Shop All DNA⁄RNA Cell Stains

Vybrant™ DyeCycle™ Violet Stain (Invitrogen™)

Vybrant® DyeCycle™ Violet Stain is a cell permeable DNA dye that can be used for cell cycle analysis and stem cell side population by flow cytometry.

• Precise—accurate cell cycle analysis in living cells

• Safe—low cytotoxicity for cell sorting and additional live cell experiments

• Minimal compensation—easier multiplexing

• Flexible

• Simple, robust staining protocol

View a selection guide for all products related to cell cycle analysis of fixed and live cells in flow cytometry.

Precise

Successful cell cycle analysis requires a dye that is DNA selective and can stain cells in a homogeneous pattern minimizing fluorescence variability. The Vybrant® DyeCycle™ Violet Stain is an ideal tool for DNA content analysis in living cells since the stain is cell permeable and, after binding double-stranded DNA, emits a fluorescent signal that is proportional to the DNA mass (see figure).

Low Cytotoxicity

Unlike stains that require high concentrations or have chemical structures that are toxic to cells, Vybrant® DyeCycle™ stains exhibit relatively low cytotoxicity, allowing the possibility of sorting based on the phase of the cell cycle.

Minimal Compensation

Well-suited for the popular violet laser line, the Vybrant® DyeCycle™ Violet Stain/DNA complex has fluorescence excitation and emission maxima of 369/437 nm, respectively (see figure).

The violet excitation and narrow emission of Vybrant® DyeCycle™ Violet Stain make it ideal for multiplexing due to the limited spectral overlap with other common dyes (Alexa Fluor® 488, FITC, and RPE) and fluorescent proteins (Green Fluorescent Protein (GFP) and mCherry) . Vybrant® DyeCycle™ Violet Stain can also be used with UV excitation, having emission at ~440 nm.

Flexible

Vybrant® DyeCycle™ Violet Stain has been shown to not only work for both live cells and fixed cells in cell cycle assays, but to identify stem cell side populations and early progenitors in mammalian hematopoietic tissues (see figure).

Simple, Robust Staining Protocol

For cell analysis, simply prepare flow cytometry tubes each containing 1 mL of cells suspended in complete media at a cell concentration of 1 × 106 cells/mL. To each tube, add 1 µL of Vybrant® DyeCycle™ Violet Stain and mix well. Final stain concentration is 5 µM. Incubate at 37°C for 30 minutes, protected from light. Keep cells at 37°C until acquisition. Analyze samples without washing or fixing on a flow cytometer using ~405 nm excitation and ~440 nm emission.

Vybrant™ DyeCycle™ Green Stain (Invitrogen™)

Vybrant® DyeCycle™ Green Stain is a cell-permeable DNA dye that can be used for cell cycle analysis on a 488 nm spectral line of the argon-ion laser, which is commonly used on all flow cytometers.

• Precise—accurate cell cycle analysis in living cells

• Safe—low cytotoxicity for cell sorting and additional live cell experiments

• Simple, robust staining protocol

View a selection guide for all products related to cell cycle analysis of fixed and live cells in flow cytometry.

Precise

Successful cell cycle analysis requires a dye that is DNA selective and can stain cells in a homogeneous pattern minimizing fluorescence variability. The Vybrant® DyeCycle™ Green Stain is an ideal tool for DNA content analysis in living cells since the stains are cell permeable and, after binding double-stranded DNA, emit a fluorescent signal that is proportional to the DNA mass (see figure).

Low Cytotoxicity

Unlike stains that require high concentrations or have chemical structures that are toxic to cells, the Vybrant® DyeCycle™ Green Stain exhibits relatively low cytotoxicity, allowing the possibility of sorting based on the phase of the cell cycle.

Simple, Robust Staining Protocol

For cell analysis, simply prepare flow cytometry tubes containing 1 mL of cells suspended in complete media at a concentration of 1 × 106 cells/mL. To each tube add 2 µL of Vybrant® DyeCycle™ Green Stain. Final stain concentration is 10 µM. Incubate at 37°C for 30 minutes, protected from light. Analyze samples on a flow cytometer using 488 nm excitation and green emission.

Vybrant™ DyeCycle™ Orange Stain (Invitrogen™)

Vybrant® DyeCycle™ Orange Stain is a cell permeable DNA dye that can be used for cell cycle analysis on 488 nm or 532 nm laser lines.

• Precise—accurate cell cycle analysis in living cells

• Safe—low cytotoxicity for cell sorting and additional live cell experiments

• Simple, robust staining protocol

View a selection guide for all products related to cell cycle analysis of fixed and live cells in flow cytometry.

Precise

Successful cell cycle analysis requires a dye that is DNA selective and can stain cells in a homogeneous pattern minimizing fluorescence variability. The Vybrant® DyeCycle™ Orange Stain is an ideal tool for DNA content analysis in living cells since the stains are cell permeable and, after binding double-stranded DNA, emit a fluorescent signal that is proportional to the DNA mass (see figure).

Low Cytotoxicity

Unlike stains that require high concentrations or have chemical structures that are toxic to cells, the Vybrant® DyeCycle™ Orange Stain exhibits relatively low cytotoxicity, allowing the possibility of sorting based on the phase of the cell cycle.

Simple, Robust Staining Protocol

For cell analysis, simply prepare flow cytometry tubes containing 1 mL of cells suspended in complete media at a concentration of 1 × 106 cells/mL. To each tube add 2 µL of Vybrant® DyeCycle™ Orange Stain. Final stain concentration is 10 µM. Incubate at 37°C for 30 minutes, protected from light. Analyze samples on flow cytometer using 488 nm excitation and orange emission.

7-AAD (7-Aminoactinomycin D) (Invitrogen™)

7-aminoactinomycin D (7-AAD) is a fluorescent intercalator that undergoes a spectral shift upon association with DNA. 7-AAD/DNA complexes can be excited by the 488 nm laser and has an emission maxima of 647 nm, making this nucleic acid stain useful for multicolor fluorescence microscopy and flow cytometry. 7-AAD appears to be generally excluded from live cells, but can be used with cells that have been fixed and permeabilized. 7-AAD has been used for cell cycle analysis by flow cytometry. 7-AAD also binds selectively to GC regions of DNA yielding a distinct banding pattern in polytene chromosomes and chromatin for use in chromosome banding studies.

View a selection guide for all nonfixable viability dyes for flow cytometry.

eBioscience™ Propidium Iodide (Invitrogen™)

Propidium Iodide (PI) is a standard reagent used for assessing cell viability and exclusion of non-viable cells in flow cytometry. PI binds to double stranded DNA, but is excluded from cells with intact plasma membranes. PI should be analyzed in the PE channel when used as a counterstain for Annexin V FITC. 7-AAD can be used in place of PI when using Annexin V PE. The advantage of 7-AAD over PI is that there is minimal spectral overlap between these emissions. Choose propidium Iodide as a counterstain with Annexin V apoptosis assays.

Reactivity/Species
Human, Mouse, Rat

Hoechst 33258, Pentahydrate (bis-Benzimide) - 10 mg/mL Solution in Water (Invitrogen™)

Hoechst 33258 nucleic acid stain is a popular nuclear counterstain that emits blue fluorescence when bound to dsDNA. Its uses are similar to Hoechst 33342 (H-1399) for counterstaining, apoptosis and cell cycle studies, but Hoechst 33258 is reportedly less cell-permeant.

BOBO™-3 Iodide (570/602), 1 mM solution in DMSO (Invitrogen™)

Molecular Probes® dimeric cyanine nucleic acid dyes are among the highest sensitivity fluorescent probes available fornucleic acid staining. In addition to their high affinity for nucleic acids, cyanine dimers are essentially nonfluorescent in the absence of nucleic acids and exhibit 100- to 1000-fold fluorescence enhancements upon binding to DNA. The extinction coefficients and fluorescence quantum yields of the cyanine dimers bound to DNA are high, resulting in very bright fluorescence signals.

The dimeric cyanine dyes are useful for many applications. Their bright fluorescence signals and low backgrounds make them ideal for staining nucleic acids on solid supports, such as microarrays. They are also useful as nuclear and chromosome counterstains for multicolor fluorescence labeling experiments. The extraordinary stability of the dye–nucleic acid complexes makes it possible to prestain nucleic acid samples prior to gel or capillary electrophoresis.

The dimeric cyanine nucleic acid stains are supplied in a unit size of 200 µL as 1 mM solutions in dimethylsulfoxide (DMSO).

Vybrant™ DyeCycle™ Ruby Stain (Invitrogen™)

Vybrant® DyeCycle™ Ruby Stain is a cell permeable DNA dye that can be used for cell cycle analysis on a 488 nm or 635 nm red diode laser.

• Precise—accurate cell cycle analysis in living cells

• Safe—low cytotoxicity for cell sorting and additional live cell experiments

• Minimal compensation—easier multiplexing

• Simple, robust staining protocol

View a selection guide for all products related to cell cycle analysis of fixed and live cells in flow cytometry.

Precise

Successful cell cycle analysis requires a dye that is DNA selective and can stain cells in a homogeneous pattern minimizing fluorescence variability. The Vybrant® DyeCycle™ Ruby Stain is an ideal tool for DNA content analysis in living cells since the stain is cell permeable and, after binding double-stranded DNA, emits a fluorescent signal that is proportional to the DNA mass (see figure).

Low Cytotoxicity

Unlike stains that require high concentrations or have chemical structures that are toxic to cells, Vybrant® DyeCycle™ Ruby Stain exhibits relatively low cytotoxicity, allowing the possibility of sorting based on the phase of the cell cycle.

Minimal Compensation

Well-suited for the popular red 633 nm laser line, the Vybrant® DyeCycle™ Ruby Stain/DNA complex has fluorescence excitation and emission maxima of 638/686 nm, respectively (see figure). The spectral characteristics allow use of the red laser for cell cycle analysis and frees up other channels for additional parameters.

The red excitation and narrow emission of Vybrant® DyeCycle™ Ruby Stain make it ideal for multiplexing due to the limited spectral overlap with other common dyes (Alexa Fluor® 488, FITC, and RPE) and fluorescent proteins (Green Fluorescent Protein (GFP)).

Simple, Robust Staining Protocol

For cell analysis, simply prepare flow cytometry tubes containing 0.5 mL of cells suspended in complete media at a concentration of 5 × 105 cells/mL. To each tube, add 1 µL of Vybrant® DyeCycle™ Ruby Stain and mix well. Final stain concentration is 5 µM. Incubate at 37°C for 15–30 minutes, protected from light. Analyze without washing cells on a flow cytometer using 488 nm or 633/5 nm excitation and >670 nm emission.

Propidium Iodide ReadyProbes™ Reagent (Invitrogen™)

Propidium iodide is a commonly used dead-cell stain that emits red fluorescence when bound to DNA. Propidium iodide is also used as a counterstain in multicolor fluorescent techniques. With Propidium Iodide ReadyProbes® Reagent, we provide a room temperature-stable solution of classic DNA stain that comes in a convenient-to-use dropper bottle. Just tip and drip two drops per ml to stain your cells.

Features of Propidium Iodide ReadyProbes® Reagent:
• Ready-to-use liquid propidium iodide formulation
• Rapid staining of dead cells without wash steps
• Ready-to-use liquid formulation in convenient dropper bottle—no need to dilute, weigh, or pipette
• Stable at room temperature—keep handy at your work station or cell culture area

Classic Dead Cell Stain
Propidium iodide is a classic fluorescent dye used extensively for staining of dead cells (Figure 1). It exhibits a sufficiently large Stokes shift to allow simultaneous detection of nuclear DNA and FITC or Alexa Fluor® 488-labeled antibodies.

Packaged for Convenience
Propidium Iodide ReadyProbes® Reagent is supplied ready-to-use and can be stored right next to your flow cytometer or in your cell culture lab. A liquid formulation in an ultra-convenient dropper bottle (Figure 2) allows you to stain your cells whenever and wherever they are ready. Just add two drops per ml for optimally bright and distinct nuclear counter-staining.

Multiple Applications
Propidium iodide is membrane-impermeant and excluded from viable cells. It is therefore commonly used for identifying dead cells in a population. Its spectral properties, selectivity for dsDNA, and increased fluorescence when bound to DNA, make propidium iodide ideal for use with green (Alexa Fluor® 488, FITC, GFP) fluorophores in multicolor experiments. Because of its high affinity for DNA, it is also frequently used for counting cells, measuring apoptosis, and sorting cells based on DNA content.

Suggestions for Use
• In most cases, 2 drops/1×106 cells of Propidium Iodide ReadyProbes® Reagent and an incubation time of 15 to 30 minutes will produce bright nuclear staining; however, optimization may be needed for some cell types, conditions, and applications. In such cases, simply add more or fewer drops until the optimal staining intensity is obtained.
• When bound to nucleic acids, the fluorescence excitation maximum for propidium iodide is 535 nm and the emission maximum is 617 nm. Propidium iodide can be excited with a xenon or mercury-arc lamp or with the 488 line of an argon-ion laser. Generally, propidium iodide fluorescence is detected in the FL2 channel of flow cytometers.
• As a preferred red nuclear stain in dead cell analyses using flow cytometry, Propidium Iodide ReadyProbes® Reagent is ideal for use with antibody-based applications.

See other Molecular Probes® imaging tools and reagents.

Hoechst 33342, Trihydrochloride, Trihydrate - 10 mg/mL Solution in Water (Invitrogen™)

Hoechst 33342 nucleic acid stain is a popular cell-permeant nuclear counterstain that emits blue fluorescence when bound to dsDNA. This dye is often used to distinguish condensed pycnotic nuclei in apoptotic cells and for cell-cycle studies in combination with BrdU.

YOYO™-1 Iodide (491/509) - 1 mM Solution in DMSO (Invitrogen™)

One of our highest affinity nucleic acid stains, the cell-impermeant YOYO-1 stain shows over a thousand-fold increase in its green fluorescence when bound to dsDNA. YOYO-1 stain has proved extremely useful in the analysis of single molecules of DNA.

SYTO™ 9 Green Fluorescent Nucleic Acid Stain (Invitrogen™)

SYTO 9 green fluorescent nucleic acid stain has been shown to stain live and dead Gram-positive and Gram-negative bacteria, and it is a component of the LIVE/DEAD BacLight Bacterial Viability Kits (L-7007, L-7012, L-13152).

NucGreen™ Dead 488 ReadyProbes™ Reagent (Invitrogen™)

NucGreen Dead 488 ReadyProbes Reagent is a room temperature-stable solution of SYTOX Green Nucleic Acid Stain (Cat. No. S7020), which is a cell-impermeant stain that emits exceptionally bright, green fluorescence when bound to DNA. Cells that have lost plasma membrane integrity are stained within minutes, making this an extremely useful stain to estimate live/dead cell ratios and to measure cytotoxicity in kinetic live-cell assays. It is also suitable for staining nuclei in fixed cell preparations and tissue sections.

• Exceptionally bright green fluorescence upon binding to DNA
• Rapid staining of damaged, dead, or fixed cells without wash steps
• Ready-to-use liquid formulation in convenient dropper bottle—no need to dilute, weigh, or pipette
• Stability at room temperature—keep handy at your scope or cell

See other ReadyProbes reagents for cell staining
See other nuclear stains for imaging

Cell imaging applications
The membrane-impermeable NucGreen Dead 488 reagent is a high-affinity DNA stain that easily stains cells with compromised cell membranes, yet does not enter living cells. It is therefore ideal for discrimination of live and dead cells. The fluorescence increases more than 500-fold on binding to dsDNA in cells with compromised cell membranes (dying or dead cells), in fixed cells, and tissue slices. The spectral properties, with excitation/emission at 504/523 nm when bound to DNA, are ideal for standard FITC filters. .

Suggestions for use
• NucGreen Dead 488 reagent may be added directly to cells in full media or buffer solutions
• It easily stains nuclei of fixed cells and tissue slices
• In most cases, 2 drops/ml and an incubation time of 15 to 30 minutes will give bright nuclear staining; however, optimization may be needed for some cell types, conditions, and applications. In such cases, simply add more or fewer drops until the optimal staining intensity is obtained. In most cases, staining intensity increases with time if cells are not washed prior to imaging.
• NucGreen Dead 488 dye is excited with a maximum at 504 nm when bound to DNA, with an emission maximum at 523 nm. It is detected through standard GFP and FITC filters.

SYTO™ 61 Red Fluorescent Nucleic Acid Stain - 5 mM Solution in DMSO (Invitrogen™)

The cell-permeant SYTO 61 red fluorescent nucleic acid stain exhibits bright, red fluorescence upon binding to nucleic acids. Because the staining pattern of the SYTO dyes in live cells may vary between cell types, we offer the SYTO Red Fluorescent Nucleic Acid Stain Sampler Kit (S-11340) to enable researchers to find the most appropriate red-fluorescent SYTO stain for their system.

Ethidium Homodimer-2 (EthD-2) - 1 mM Solution in DMSO (Invitrogen™)

The cell-impermeant viability indicator ethdium homodimer-2 (EthD-2) is a high-affinity nucleic acid stain that is weakly fluorescent until bound to DNA and emits red fluorescence (excitation/emission maxima ~535/624).