.
8
4 6 diamidino 2 phenylindole (dapi) by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, Japan, China, Canada, Italy, Australia, France, Switzerland, Spain, Belgium, Denmark, Panama, Poland, Singapore, Austria, Morocco, Netherlands, Sweden, Argentina, India, Finland, Pakistan, Cameroon, New Zealand
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.
9
Facscalibur by BD
Sourced in United States, Germany, United Kingdom, China, Canada, Japan, Italy, France, Belgium, Switzerland, Singapore, Uruguay, Australia, Spain, Poland, India, Austria, Denmark, Netherlands, Jersey, Finland, Sweden
The FACSCalibur is a flow cytometry system designed for multi-parameter analysis of cells and other particles. It features a blue (488 nm) and a red (635 nm) laser for excitation of fluorescent dyes. The instrument is capable of detecting forward scatter, side scatter, and up to four fluorescent parameters simultaneously.
10
Facscanto 2 by BD
Sourced in United States, Germany, United Kingdom, Belgium, China, Australia, France, Japan, Italy, Spain, Switzerland, Canada, Uruguay, Netherlands, Czechia, Jersey, Brazil, Denmark, Singapore, Austria, India, Panama
The FACSCanto II is a flow cytometer instrument designed for multi-parameter analysis of single cells. It features a solid-state diode laser and up to four fluorescence detectors for simultaneous measurement of multiple cellular parameters.

More about "BODIPY"

BODIPY (4,4-Difluoro-4-bora-3a,4a-diaza-s-indacene) is a family of fluorescent dye molecules widely used in biological research.
These dyes, also known as BODIPY 581/591 C11, BODIPY 493/503, and C11-BODIPY, offer excellent photostability, high quantum yields, and tunable spectral properties, making them valuable tools for labeling, imaging, and sensing applications.
The ALDEFLUOR kit, which utilizes BODIPY-based fluorescent dyes, is commonly used for the identification and isolation of stem and progenitor cells.
C11-BODIPY581/591, a BODIPY-derived dye, is a popular choice for monitoring lipid peroxidation in cells and tissues.
Researchers can optimize their BODIPY experiments by utilizing PubCompare.ai's AI-driven platform.
This intelligent system helps users locate the best protocols and products from literature, preprints, and patents, enhancing reproducibility and accuracy.
The platform's comparisons ensure reliable results, empowering researchers to make informed decisions and advance their BODIPY-related studies.
Beyond BODIPY, researchers may also use other fluorescent dyes like Hoechst 33342 and DAPI for nuclear staining, as well as flow cytometry instruments like FACSCalibur and FACSCanto II for cell analysis and sorting.
By combining the power of BODIPY dyes with cutting-edge research optimization tools and complementary techniques, scientists can unlock new insights and drive progress in their fields of study.