Organelle Dyes

BODIPY493/503 is a BODIPY dye. BODIPY dye is a small molecule dye with strong ultraviolet absorption ability, its fluorescence peak is relatively sharp, and the quantum yield is high. They are relatively insensitive to the polarity and pH of the environment and are relatively stable under different physiological conditions. Due to its structural asymmetry, BODIPY derives a variety of structural products. BODIPY lipid droplet dyes can well pass through the cell membrane into the cell, and localize the neutral lipids in the cell to specifically stain the lipid droplets, which can be used for labeling of live cells and fixed cells. Maximum excitation/emission wavelength: 493/503 nm.

DiR is a long-chain carbocyanine dye. Carbocyanine dyes are widely used as Di to label cells, organelles, liposomes, viruses and lipoproteins.

Hoechst 33342 is a marker dye in Hoechst series. Hoechst is A live nuclear marker dye. Hoechst binds to the grooves in the DNA double strand, which tends to be A/ T-rich DNA strand. Although it binds to all nucleic acids, the A/ T-rich double strand DNA significantly enhances fluorescence intensity Therefore,Hoechst dye can be used for living cell labeling. The fluorescence intensity of Hoechst dye increases with the increase of pH of solution.

CFDA-SE is a fluorescent dye that can penetrate the cell membrane. It can react with the free amine group in the cytoskeleton protein inside the cell, and finally form a protein complex with fluorescence. After entering the cell, CFDA-SE locates in the cell membrane, cytoplasm and nucleus, and the fluorescence staining is strongest in the nucleus. CFDA-SE dye can be uniformly inherited by the cells with cell division and proliferation, and its attenuation is proportional to the number of cell divisions. This phenomenon can be detected and analyzed by flow cytometry under the excitation light of 488 nm, and can be used to detect the proliferation of cells.

JC-1 (CBIC2) is an ideal fluorescent probe widely used to detect mitochondrial membrane potential. JC-1 accumulates in mitochondria in a potential dependent manner and can be used to detect the membrane potential of cells or purified mitochondria. In normal mitochondria, JC-1 aggregates in the mitochondrial matrix to form a polymer, which emits strong red fluorescence (Ex=585 nm, Em=590 nm); When the mitochondrial membrane potential is low, JC-1 cannot aggregate in the matrix of mitochondria and produce green fluorescence (ex=510 nm, em= 527 nm).

Di-4-ANEPPDHQ (solution) is a polarity-sensitive membrane probe with a doubly positive charge that can be used to visualize membrane microdomains in living Arabidopsis cells. Di-4-ANEPPDHQ produces a fluorescence spectrum shift by changing the polarity of the lipid environment after embedding into the cell membrane, thereby quantifying the degree of lipid accumulation. The excitation wavelength of Di-4-ANEPPDHQ is 488 nm, and the emission wavelengths are 560 nm and 650 nm in the liquid ordered and disordered phases, respectively. Di-4-ANEPPDHQ is often used for fluorescence imaging studies of membrane microstructure, lipid order, and membrane tension response in living cells[1][2][3].
Solvent and concentration: DMSO: 5 mM

DAPI (4',6-Diamidino-2-phenylindole) dihydrochloride (solution) is a DAPI dye. DAPI is a fluorescent dye that binds strongly to DNA. It binds to the AT base pair of the double-stranded DNA minor groove, and one DAPI molecule can occupy three base pair positions. The fluorescence intensity of DAPI molecules bound to double-stranded DNA is increased by about 20 times, and it is commonly observed with fluorescence microscopy, and the amount of DNA can be determined based on the intensity of fluorescence. DAPI cannot penetrate intact cell membranes and is commonly used for staining damaged and fixed cells. DAPI (Compound 3) is an acid-sensing ion channel 3 (ASIC3) inhibitor. DAPI binds to ASIC3 and blocks the channel function. DAPI can be used in the study of chronic pain treatment (Ex/Em = 356/451 nm).
Solvent and concentration: ddH2O: 5 mg/mL

Fluo-3AM (solution) is a fluorecent Ca²⁺ chelator, with high affinity for calcium. Fluo-3 AM can specifically identify intracellular calcium ions, with high sensitivity, low cytotoxicity, increased AM acetylmethyl ester can enter the cell well, after being sheared by the intracellular esterase stay in the cell to bind to calcium ions, produce strong fluorescence.
Solvent and concentration: DMSO: 5 mM

Nile red (Nile blue oxazone) is a lipophilic stain. Nile red has environment-sensitive fluorescence. Nile red is intensely fluorescent in a lipid-rich environment while it has minimal fluorescence in aqueous media. Nile red is an excellent vital stain for the detection of intracellular lipid droplets by fluorescence microscopy and flow cytof uorometry. Nile red stains intracellular lipid droplets red. The fluorescence wavelength is 559/635 nm.

Dihydroethidium, also known as DHE, is a peroxide indicator. Dihydroethidium penetrates cell membranes to form a fluorescent protein complex with blue fluoresces. After entering the cells, Dihydroethidium is mainly localized in the cell membrane, cytoplasm and nucleus, and the staining effect is the strongest in the nucleus. Dihydroethidium produces inherent blue fluorescence with a maximum excitation wavelength of 370 nm and a maximum emission wavelength of 420 nm; after dehydrogenation, Dihydroethidium combines with RNA or DNA to produce red fluorescence with a maximum excitation wavelength of 300 nm and a maximum emission wavelength of 610 nm. 535 nm can also be used as the excitation wavelength for actual observation.

Propidium Iodide (PI) is a nuclear staining agent that stains DNA. Propidium Iodide is an analogue of ethidine bromide that emits red fluorescence upon embedding in double-stranded DNA. Propidium Iodide cannot pass through living cell membranes, but it can pass through damaged cell membranes to stain the nucleus. Propidium Iodide has a fluorescence wavelength of 493/617 nm and a wavelength of 536/635 nm after Mosaic with DNA. Propidium Iodide is commonly used in the detection of apoptosis (apoptosis) or necrosis (necrosis), and is often used in flow cytometry analysis.

DiI is a long-chain carbocyanine dye. Carbocyanine dyes are widely used as Di to label cells, organelles, liposomes, viruses and lipoproteins.

DAPI (4',6-Diamidino-2-phenylindole) dihydrochloride is a DAPI dye. DAPI is a fluorescent dye that binds strongly to DNA. It binds to the AT base pair of the double-stranded DNA minor groove, and one DAPI molecule can occupy three base pair positions. The fluorescence intensity of DAPI molecules bound to double-stranded DNA is increased by about 20 times, and it is commonly observed with fluorescence microscopy, and the amount of DNA can be determined based on the intensity of fluorescence. DAPI cannot penetrate intact cell membranes and is commonly used for staining damaged and fixed cells. DAPI (Compound 3) is an acid-sensing ion channel 3 (ASIC3) inhibitor. DAPI binds to ASIC3 and blocks the channel function. DAPI can be used in the study of chronic pain treatment (Ex/Em = 356/451 nm).

DiO is a long-chain carbocyanine dye. Carbocyanine dyes are widely used as Di to label cells, organelles, liposomes, viruses and lipoproteins.

DiD is a long-chain carbocyanine dye. Carbocyanine dyes are widely used as Di to label cells, organelles, liposomes, viruses and lipoproteins (Ex/Em = 633/665 nm).

Rhodamine dyes are membrane-permeable cationic fluorescent probes that specifically recognize mitochondrial membrane potentials, thereby attaching to mitochondria and producing bright fluorescence, and at certain concentrations, rhodamine dyes have low toxicity to cells, so they are commonly used to detect mitochondria in animal cells, plant cells, and microorganisms.

Mito-Tracker Green is a green fluorescent dye that selectively accumulates in the mitochondrial matrix. MitoTracker Green FM covalently binds mitochondrial proteins by reacting with free mercaptan of cysteine residues, allowing staining of mitochondrial membrane potential independent of membrane potential. Excitation/emission wavelength 490/523 nm.

MitoTracker Deep Red (MTDR) FM fluorescent dye that selectively accumulates in the mitochondrial matrix. MitoTracker Deep Red FM covalently binds mitochondrial proteins by reacting with free mercaptan of cysteine residues, allowing staining of mitochondrial membrane potential independent of membrane potential. Excitation/emission wavelength 644/665 nm. MitoTracker Deep Red dyes have an excitation/emission wavelength of 633/650-750 nm.
The Ex/Em of MitoTracker Deep Red (MTDR) FM is 644/665 nm.

Rhodamine dyes are membrane-permeable cationic fluorescent probes that specifically recognize mitochondrial membrane potentials, thereby attaching to mitochondria and producing bright fluorescence, and at certain concentrations, rhodamine dyes have low toxicity to cells, so they are commonly used to detect mitochondria in animal cells, plant cells, and microorganisms.

RhoNox-1 is a fluorescent probe for the specific detection of divalent iron ions, and when RhoNox-1 reacts with Fe²⁺. RhoNox-1 can generate an irreversible orange (red) fluorescent product (Ex/Em：540/575 nm) . FeRhoNox-1 can enter the cell well, suitable for the detection of Fe²⁺ in living cells, and tends to be localized in the Golgi apparatus.