Shop All DNA⁄RNA Cell Stains

POPO™-1 Iodide (434/456) - 1 mM Solution in DMSO (Invitrogen™)

POPO™-1 iodide is a high-affinity nucleic acid stain based upon a symmetric cyanine dye dimer that is essentially nonfluorescent in the absence of nucleic acids that exhibits excitation/emission maxima ~434/456 nm when bound to nucleic acids.

PO-PRO™-1 Iodide (435/455) - 1 mM Solution in DMSO (Invitrogen™)

One of our carbocyanine monomers, PO-PRO™-1 stain is a useful counterstain and dead cell indicator, with blue fluorescence (excitation/emission maxima ~435/455 nm).

POPO™-3 Iodide (534/570) - 1 mM Solution in DMF (Invitrogen™)

POPO™-3 iodide is a high-affinity nucleic acid stain based upon a symmetric cyanine dye dimer that is essentially nonfluorescent in the absence of nucleic acids that exhibits excitation/emission maxima ~534/570 nm when bound to nucleic acids.

YO-PRO™-1 Iodide (491/509) (Invitrogen™)

One of our proprietary carbocyanine nucleic acid stains, the green-fluorescent YO-PRO®-1 stain has found a niche in identifying apoptotic cells. Apoptotic cells become permeant to YO-PRO®-1, but remain impermeant to propidium iodide (P-3566), a dead cell stain. Live cells are not stained with YO-PRO®-1, allowing them to be used in subsequent experiments. We also offer the nucleic acid stain in our Vybrant® Apoptosis Assay Kits #4 (V-13243) and #7 (V-23201).

TOTO™-3 Iodide (642/660) - 1 mM Solution in DMSO (Invitrogen™)

TOTO®-3 stain is a carbocyanine dimer with far-red fluorescence similar to Alexa Fluor® 647 or Cy® 5 dyes that is easily distinguished from fluorescein and rhodamine. It is useful as a nuclear counterstain and dead cell indicator, and is among the highest-sensitivity probes for nucleic acid detection.

Important Features of TOTO®-3 Include:

• Nonfluorescent in the absence of nucleic acids
• Very bright fluorescence signal
• Ideal for flow cytometry and fluorescence microscopy
• Long-wavelength fluorescence is well separated from green and red fluorophores
• Cell-impermeant
• Excitation⁄Emission: 640⁄660 nm


Many Applications
TOTO®-3 stain and the other dimeric cyanine stains have wide applicability due to their low background and bright fluorescence. Uses include staining of nucleic acids on solid supports, prestaining of samples for gel or capillary electrophoresis, and nuclear counterstaining in multiple-label experiments. Electrophoresis of samples prestained with TOTO®-3 or other dimeric cyanine dyes is possible due to the unusual stability of the dye-Nucleic Acid complexes.

TOTO®-3 Stain has High Selectivity for Nuclear Over Cytoplasmic Staining
TOTO®-3 stain gives strong and selective nuclear staining in cultured cells and in paraffin sections. TOTO®-3 stain and other carbocyanine dimers have very strong binding affinity for dsDNA, with dissociation constants in the micromolar range.

Use TOTO®-3 Stain for 2-Color Viability Staining
Simultaneous labeling with a green-fluorescent SYTO® dye and cell-impermeant TOTO®-3 or TO-PRO®-3 stains are frequently used to assess cell viability. TOTO®-3 and TO-PRO®-3 stains both have much greater extinction coefficients than that of DNA-bound propidium iodide.

Extend Your Possibilities for Multicolor Labeling
The long-wavelength fluorescence of TOTO®-3 stain is well separated from that of commonly used fluorophores, such as our popular Alexa Fluor® dyes, Oregon Green, ® fluorescein (FITC), rhodamine (TRITC), Texas Red, coumarin (AMCA), Marina Blue™ and Pacific Blue™ dyes. Additionally, long-wavelength light–absorbing dyes such as TOTO®-3 stain have the advantage that their fluorescence is usually not obscured by the autofluorescence of tissues.
Explore other probes for the nucleus

Learn more about nucleic acid detection on gels, blots, and arrays.

Read more about cyanine dyes and other nucleic acid stains.

Find out more about viability and cytotoxicity assay reagents.

Plot the TOTO®-3 spectra and check spectral compatibility with other fluorophores

For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use.

eBioscience™ Propidium Iodide Staining Solution (Invitrogen™)

Propidium Iodide (PI) is a ready-to-use solution for the exclusion of nonviable cells in flow cytometric analysis. PI binds to double stranded DNA by intercalating between basepairs, but is excluded from cells with intact plasma membranes. PI can be used in FL3 for inviability exclusion, but should be analyzed in FL2 when used as a counterstain for FITC Annexin V.

Reported Application
Flow Cytometric Analysis

YOYO™-3 Iodide (612/631) - 1 mM Solution in DMSO (Invitrogen™)

YOYO®-3 iodide is a cell-impermeant, high-affinity nucleic acid stain based upon a symmetric cyanine dye dimer that is essentially nonfluorescent in the absence of nucleic acids that exhibits excitation/emission maxima ~612/631 nm when bound to nucleic acids.

TO-PRO™-3 Iodide (642/661) - 1 mM Solution in DMSO (Invitrogen™)

TO-PRO®-3 stain is a carbocyanine monomer nucleic acid stain with far-red fluorescence similar to Alexa Fluor® 647 or Cy®5 dyes. It is useful as a nuclear counterstain and dead cell indicator, and is among the highest-sensitivity probes for nucleic acid detection.

Important Features of TO-PRO®-3 Stain Include:

• Ultrasensitive detection of dsDNA (double-stranded nucleic acids)
• Ideal for flow cytometry and fluorescence microscopy
• Long-wavelength fluorescence well separated from green and red fluorophores
• Excitation⁄Emission: 642⁄661 nm
• Cell impermeant

Many Applications
TO-PRO®-3 and the other monomeric cyanine stains have wide applicability due to their low background and bright fluorescence. Uses include staining of nucleic acids on solid supports, prestaining of samples for gel or capillary electrophoresis, viability detection and counterstaining in multiple-label experiments.

TO-PRO®-3 Stain has High Selectivity for Nuclear Over Cytoplasmic Staining
TO-PRO®-3 gives strong and selective staining of the nucleus in cultured cells and in paraffin sections. TO-PRO®-3 and other carbocyanine monomers have very strong binding affinity for dsDNA, with dissociation constants in the micromolar range.

Use TO-PRO®-3 Stain for 2-Color Viability Staining
Simultaneous labeling with a green-fluorescent SYTO® dye and cell-impermeant TO-PRO®-3 stain is frequently used to assess cell viability. TO-PRO®-3 and TOTO®-3 stains both have much greater extinction coefficients than DNA-bound propidium iodide.

Expand Your Options for Multicolor Labeling
The long-wavelength fluorescence of TO-PRO®-3 stain is well separated from that of commonly used fluorophores, such as our popular Alexa Fluor® dyes, Oregon Green®, fluorescein (FITC), rhodamine (TRITC), Texas Red®, coumarin (AMCA), Marina Blue™ and Pacific Blue™ dyes. Additionally, long-wavelength light–absorbing dyes such as TO-PRO®-3 stain have the advantage that their fluorescence is usually not obscured by the autofluorescence of tissues.
Explore other probes for the nucleus

Learn more about nucleic acid detection on gels, blots, and arrays.

Read more about cyanine dyes and other nucleic acid stains.

Find out more about viability and cytotoxicity assay reagents.

Plot the TO-PRO®-3 spectra and check spectral compatibility with other fluorophores

LDS 751 (Invitrogen™)

LDS 751 is a cell-permeant nucleic acid stain that has a peak excitation at ~543 nm on dsDNA and is particular useful in multicolor analyses due to its long wavelength emission maximum (~712 nm). Binding of LDS 751 to dsDNA results in a ~20-fold fluorescence enhancement.

View a selection guide for all Cell Viaibility Assays for Flow Cytometry.

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.

SYTOX™ Blue Dead Cell Stain, for flow cytometry (Invitrogen™)

SYTOX™ Blue dead cell stain is a simple and quantitative single-step dead-cell indicator for use with violet laser equipped flow cytometers. SYTOX™ Blue dead cell stain is a high-affinity nucleic acid stain that easily penetrates cells with compromised plasma membranes but will not cross uncompromised cell membranes. After brief incubation with SYTOX™ Blue stain, the nucleic acids of dead cells fluoresce bright blue when excited with 405 nm violet laser light. The violet-excited fluorescence emission of SYTOX™ Blue stain permits clear discrimination from probes excited by most other laser lines, facilitating the development of multicolor assays with minimal spectral overlap between signals. SYTOX™ Blue dead cell stain is supplied as a 1 mM solution in dimethylsulfoxide (DMSO) in a unit size of 1 mL.

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

FxCycle™ Violet Stain (Invitrogen™)

FxCycle™ Violet stain (F10347) is used for flow cytometric analysis of DNA content in fixed cells. This dye is excited with a 405⁄407 nm laser with emission collected in the 450⁄50 BP filter or equilavent. This dye is DNA selective so RNAse is not required. With multicolor cell cycle studies possible using flow cytometry, it is often necessary to analyze DNA content on alternative lasers to preserve the common 488 nm laser and detection channels for other markers. Well suited for the popular violet laser line, FxCycle™ Violet stain is a good choice for DNA content analysis in multicolor cell cycle studies.

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

eBioscience™ 7-AAD Viability Staining Solution (Invitrogen™)

7-AAD (7-amino-actinomycin D) is a ready-to-use solution for the exclusion of nonviable cells in flow cytometric analysis. 7-AAD can be used in place of PI (propidium iodide). This solution can be used in combination with PE (phycoerythrin) and FITC (fluorescein isothiocyanate) conjugated antibodies in 2-color analysis. The advantage of 7-AAD over PI is that there is minimal spectral overlap between these emissions. Fluorescence is detected in the far red range of the spectrum (650 nm long-pass filter).

Reported Application
Flow Cytometric Analysis

YO-PRO™-3 Iodide (612/631) - 1 mM Solution in DMSO (Invitrogen™)

One of our carbocyanine monomers, YO-PRO®-3 iodide is a useful counterstain and dead cell indicator, with excitation/emission maxima ~612/631 nm.

SYTO™ 21 Green Fluorescent Nucleic Acid Stain - 5 mM Solution in DMSO (Invitrogen™)

The cell-permeant SYTO 21 green fluorescent nucleic acid stain exhibits bright, green 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 Green Fluorescent Nucleic Acid Stain Sampler Kit #2 (S-7554) to enable researchers to find the most appropriate green-fluorescent SYTO stain for their system.