Cell Organelle Stains For Targeted Cell Structure Analysis

Cell Stains

AAT Bioquest® offers an extensive selection of high-quality cellular stains designed to meet a variety of research needs. Our product line includes specialized dyes for specific cellular structures, as well as powerful solutions for distinguishing between healthy, apoptotic, and necrotic cells. Optimized for multicolor analysis, our stains enable you to achieve clear, detailed results in complex cell staining experiments. Explore our full range of Cellular Stains and elevate the precision and efficiency of your cell-based assays.

Cell Lines and Organisms Validated for Most Stains:

Mammalian Cells: HeLa
Yest: Saccharomyces cerevisiae
Gram+ Bacteria: Staphylococcus epidermidis
Gram- Bacteria E. coli

Compatibility Table for Cellular Stains and Dyes

This table offers a comprehensive overview of the compatibility of various stains and dyes with different cell types, including mammalian cells, yeast, Gram-positive, and Gram-negative bacteria. Compatibility is rated as high (+++), moderate (++), low (+), or not compatible (-). Compounds marked with (*) may interact non-specifically with acidic bacterial components due to their activation under acidic conditions. The table also indicates whether each stain or dye is suitable for live cell imaging, fixed cell imaging, and whether it is fixable (Yes/No), helping you select the best option for your research requirements.

Disclaimer: The compatibility ratings are based on literature and experimental data; however, actual performance may vary depending on specific experimental conditions and cell types. Users are encouraged to validate the suitability of stains and dyes for their particular applications.

Localization	Dye	Mammalian	Yeast	Gram+ Bacteria	Gram- Bacteria	Live Cell Compatibility	Fixed Cell Compatibility	Dye Fixability	Principle
Cell Surface	iFluor® WGA Conjugates	+ + +	+ + +	+	-	Yes	Yes	Yes	Bind to glycoproteins and polysaccharides present on cell surfaces, especially those containing N-acetylglucosamine (GlcNAc) residues.
	iFluor® ConA Conjugates	+ + +	+ + +	+	+ +	Yes	Yes	Yes	Concanavalin A (ConA) is a lectin that binds to α-D-mannose and α-D-glucose residues found on glycoproteins and glycolipids.
	Cell Navigator® Cell Plasma Membrane Stains	+ + +	+ +	+ +	+ +	Yes	Yes	Yes	High affinity for the lipid bilayer of the plasma membrane.
	CellPaint™ TSP membrane stain	+ + +	+ +	-	-	Yes	Yes	Yes	High affinity for the lipid bilayer of the plasma membrane.
	DiA	+ + +	+ + +	+ +	+ +	Yes	Yes	Yes	Lipophilic, carbocyanine dye commonly used for staining cell membranes and intracellular membrane.
	Dil	+ + +	+ + +	+ +	+ +	Yes	Yes	Yes	Lipophilic carbocyanine dye widely used for labeling cell membranes and neuronal tracing.
	DiO	+ + +	+ + +	+ +	+ +	Yes	Yes	Yes	Lipophilic carbocyanine dye family, similar to DiI.
	DiD	+ + +	+ + +	+ +	+ +	Yes	Yes	Yes	Lipophilic carbocyanine dye used for staining cell membranes.
	DiR	+ + +	+ + +	+ +	+ +	Yes	Yes	Yes	Lipophilic carbocyanine dye used for deep-tissue imaging due to its near-infrared fluorescence.
Nucleus	Nuclear™ LCS1 Stains	+ + +	+ +	-	-	Yes	Yes	Yes	Nuclear LCS1 series dyes are fluorogenic and cell-permeant dye that selectively binds to DNA.
	Hoechst 33342 / Hoechst Ultrapure	+ + +	+ +	+ +	+ +	Yes	Yes	Yes	Binds to A-T regions of DNA, fluorescing under UV light.
	DAPI	+ + +	+ +	+ +	+ +	Yes	Yes	Yes	Binds to DNA, emitting blue fluorescence when excited by UV light.
	MycoLight™ Green JJ98	+ + +	+ + +	+ + +	+ + +	Yes	Yes	Yes	A green-fluorescent stain that binds to DNA, permeating both prokaryotic and eukaryotic cell membranes.
	MycoLight™ Red JJ94	+ + +	+ + +	+ + +	+ + +	Yes	Yes	Yes	Similar mechanism as MycoLight™ Green, with enhanced red fluorescence.
	MycoLight™ Green JJ99	+ + +	+ + +	+ + +	+ + +	Yes	Yes	Yes	Functions similarly to MycoLight™ Green JJ98 with slightly different spectral properties.
	Thiazole orange	+ + +	+ +	+ +	+ +	Yes	Yes	Yes	Intercalates between base pairs in DNA, providing fluorescence upon binding.
	Cyto-13	+ + +	+ +	+ +	+ +	Yes	Yes	Yes	Binds to DNA and RNA, resulting in a fluorescent signal upon excitation.
Dead Cell Stain	Live or Dead™ Fixable Dead Cell Staining Kits	+ + +	+ +	+ + +	+ +	Yes	Yes	Yes	Two-color fluorescence assays where live bacteria emit the selected dye's fluorescence, while dead bacteria fluoresce red from propidium iodide.
	Live or Dead™ Yeast Viability Assay Kit	+ + +	+ +	+ + +	+ + +	Yes	Yes	Yes	Two-color fluorescence assay where live yeast fluoresce green from MycoLight™ Green JJ98, and dead yeast fluoresce red from propidium iodide.
	MycoLight™ Fluorescence Live/Dead Bacterial Imaging Kit	+ + +	+ + +	+ + +	+ + +	Yes	Yes	No	Two-color fluorescence assay, where live bacteria fluoresce green from MycoLight™ 520 due to esterase activity, while dead bacteria fluoresce red from propidium iodide.
	Nuclear™ DCS1 Stains	+ + +	+ +	+ + +	+ +	No	Yes	Yes	Binds to dead cell nuclei and emits fluorescence upon binding.
	Propidium Iodide	+ + +	+ + +	+ +	+ +	No	Yes	Yes	Intercalates with DNA of dead cells, fluorescing upon excitation.
	7-AAD	+ + +	+ +	+ + +	+ + +	No	Yes	Yes	Intercalates with DNA in dead cells, enabling fluorescence detection.
	DiYO™-1	+ + +	+ +	+ +	+ +	No	Yes	Yes	Fluorescent dye that stains dead cells by penetrating compromised membranes.
	DiYO™-3	+ + +	+ +	+ +	+ +	No	Yes	Yes	Similar to DiYO™-1, with a different spectral profile for dead cell staining.
	DiTO™-1	+ + +	+ +	+ +	+ +	No	Yes	Yes	Fluorescent dye for dead cell detection, emitting upon membrane compromise.
	DiTO™-3	+ + +	+ +	+ +	+ +	No	Yes	Yes	Similar to DiTO™-1, designed for detecting dead cells with fluorescence.
	TWO-PRO™ 1	+ + +	+ +	+ + +	+ +	No	Yes	Yes	Selectively stains nuclei in dead cells or permeabilized samples.
	TWO-PRO™ 3	+ + +	+ +	+ + +	+ +	No	Yes	Yes	Selectively stains nuclei in dead cells or permeabilized samples.
Cytoplasm	Calcein AM	+ + +	+ +	+ +	+ +	Yes	No	No	Cell-permeable dye that fluoresces green upon hydrolysis in live cells.
	CytoTell™ Blue	+ + +	+ +	+	+	Yes	No	No	Releases fluorescence via a blocker, allowing for retention in live cells.
	CytoTell™ Green	+ + +	+ +	+	+	Yes	Yes	Yes	Similar to CFSE, it is retained in cells and allows fluorescence measurement for viability.
	CytoTell™ Orange	+ + +	+ +	+	+	Yes	No	No	Retained in live cells, providing a means to analyze health and proliferation.
	CytoTell™ Red 590	+ + +	+ +	+	+	Yes	No	No	Functions by being retained within live cells for monitoring activities.
	CytoTell™ Red 650	+ + +	+ +	+	+	Yes	Yes	Yes	Enables effective analysis of viability and behavior by being retained in cells.
	CytoTell™ UltraGreen	+ + +	+ +	+	+	Yes	No	No	Indicates health and proliferation by being retained in live cells.
	CytoTell™ Violet 500	+ + +	+ +	+	+	Yes	No	No	Penetrates live cells and releases fluorescence for analyzing functions and viability.
	CFSE	+ + +	+ +	+ + +	+ + +	Yes	No	Yes	Dilutes its fluorescence upon cell division, enabling tracking of proliferation.
	MycoLight™ Live Bacteria Stain	+ + +	+ + +	+ + +	+ + +	Yes	No	No	Specifically stains live bacteria, emitting fluorescence to distinguish populations. Other MycoLight™ kits are available for a wide range of applications.
Lysosomes	Cell Navigator® Lysosome Staining Kits	+ + +	+	∗	∗	Yes	No	No	Selectively labels lysosomes in live cells with using proprietary lysotropic dyes that accumulates via the pH gradient.
	LysoBrite™ Blue	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	LysoBrite™ Green	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	LysoBrite™ Orange	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	LysoBrite™ Red DND-99	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	LysoBrite™ Red	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	LysoBrite™ Deep Red	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	LysoBrite™ NIR	+ + +	+	∗	∗	Yes	No	No	Fluorescent dye that accumulates in lysosomes; emits fluorescence upon excitation.
	CytoFix™ Red Fixable Lysosomal Stain	+ + +	+	∗	∗	Yes	Yes	Yes	Fluorescent stain for lysosomes that is fixable, allowing for analysis post-fixation.
	LysoBrite™ Green DND-26	+ + +	+	∗	∗	Yes	No	No	Fluorescent probe designed for lysosomal staining with green emission.
	Protonex™ Lyso-Red 670	+ + +	+	∗	∗	Yes	No	No	Selectively accumulates in lysosomes, emitting red fluorescence, designed for imaging acidic organelles.
	Protonex™ Lyso-NIR 770	+ + +	+	∗	∗	Yes	No	No	Near-infrared fluorescent dye for lysosomal imaging, useful in multi-parameter assays.
Mitochondria	Cell Navigator® Mitochondrion Staining Kits	+ + +	+ +	-	-	Yes	No	Yes³	Selectively labels mitochondria using proprietary dyes that selectively accumulate via the mitochondrial membrane potential.
	MitoLite™ Blue FX490	+ + +	+	-	-	Yes	Yes	Yes	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ Green FM	+ + +	+	-	-	Yes	No	No	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ Green EX488	+ + +	+	-	-	Yes	No	No	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ Orange EX405	+ + +	+	-	-	Yes	No	No	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ Orange FX570	+ + +	+	-	-	Yes	No	Yes	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ Red FX600	+ + +	+	-	-	Yes	Yes	Yes	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ Deep Red FX660	+ + +	+	-	-	Yes	Yes	Yes	Stains mitochondria by accumulating based on membrane potential.
	MitoLite™ NIR FX690	+ + +	+	-	-	Yes	Yes	Yes	Stains mitochondria by accumulating based on membrane potential.
	CytoFix™ Red Fixable Mitochondrial Stain	+ + +	+ +	-	-	Yes	Yes	Yes	Fixable mitochondrial stain that provides red fluorescence.
	JC-1	+ + +	+ +	-	-	Yes	No	No	A cationic dye that changes color from green to red in response to mitochondrial membrane potential changes.
	JC-10	+ + +	+ +	-	-	Yes	No	No	Similar to JC-1, utilized for detecting mitochondrial membrane potential in live cells.
	TMRE	+ + +	+ +	-	-	Yes	No	No	A lipophilic cationic dye that accumulates in active mitochondria, based on membrane potential.
	TMRM	+ + +	+ +	-	-	Yes	No	No	Similar to TMRE, used for assessing mitochondrial membrane potential.
	MitoDNA™ Blue 470	+ + +	+ +	-	-	Yes	Yes	Yes	Stains mitochondrial DNA with fluorescence.
	MitoDNA™ Red 610	+ + +	+ +	-	-	Yes	Yes	No	Stains mitochondrial DNA with fluorescence.
	MitoDNA™ Red 680	+ + +	+ +	-	-	Yes	ND¹	No	Stains mitochondrial DNA with fluorescence.
	MitoDNA™ Red710	+ + +	+ +	-	-	Yes	ND	No	Stains mitochondrial DNA with fluorescence.
	MitoROS Brite™ 570	+ + +	+ +	-	-	Yes	No	No	Selectively accumulates in mitochondria and fluoresces bright orange upon detection of mitochondrial reactive oxygen species (mtROS).
	MitoROS Brite™ 670	+ + +	+ +	-	-	Yes	No	No	Selectively accumulates in mitochondria and fluoresces bright red upon detection of mitochondrial reactive oxygen species (mtROS).
	MitoROS Brite™ NIR 780	+ + +	+ +	-	-	Yes	No	No	Selectively accumulates in mitochondria and emits near-infrared fluorescence upon detection of mitochondrial reactive oxygen species (mtROS).
Cytoskeleton (F-Actin/Tublin)	Phalloidin-iFluor® Conjugates	+ + +	+ +	+ +	+ +	No	Yes	N/A²	Stains F-actin in cells for cytoskeleton visualization.
	Cell Navigator® Live Cell Tubulin Staining Kit	+ + +	+ +	-	-	Yes	No	No	Labels tubulins in live cells with Tubulite™ Red without needing fixation.
	OG488 Taxol Conjugate	+ + +	+ +	-	-	No	Yes	N/A	Binds to and stabilizes microtubules for visualization.
	OG488 Diacetate Taxol Conjugate Cell-Pemeable	+ + +	+ +	-	-	Yes	No	Yes	Same as OG488 Taxol Conjugate but designed for live-cell imaging.
	Tublite™ Green Cell-Pemeable	+ + +	+ +	-	-	Yes	No	No	Stains microtubules, allowing visualization in live cells.
	Tublite™ Red Cell-Pemeable	+ + +	+ +	-	-	Yes	No	No	Stains microtubules, allowing visualization in live cells.
	Tublite™ Deep Red Cell-Pemeable	+ + +	+ +	-	-	Yes	No	No	Stains microtubules, allowing visualization in live cells.
Endoplasmic Reticulum	Cell Navigator® Live Cell ER Stains	+ + +	-	-	-	Yes	Yes⁴	Yes	Stains the endoplasmic reticulum (ER) in live cells. Available in blue, green, and red.
Golgi	Cell Navigator® NBD Ceramide Golgi Stain	+ + +	+ +	-	-	Yes	Yes	Yes	Specifically stains the Golgi apparatus, allowing visualization of ceramide localization.
Golgi	Cell Navigator® TMR Ceramide Golgi Stain	+ + +	+ +	-	-	Yes	No	Yes	Similar to NBD, targets the Golgi apparatus but with different ceramide analogs.
Not determined. Not applicable. With the exception of the Green and Orange mitochondrial staining kits, which do not have fixable dyes. Blue ER staining kit can be used on fixed cells. Red and Green can not.

On the banner:

Live HeLa cells were stained with DiR for the plasma membrane, and nuclei were co-stained with Hoechst 33342 UltraPure.
Multicolor fluorescence imaging of HeLa cells fixed with 4% formaldehyde, followed by staining with 1 µg/mL mouse anti-tubulin antibody IgG-iFluor® 488 (green). Cells were also stained with Phalloidin-iFluor® 647 (red) and 2 µM DAPI (blue) for 5 minutes before imaging.

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Original created on November 13, 2024, last updated on November 21, 2024
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Compatibility Table for Cellular Stains and Dyes

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