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Cellular Stains Selection Guides

Find the right dye for your application

Compare applications, fixability, cellular targets, and staining in different organisms at a glance.

For more detailed information, see our Cellular Stains Technology Page and Membrane & Cell Surface Stains Comparison. Download our Cellular Stains Brochure or visit our Brochure Library to browse our product flyers.



Nuclear Stains

Product Stains live
cells
Fix after
staining
Permeabilize
after staining
Fix before
staining
Non-
cytotoxic
Color
(Ex/Em)1
Applications / Notes
DAPI
Hoechst 33342
Hoechst 33258
Yes Yes Yes Yes Yes Blue
(352/461 nm)
• Classic blue nuclear stains
• No-wash, nontoxic, stable for several days
• Use DAPI in antifade mounting medium
NucSpot® Live 488 Yes Yes Yes Yes Yes Green
(500/515 nm)
• Green nuclear stain for live or fixed cells
• No-wash, nontoxic for real-time imaging
Thiazole Green (SYBR® Green I) Yes No2 No2 No2 No Green
(498/522 nm)
• Structurally identical to SYBR® Green I
Oxazole Gold (SYBR® Gold) Yes No2 No2 No2 No Green
(496/539 nm)
• Structurally identical to SYBR® Gold
• Live cell staining of nuclei and mitochondrial DNA
NucSpot® 470 Dead cell-
selective
No No Yes Yes Green
(460/546 nm)
• No-wash green nuclear stain
• Dead-cell selective in unfixed cells
NucSpot® 555/570 Dead cell-
selective
No No Yes Yes Red
(559/566 nm)
• Nuclear-specific red counterstain for fixed cells
• Specifically stains dead cells in live cultures
NucSpot® 568/580 Dead cell-
selective
No No Yes Yes Dark red
(572/583 nm)
• Nuclear-specific red counterstain for fixed cells
• Specifically stains dead cells in live cultures
• Suitable for multi-day live cell imaging
NucSpot® 594/615 Dead cell-
selective
No No Yes Yes Deep red
(603/613 nm)
• Nuclear-specific red counterstain for fixed cells
• Specifically stains dead cells in live cultures
• Suitable for multi-day live cell imaging
NucSpot® 650/665 Dead cell-
selective
No No Yes Yes Pink
(653/671 nm)
• Nuclear-specific far-red counterstain for fixed cells
• Specifically stains dead cells in live cultures
NucSpot® Live 650 Yes Yes Yes Yes Yes Far-red
(650/675 nm)
• Far-red nuclear stain for live or fixed cells
• No-wash, nontoxic for real-time imaging
RedDot™1 Far-Red Nuclear Stain Yes No No No2 No Far-red
(662/694 nm)
• No wash, far-red nuclear stain
• Compare to Draq5™
• Endpoint only; toxic after several hours
RedDot™2 Far-Red Nuclear Stain Dead cell-
selective
No No Yes Yes Far-red
(650/675 nm)
• No-wash, far-red nuclear stain
• Dead cell-selective in unfixed cells
• Compare to Draq7™
NucSpot® 680/700 Dead cell-
selective
No No Yes Yes Near IR
(683/707 nm)
• Nuclear-specific near-IR counterstain for fixed cells
• Specifically stains dead cells in live cultures
NucSpot® 750/780 Dead cell-
selective
No No Yes Yes Near IR
(750/780 nm)
• Nuclear-specific near-IR counterstain for fixed cells
• Specifically stains dead cells in live cultures
• Suitable for multi-day live cell imaging
Cell-Membrane
Impermeant Nucleic Acid Dyes

Dead cell-
selective
No No No2 Yes Multiple colors
Blue to Far-Red
• PI, EthDIII, dimeric cyanine dyes, etc.
• See Dead Cell & Apoptosis Stains
• Nuclear staining in fixed cells requires RNase treatment
1 With DNA
2 Not nuclear-specific in fixed cells
SYBR is a registered trademark of Thermo Fisher Scientific

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Live Cell Stains

Product Localization Fix after
staining
Permeabilize
after staining
Fix before
staining
Non-
cytotoxic
Staining stability1 Colors Applications / Notes
DAPI
Hoechst 33342
Hoechst 33258
Nucleus Yes Yes Yes Yes Days Blue (352/461 nm) • No-wash, nontoxic, stable for several days
NucSpot® Live Nuclear Stains Nucleus Yes Yes Yes Yes Days Green (500/515 nm)
Far-red (650/675 nm)
• No-wash, nontoxic for real-time imaging
Thiazole Green Nucleus
& cytoplasm
Yes Yes Yes No < 4 hours Green (498/522 nm) • Structurally identical to SYBR® Green I
• Very bright, no-wash staining of DNA
• Shows some mitochondrial & cytoplasmic staining
• Toxic after several hours
RedDot™1 Far-Red
Nuclear Stain
Nucleus No No No No < 4 hours Far-red (662/694 nm) • Compare to Draq5™
• Toxic after several hours
ViaFluor® Live Cell
Microtubule Stains
Microtubules No No No Possibly
toxic
Days Blue (408/452 nm)
Green (500/515 nm)
Far-red (650/675 nm)
• No-wash, live cell microtubule stains
• Low toxicity, stain for 48 hours or longer
ViaFluor® SE Cell
Proliferation Dyes
Cell interior Yes Yes No Yes Days Blue (408/452 nm)
Green (493/532 nm)
• Stable, whole-cell labeling of live cells
• Non-toxic for tracking multiple cell divisions
• Excellent choice for cell tracing or co-cultures
Calcein-AM Cell interior /
Cell viability
No No No Yes ≤ 24 h Green (494/517 nm) • Short-term, whole-cell labeling of live cells
• For cell viability or dye efflux assays
Acridine Orange Nucleus &
Cytoplasm
Yes Yes Yes Possibly
toxic
Days Green ( DNA)
Red ( RNA)
• Membrane permeant nucleic acid dye
• Stains DNA green (Ex/Em 500/526 nm),
RNA red (Ex/Em 496/650 nm)
CellBrite® Steady
Membrane Staining Kits
Membrane/
Cell Surface
No No No Yes Days 5 Colors
Blue to Near-IR
• Image live cell surface for ≥24 hours
• Optional Enhancer masks intracellular signal
• Fast, even staining in complete medium
• STORM-compatible options
CellBrite® Cytoplasmic Membrane Dyes
CellBrite® NIR Cytoplasmic Membrane Stains
Membranes3 Yes2 No2 Yes2 Yes Days to
weeks3
8 Colors
Blue to Near-IR
• Lipophilic carbocyanine membrane dyes
• Fix before or after labeling2
• Stable & non-toxic for cell tracking3
CellBrite® Fix
Membrane Stains
Membrane/
Cell Surface3
Yes Yes No Yes Days3 Green (480/513 nm)
Red (542/571 nm)
Far-Red (638/667 nm)
• Covalent membrane labeling
• More uniform staining than lipophilic dyes
• Stain yeast and bacteria
MemBrite® Fix
Cell Surface Stains
Cell surface3 Yes Yes No Yes Days3 8 colors
Blue to Near-IR
• Covalent labeling of surface proteins
• Rapid, uniform cell surface staining
• STORM-compatible dye options
• Stain yeast and gram-positive bacteria
SynaptoGreen™ & SynaptoRed™
Nerve Terminal Dyes
Vesicles Yes4 Yes4 No Yes Minutes
to hours
Green (~480/600 nm)
Red (~510/750 nm)
• Cationic styryl membrane dyes
• Track vesicle trafficking & release
• Dye options with fixable amine group
• Equivalent to FM® dyes
CF® Dye Cholera Toxin
Conjugates
Lipid rafts Yes Yes Yes Yes ≤ 24 h 6 colors
Green to Near-IR
• Binds GM1 ganglioside in lipid rafts
• For cell surface labeling or neuronal tracing
• Staining can be heterogeneous in cultured cells
CF® Dye Transferrin
Conjugates
Endocytic
tracer
Yes Yes No Yes ≤ 24 h 7 colors
Green to Near-IR
• Transferrin receptor ligand
• Traffics to recycling endosomes
CF® Dye Dextrans Fluid phase
tracer
Yes No No Yes ≤ 24 h Wide selection
Green to Near-IR
• Fluid phase endocytosis & permeability tracers
• Range of molecular weights
WGA Conjugates
ConA Conjugates
PNA Conjugates
Glycoproteins Yes Yes Yes Possibly
toxic
≤ 24 h Wide selection
UV to Near-IR
• Bind to cell surface glycoproteins3
• Binding/biological effects vary by cell type
• See Stains in Different Organisms for bacteria/yeast
• Wide choice of CF® dye colors
LipidSpot™ Lipid
Droplet Stains
Lipid droplets /
Neutral lipids
Yes Yes Yes Yes ≥24 h Green (427/585 nm)
Far-red (610/663 nm)
• No wash, live or fixed cell staining
• Tolerates permeabilization
LysoView™ Dyes Lysosomes No No No Yes Days Blue, Green, Orange, Far-Red • No wash, live cell staining of lysosomes
MitoView™ Dyes Mitochondria/
Cell viability
No5 No No5 Yes Days Blue, Green, Far-Red, Near-IR • No wash, live cell staining of mitochondria
• MitoView™ 633 is potential-dependent
MitoView™ Fix 640 Mitochondria/
Cell viability
Yes Yes No Yes Days Far-red (644/665 nm) • No wash, non-toxic mitochondria staining
• Stable for several days
• Tolerates fixation and permeabilization
Aquaphile™ JC-1
JC-1, Iodide
JC-1, Chloride
JC-1 Mitochondrial Membrane Kit
Mitochondria/
Cell viability
No No No Yes Days Green (510/527 nm, cytoplasm),
Red (585/590 nm,
healthy mitochondria)
• No wash, live cell staining of mitochondria
• Measure mitochondrial potential/cell health
• Green fluorescence in cytoplasm, red fluorescence in polarized mitochondria
TMRM
TMRE
Mitochondria/
Cell viability
No No No Yes Days Red (548/573 nm) • No wash, live cell staining of mitochondria
• Preferred dyes for quantitative mitochondrial membrane potential measurement
Annexin V
Conjugates
Apoptotic cell membranes Yes No No Yes Days Wide selection
UV to Near-IR
• Stain cell surface of apoptotic cells
• Washing is optional
• Azide-free options for real-time imaging
NucView® Caspase-3
Substrates
Apoptotic cell
nuclei
Yes Yes No Yes Days Blue (429/469 nm)
Green (500/530 nm)
Orange (528/563 nm)
• Detect caspase-3 activity in intact cells
• No-wash assay for endpoint or real-time analysis
• NucView® 488 tested in >100 cell types & 200 papers
Cell-Membrane-
Impermeant
Nucleic Acid Dyes
Necrotic cells6 No No No6 Yes Days Wide selection
Green to Far-Red
• No wash staining for real-time imaging
• See Dead Cell & Apoptosis Stains
1 Stability of staining is a general guideline only, actual stability may depend on cell type/experimental system.
2 Formaldehyde fixation only, dyes do not tolerate alcohol/solvent treatment; dyes have poor tolerance for detergent, but cells can be stained after fixation/permeabilization with good results.
3 Surface staining is internalized by endocytosis, becoming mostly intracellular after several hours.
4 Dye options with formaldehyde-fixable amine groups; can be used with a low-detergent permeabilization protocol.
5 Cells can be fixed before or after MitoView™ Green staining, but dye localization will not be as specific as in live cells. We recommend mitochondrial marker antibodies for fixed cell staining.
6 Necrotic cell stains also stain late apoptotic cells with leaky membranes; staining is not dead cell-selective in fixed samples.

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Stains for Fixed Cells or Tissue Sections

Product Target Also stains
live cells?
Color (Ex/Em) Applications / Notes
Phalloidin Conjugates F-actin No Wide selection
UV to Near-IR
• Widely used stain for actin filaments
• Formaldehyde-fixation only (no methanol fixation)
CF® Dye α-Bungarotoxin Conjugates Nicotinic acetylcholine receptor Yes Wide selection
UV to Near-IR
• Labels neuromuscular junctions
CellBrite® Cytoplasmic Membrane Dyes
CellBrite® NIR Cytoplasmic Membrane Stains
Cell Membrane Yes 8 colors
Blue to Near-IR
• Lipophilic dyes for stable, non-toxic membrane labeling
• Fix before or after labeling1
CF® Dye WGA Conjugates
CF® Dye ConA Conjugates
CF® Dye PNA Conjugates
Glycoproteins Yes Wide selection
UV to Near-IR
• Bind to cell surface glycoproteins
• May stain intracellular targets in permeabilized cells
• Staining is tissue- and cell-type dependent
CF® Dye Cholera Toxin Conjugates GM1 ganglioside in lipid rafts Yes 6 colors
Green to Near-IR
• For cell surface labeling or neuronal tracing
• Expression/staining can be heterogeneous in cultured cells
LipidSpot™ Lipid Droplet Stains Lipid droplets /
Neutral lipids
Yes Green (427/585 nm) and
Far-red (610/663 nm
in vegetable oil,
~592/638 nm in cells)
• Stain before or after fixation
• Tolerates permeabilization after fixation
Organelle marker antibodies Mitochondria, nuclear envelope,
nucleoli, Golgi and more
No Wide selection
Blue to Near-IR
• Best options for fixed cell organelle staining
MitoView™ Green Mitochondria Yes Green • Can be used if suitable mitochondria antibody not available
• Staining not as specific as in live cells
1 Formaldehyde fixation only, dyes do not tolerate alcohol/solvent treatment; dyes have poor tolerance for detergent, but cells can be stained after fixation/permeabilization with good results.

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Dead Cell & Apoptosis Stains

Product Target Nuclear-
specific
Fix
after staining
Permeabilize
after staining
Color (Ex/Em) Applications / Notes
Oxazole Blue Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Blue (434/457 nm)2 • Cell-impermeant monomeric nucleic acid dye
• Reported to selectively stain early apoptotic cells
• Equivalent to PO-PRO™-1
Oxazole Blue Homodimer Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Blue (433/457 nm)2 • Cell-impermeant monomeric nucleic acid dye
• Equivalent to POPO™-1
NucView® Caspase-3 Substrates Apoptotic cells
Caspase activity
Yes Yes Yes Blue (429/469 nm)2
Green (500/530 nm)2
Orange (528/563 nm)2
• Detect caspase-3 activity in intact cells
• No-wash assay for endpoint assay or real-time analysis
• NucView® 488 validated in >100 cell types & 200 papers
CF® Dye Annexin Conjugates Apoptotic cells
Phosphatidylserine
No Yes No Wide selection
UV to Near-IR
• Annexin V with CF® dyes & other labels
• Available preservative-free for real-time cell imaging
Live-or-Dye™ Fixable Viability Stains Necrotic cells1
Cell-impermeant reactive dyes
No Yes Yes 8 Colors
UV to Near-IR
• Covalent labeling of dead cell cytoplasm
• Excellent tolerance for fixation/permeabilization
• Wash required after staining
NucSpot® Nuclear Stains Necrotic cells1
Cell-impermeant DNA dyes
Yes No No 7 Colors
UV to Near-IR
• Nuclear-specific counterstains or dead cell stains
• No-wash staining, compatible with real-time imaging
• Options for cell cycle analysis in fixed cells
Oxazole Yellow Early apoptotic cells
Cell-impermeant DNA/RNA dye
No No No Green (491/506 nm)2 • Equivalent to YO-PRO®-1 Iodide
• Reported to selectively stain early apoptotic cells
• No-wash staining, compatible with real-time imaging
Oxazole Yellow Homodimer Early apoptotic cells
Cell-impermeant DNA/RNA dye
No No No Green (491/508 nm)2 • Equivalent to YOYO®-1 Iodide
• No-wash staining, compatible with real-time imaging
TO Iodide Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Green (515/531 nm)2 • Equivalent to TO-PRO®-1 Iodide
• No-wash staining, compatible with real-time imaging
Thiazole Orange Homodimer Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Green (514/531 nm)2 • High-affinity dimeric cyanine DNA/RNA dye
• Equivalent to TOTO®-1 Iodide
• No-wash staining, compatible with real-time imaging
PathoGreen™ Histofluorescent Stain Degenerating neurons No N/A N/A Green (497/520 nm) • For fixed neuronal cells/tissue sections
CF® Dye TUNEL Assay Apoptotic cells
DNA strand breaks
Yes N/A N/A Green (490/515 nm)
Red (593/614 nm)
Far-red (642/662 nm)
• Label dsDNA breaks with bright, photostable CF® dyes
• For fixed cells or tissue sections
Live-or-Dye NucFix™ Red Necrotic cells1
Cell-impermeant DNA/RNA dye
Yes3 Yes Yes Red (520/610 nm)2 • Covalent, red fluorescent dead cell nuclear stain
• The only fixable dead cell nuclear stain
• Wash after staining required
Ethidium Homodimer III Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Red (530/620 nm)2 • Developed at Biotium as an alternative to EthDI
• 45% brighter than EthDI when bound to DNA
Ethidium Homodimer I Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Red (528/616 nm)2 • High-affinity membrane-impermeant DNA/RNA stain
• >30-fold fluorescence enhancement upon binding DNA
Propidium Iodide Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Red (535/617 nm)2 • Can be excited at 488 nm for the PE channel
• Useful for cell cycle analysis in fixed cells (with RNase)
RedDot™2 Far-Red Nuclear Stain Necrotic cells1
Cell-impermeant DNA/RNA dye
Yes No No Far-red (662/694 nm)2 • Far-red nuclear counterstain or dead cell stain
• Compare to Draq7™
• No-wash staining, compatible with real-time imaging
Thiazole Red Homodimer Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Far-red (642/661 nm)2 • High-affinity dimeric cyanine DNA/RNA dye
• Equivalent to TOTO®-3 Iodide
• No-wash staining, compatible with real-time imaging
Thiazole Red Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Far-red (642/657 nm)2 • Equivalent to TO-PRO®-1 Iodide
• No-wash staining, compatible with real-time imaging
7-AAD Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Far-Red (546/647 nm)2 • Far-red dye for the PE-Cy®5 flow cytometry channel
• Can be excited by the 488 nm or 532 nm laser line
• Useful for cell cycle analysis in fixed cells
NucSpot® Far-Red Necrotic cells1
Cell-impermeant DNA/RNA dye
No No No Far-Red (597/667 nm)2 • Designed as improved replacement for 7-AAD
• For flow cytometry in the PE-Cy®5 or APC channel
• Less bleed into the PE-Texas Red® channel
• Useful for cell cycle analysis in fixed cells
1 Necrotic cell stains also stain late apoptotic cells with leaky cell membranes.
2 With DNA.
2 Not nuclear-specific in yeast.
Cy Dye is a registered trademark of Cytiva; POPO, TOTO, YOYO, TO-PRO, PO-PRO, and YO-PRO are trademarks or registered trademarks of Thermo Fisher Scientific; Draq5 and Draq7 are trademarks of Biostatus, Ltd.

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Stains for Cell Cycle Analysis by Flow Cytometry

Product Live or Fixed Cells? RNase treatment required? Color
(Ex/Em)1
Applications / Notes
NucSpot® 470 Fixed No Green
(460/546 nm)
• Nuclear-specific green counterstain for fixed cells
• Selectively stains dead cells in live cultures
• Excellent match for blue LED excitation sources
Propidium Iodide Fixed Yes Red (535/617 nm) • Widely used dead cell stain
• Can be excited by 488 nm laser line for detection in the PE channel
7-AAD Fixed No Far-Red (546/647 nm) • Far-red dye for detection in the PE-Cy®5 channel
• Can be excited by the 488 nm or 532 nm laser line
NucSpot® Far-Red Fixed No Far-Red (597/667 nm) • Designed as improved replacement for 7-AAD
• For the PE-Cy®5 or APC channel
• Less bleed into the PE-Texas Red® channel
RedDot™1 Far-Red Nuclear Stain Live No Far-red
(662/694 nm)
• For short-term live cell staining (≤4 hours)
• Useful for cell number normalization for In Cell Western®
• Can be excited at wavelengths between 488 and 647 nm
• Detect in Cy®5 or APC channel
1 With DNA
Cy Dye is a registered trademark of Cytiva. In Cell Western is a registered trademarks of LI-COR Inc.

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Stains for Spheroids, 3D Cultures, or Matrigel® Cultures

Product Target Fixable? Tolerates optical
clearing?
Applications / Notes
Hoechst 33342
Hoechst 33258
All cell nuclei Yes Yes • See Nuclear Stains
NucSpot® Live Nuclear Stains All cell nuclei Yes ND • See Nuclear Stains
CellBrite® Cytoplasmic Membrane Dyes
CellBrite® NIR Cytoplasmic Membrane Stains
Cell membranes Yes1 No • Lipophilic carbocyanine dye have been used for labeling cells before or after spheroid formation
• See Live Cell Stains
MitoView™ Dyes Mitochondria No No • See Live Cell Stains
NucView® 488
Caspase-3 Substrate
Apoptotic cells Yes Yes • See Dead Cell & Apoptosis Stains
Calcein-AM Viable cells
(whole cell interior)
No No • Commonly used to stain cells in Matrigel® or spheroids
• See Live Cell Stains
Cell-Membrane
Impermeant Nucleic Acid Dyes
Necrotic cells2 No No • See Dead Cell & Apoptosis Stains
ViaFluor® SE Cell
Proliferation Dyes
Whole cell interior Yes Yes • Can be used to label cells before seeding in Matrigel® or spheroids
• See Live Cell Stains
LipidSpot™ Lipid
Droplet Stains
Lipid droplets Yes1 ND • LipidSpot™ 488 has been validated for staining 3D cell spheroids
ViaFluor® Live Cell
Microtubule Stains


CellBrite® Steady
Membrane Staining Kits


LysoView™ Dyes
Membrane and various organelles No ND • May be suitable for staining spheroids, 3D cultures, or Matrigel® cultures, but have not yet been validated
1 Formaldehyde fixation only, dyes do not tolerate alcohol/solvent treatment; dyes have poor tolerance for detergent, but cells can be stained after fixation/permeabilization with good results.
2 Necrotic cell stains also stain late apoptotic cells with leaky membranes; staining is not dead cell-selective in fixed samples.
Matrigel is a registered trademark of Corning, Inc.

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Cellular Stains in Different Organisms

The table below lists the application of several cellular stains for various organisms. A “Yes” indicates the stain is validated for the organism and may be used for reliable analysis. A “No” indicates that we do not recommend this stain for that organism; however some staining may still occur. See our FAQ for more information.

Localization Product Mammalian
Cells
Yeast Gram+
Bacteria
Gram-
Bacteria
Notes / Applications
Cell Surface CellBrite® Cytoplasmic Membrane Dyes Yes No No No • See Live Cell Stains
• See Stains for Fixed Cells & Tissue Sections
CellBrite® Steady Membrane Dyes Yes No No No • See Live Cell Stains
CellBrite® Fix Membrane Stains Yes Yes Yes Yes • See Live Cell Stains
MemBrite® Fix Membrane Stains Yes Yes Yes No • See Live Cell Stains
SynaptoGreen™ C4 (FM®1-43) Yes Yes1 Yes Yes • See Live Cell Stains
SynaptoRed™ C2 (FM®4-64) Yes Yes1 Yes Yes • See Live Cell Stains
CF® Dye WGA Conjugates Yes Yes2 Yes No • See Live Cell Stains
• See Stains for Fixed Cells & Tissue Sections
CF® Dye ConA Conjugates Yes Yes No No • See Live Cell Stains
• See Stains for Fixed Cells & Tissue Sections
Calcofluor White No Yes Yes No • See Nuclear Stains
DNA Hoechst Yes No3 Yes Yes • See Nuclear Stains
DAPI Yes No3 Yes Yes • See Nuclear Stains
NucSpot® Live Cell Nuclear Stains Yes No Yes No • See Nuclear Stains
RedDot™1 Far-Red Nuclear Stain Yes No3 Yes Yes • See Nuclear Stains
DMAO Yes4 No3 Yes Yes • Green fluorescent nucleic acid dye for live bacteria
BactoView™ Live Green Yes No3 Yes Yes • Green and red fluorescent nucleic acid dyes for live & dead bacteria
BactoView™ Live Red No3 No3 Yes Yes
Thiazole Orange Yes5 Yes11 Yes Yes • See Nuclear Stains
Dead Cells

(Yes indicates
dead cell
selectivity)
Propidium Iodide Yes Yes Yes Yes • See Nuclear Stains
Ethidium Homodimer I (EthD-I) Yes Yes Yes Yes • See Nuclear Stains
Ethidium Homodimer III (EthD-III) Yes Yes Yes Yes • See Nuclear Stains
RedDot™2 Yes Yes Yes Yes • See Nuclear Stains
Live-or-Dye™ NucFix Red Yes Yes6 No7 Yes • See Nuclear Stains
Live-or-Dye™ Fixable Viability Stains Yes Yes Yes Yes • See Nuclear Stains
NucSpot® 470 Yes Yes No7 Yes • See Nuclear Stains
Cytoplasm ViaFluor® 405 SE Cell Proliferation Dye Yes No8 Yes No • See Live Cell Stains
ViaFluor® 488 SE Cell Proliferation Dye Yes No8 Yes No • See Live Cell Stains
ViaFluor® CFSE Cell Proliferation Dye Yes Yes Yes No • See Live Cell Stains
Intracellular
Structures
MitoView™ 405 Yes Yes Yes Yes • See Live Cell Stains
MitoView™ Green Yes Yes Yes Yes • See Live Cell Stains
MitoView™ 633 Yes Yes Yes Yes • See Live Cell Stains
MitoView™ 650 Yes Yes Yes Yes • See Live Cell Stains
MitoView™ 720 Yes Yes Yes Yes • See Live Cell Stains
LysoView™ 405 Yes No9 Yes Yes • See Live Cell Stains
LysoView™ 488 Yes No Yes No • See Live Cell Stains
LysoView™ 540 Yes Yes No No • See Live Cell Stains
LysoView™ 633 Yes Yes No No • See Live Cell Stains
LysoView™ 650 Yes No No No • See Live Cell Stains
LipidSpot™ 488 Lipid Droplet Stain Yes Yes Yes No • See Live Cell Stains
LipidSpot™ 610 Lipid Droplet Stain Yes No Yes No • See Live Cell Stains
Phalloidin Conjugates Yes Yes No No • See Stains for Fixed Cells & Tissue Sections
ViaFluor® Live Cell Microtubule Stains Yes No10 No10 No10 • See Live Cell Stains
ViaVac™ Red/Green No Yes ND ND • Stains vacuoles in healthy yeast red; stains cytoplasm of all yeast green
• Equivalent to FUN®1
1 Internalizes to vacuolar membranes
2 Stains bud scars of budding yeast
3 Weak staining and not nuclear
4 Staining is not nuclear
5 Initially stains mitochondria, then redistributes to nucleus & cytoplasm
6 Dead cell specific but not nuclear
7 Stains live and dead cells
8 Not cytoplasmic, stains cell periphery
9 Staining is not lysosomal
10 Not predicted to bind yeast/bacteria cytoskeleton
11 Staining is both nuclear and cytoplasmic
FUN1 is a registered trademark of Thermo Fisher Scientific

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Faq

CellBrite® & MemBrite® Membrane & Cell Surface Stains

CellBrite® Cytoplasmic Membrane Stains are lipophilic dyes for simple, non-toxic, stable labeling of membranes in live or fixed cells. Cells can be fixed with formaldehyde before or after CellBrite® staining. But the staining has poor tolerance for permeabilization or methanol fixation, so CellBrite® staining is not easily combined with intracellular immunofluorescence (IF) staining. The dyes also do not stain bacteria or yeast. CellBrite® NIR dyes are CellBrite® dyes with near-infrared fluorescence compatible with small animal NIR imaging systems. CellBrite® Fix and MemBrite® Fix stains were developed to overcome some of these shortcomings. They are novel covalent stains that can be fixed and permeabilized for IF staining. CellBrite® Fix Membrane Stains are fluorogenic reactive membrane dyes that rapidly accumulate at the plasma membrane. When they incorporate into lipids, they become fluorescent, and at the same time react covalently with membrane proteins for stable labeling. Staining takes only 15 minutes in a single step with no wash. CellBrite® Fix stains mammalian cells, yeast, and bacteria. MemBrite® Fix Cell Surface Stains do not bind lipids, but label cell surface proteins. MemBrite® Fix requires a two-step staining protocol with washing, but offers a more extensive choice of dye colors than CellBrite® Fix. MemBrite® Fix also can be used to stain yeast. But unlike original CellBrite® dyes and lectins, CellBrite® Fix and MemBrite® Fix cannot be used on cells that are already fixed. To select a dye that’s right for your application, see our Membrane and Cell Surface Stains Comparison, or download our Membrane & Surface Stains Brochure.


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CellBrite® Cytoplasmic Membrane Dyes do not efficiently stain EVs, but CellBrite® Fix, MemBrite® Fix, CellBrite® Steady, and other stains have been used for this application. However, for optimal staining of exosome membranes we recommend our ExoBrite™ EV Membrane Stains. See our Exosome & EV Labeling Technology Page for more information.


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Biotium’s CellBrite® Cytoplasmic Membrane Dyes are dye delivery solutions that can be added directly to normal culture media to uniformly label suspended or adherent cells in culture. The PKH dyes are structurally related dyes for cell membrane labeling. But unlike CellBrite®, labeling with PKH dyes requires multiple steps and subjects cells to an iso-osmotic mannitol loading medium that can negatively affect cell membrane integrity and viability. CellBrite® Fix dyes also feature rapid and simple labeling in isotonic buffer. Cells can be fixed and permeabilized after labeling with CellBrite® Fix, unlike original CellBrite® dyes or PKH dyes, which don’t tolerate detergent.


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Microbiology: Dyes for bacteria and yeast

To date, we have not identified a fluorescent cellular stain that will detect bacteria but not mammalian cells with high specificity, or vice versa. While some mammalian cell stains show weak staining of bacteria, they usually do show some signal, and will frequently stain dead bacteria more intensely than live bacteria. We offer a selection of antibodies for specific bacterial antigens, which potentially have applications for differential staining of bacteria vs. mammalian cells, but we have not validated them in co-culture models. Also see our Viability PCR Technology Page to learn about how PMA dye can be used for highly specific detection of microbial cell viability in complex samples.


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Fixation is not recommended after staining with the Viability/Cytotoxicity Assay Kit (cat. # 30027) as the dead cell dye, EthD-III will transfer to all cells and not maintain dead cell-specific staining. Our Live-or-Dye™ NucFix™ Red (cat. # 32010) is a formaldehyde-fixable dead cell dye that can be used in bacteria. Viability qPCR (vPCR) can be an alternative strategy for quantitating live and dead bacteria. Using dead cell-specific dyes, PMA (cat. # 40019) or PMAxx (cat. # 40069) that covalently modify DNA (of only dead cells) after photo-crosslinking, a simple quantitative PCR (qPCR) amplification is used to selectively amplify live-cell DNA. Learn more about the vPCR technology.


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CellBrite® and MemBrite® Stains were originally developed for staining mammalian cells in culture, but some of the stains also have been validated for other organisms and applications. For dyes to stain yeast or bacteria membranes, see Cellular Stains in Different Organisms. For information on staining other organisms or cell types, please see our Tech Tip: Researching Applications for Membrane Dyes.


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Organelle & Cytoskeleton Stains

Cationic dyes are widely used as mitochondrial probes. They accumulate within the cell and preferentially localize in the mitochondrial matrix, induced by the greater negative membrane potential of mitochondria in live cells compared to the plasma membrane potential. Membrane potential plays a direct role in governing the distribution of the dyes across the plasma membrane: the more negative the potential, the greater the accumulation of the positively charged dyes. MitoView™ 633 is a cationic lipophilic dye that is potential-dependent and accumulates in mitochondria in proportion to the electron gradient similar to classic dyes like TMRM, TMRE and Rhodamine-123. Ratiometric dyes like JC-1 constitute another class of potential-dependent mitochondrial dyes. In normal healthy cells, JC‐1 accumulates in the mitochondria and undergoes aggregation in a potential‐dependent manner, whereas in unhealthy, apoptotic or dying cells with dissipated mitochondrial potential, the dye delocalizes to the cytosol where it dissociates to the monomeric state. The aggregated dyes (J-aggregates) fluoresce red, while the monomeric dyes fluoresce green. Some mitochondrial‐specific dyes are considered “structural” dyes, as opposed to “functional” dyes, because they are capable of staining mitochondria regardless of their polarization status. The fluorescence of cells stained with these dyes is directly proportional to their mitochondrial content or “mitochondrial mass.” MitoView™ Green is a potential-independent dye that accumulates in the mitochondria and interacts with the mitochondrial matrix via hydrophobic interactions. It can be used to stain mitochondria in live as well as formaldehyde-fixed cells. MitoView™ Green staining is not compatible with solvent-based fixatives or permeabilization. Nonyl Acridine Orange (NAO) is another potential-independent mitochondrial dye that binds specifically to cardiolipin in the inner mitochondrial membrane. However, mitochondrial dye staining of fixed cells generally is less specific compared to live cell staining. For fixed cell staining, we recommend using one our CF® Dye conjugated mitochondrial marker antibodies.


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The mechanism of binding for RedDot™ 1 and RedDot™ 2 to DNA has not been characterized. However, based on the dye structure, it may bind by a similar mechanism as DRAQ®5, which has been reported in the literature to be a concentration-dependent intercalator and minor groove binder. DRAQ is a registered trademark of Biostatus, Ltd.


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TrueBlack® and TrueBlack® Plus are hydrophobic in nature and quench lipofuscin autofluorescence mainly through hydrophobic interactions. They could therefore stain/bind to lipid structures and quench the fluorescence signal of BODIPY and other lipid droplet stains. Also, original TrueBlack® #23007 is used in 70% EtOH, which could interfere with lipid droplet morphology and affect staining. TrueBlack® Plus #23014, on the other hand, can be used in buffer instead of 70% ethanol, and may be more suitable for combining with lipid droplet staining. However, since the binding of TrueBlack® Plus is also dependent on hydrophobic interactions, we recommend testing TrueBlack® pre-treatment and post-treatment for compatibility with lipid droplet staining in your sample type.


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