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DAPI Nuclear Counterstain

A blue nuclear counterstain for fluorescence microscopy and cellular imaging.

DAPI DNA stain for cellular imaging.

Thermo Scientific Pierce DAPI Nuclear Counterstains are high-purity forms of diamidino-2-phenylindole dye for fixed-cell, fluorescent staining of DNA content and nuclei for cellular imaging techniques.

DAPI (diamidino-2-phenylindole) is a blue fluorescent probe that fluoresces brightly upon selectively binding to the minor groove of double stranded DNA, where its fluorescence is approximately 20-fold greater than in the nonbound state. Its selectivity for DNA and high cell permeability allows efficient staining of nuclei with little background from the cytoplasm. DAPI is a classic nuclear counterstain for immunofluorescence microscopy, as well as an important component of high-content screening methods requiring cell-based quantitation of DNA content.


  • DAPI dye – diamidino-2-phenylindole is a blue fluorescent stain specific for DNA
  • Convenient – choose powder or easy-to-use DAPI dye solution (1mg/mL)
  • Cellular imaging – cell-permeable dye is effective for fixed-cell staining and quantitation of DNA content
  • Counterstain – ideal for use alongside detection of specific targets with fluorescent antibodies for fluorescence microscopy or high-content screening (HCS)

Properties of DAPI Fluorescent Dye:

Structure Chemical structure of DAPI fluorescent dye
Alternative names DAPI Stain, DAPI Dye, DNA Content Counterstain
Chemical name(s) 4,6'-diamidino-2-phenylindole, dihydrochloride
4',6-diamidine-2-phenyl indole
2-(4-Amidinophenyl)-6-indolecarbamidine dihydrochloride
Molecular formula C16H15N5 2HCl
Molecular weight 350.25
Excitation wavelength 341 ±3nm (near 360nm when bound to dsDNA)
Emission wavelength 452 ±3nm (456 to 460nm when bound to dsDNA)
Extinction coefficient > 30,600/M cm at 347nm in methanol
CAS # 28718-90-3
Purity > 95% (most lots >98%) by HPLC at 240nm
Solubility > 1mg/mL in water; compound is soluble in DMF, water and various non-phosphate aqueous buffers
Storage Store solid at room temperature (RT), protected from light
Store DAPI solution (1mg/mL) at 2-8°C protected from light
Reactive groups None; binds to minor groove of double-stranded DNA

Product Details:

As a counterstain in fluorescence imaging methods, DAPI is compatible with antibodies and other probes labeled with fluorescein and rhodamine dyes, as well as with Thermo Scientific DyLight Fluors. DAPI has greater photostability than Hoechst dyes, although Hoechst 33342 can be use for live cell imaging while use of DAPI is confined to fixed cells. DAPI is offered in powdered solid and aqueous solution forms.

Cellular imaging with DAPI and phalloidin probes.
DAPI counterstaining alongside a phalloidin probe. NIH 3T3 cells were grown in 96-well plates, fixed with paraformaldehyde, and permeabilized for 15 minutes. Cells were incubated for 45 minutes with 3U/mL of DY554-Phalloidin, then for 5 minutes with 1µg/mL of DAPI. Stained cells were imaged with the Zeiss Axio Observer™ .Z1 Microscope (Obj. 20X/0.4NA). Phalloidin binds F-actin, revealing the distribution of actin filaments. DAPI stains DNA, thereby delineating the nuclei.

Cell-based fluorescent imaging with DAPI counterstain and DyLight Fluor antibodies.
Dual imaging with DAPI and antibody probes. DU145 prostate cancer cells DU145 were grown in 96-well plates, fixed with paraformaldehyde and permeabilized for 15 minutes. Cells were incubated for 1 hour at room temperature with a mouse anti-human HMGB antibody, then for 45 minutes with orange DyLight Fluor goat anti-mouse secondary antibody. Finally, DAPI was added at 1µg/mL for 5 minutes. Stained cells were imaged with the Thermo Scientific ArrayScan VTI Instrument (Obj. 20X/0.45NA).

Applications for DAPI Stain:

  • Assaying DNA in solution (ref.4)
  • Diagnosing mycoplasmal infection of cell cultures (ref.5)
  • Measuring nuclear content and sorting chromosomes in flow cytometry (ref.6)
  • Assessing apoptosis (ref.7)
  • Detecting nuclei and organellar DNA in immunofluorescent and in situ hybridization procedures (ref.2,8)
  • Replacing ethidium bromide for staining DNA in agarose gels (ref.5,9)
  • Counterstaining nuclei in histochemical methods when red-fluorescent antibodies have been used to detect specific targets (ref.8)
  • Reports also indicate that DAPI will bind to polyphosphates and other polyanions (ref.10), dextran sulfate (ref.11) and SDS (ref.12).


  1. Morikawa, K. and Yanagida, J. (1981). Visualization of individual DNA molecules in solution by light microscopy: DAPI staining method. J. Biochem. (Tokyo) 89:693-6.
  2. 2. Lawrence, M.E. and Possingham, J.V. (1986). Direct measurement of femtogram amounts of DNA in cells and chloroplasts by quantitative microspectrofluorometry. J. Histochem. Cytochem. 34:761-8.
  3. Kubista, M., et al. (1987). Characterization of interaction between DNA and 4', 6-diamidino-2-phenylindole by optical spectroscopy. Biochemistry 26:4545-53.
  4. Brunk, C.F., et al. (1979). Assay for nanogram quantities of DNA in cellular homogenates. Anal. Biochem. 92:497-500.
  5. Russell, W.C., et al. (1975). A simple cytochemical technique for demonstration of DNA in cells infected with mycoplasmas and viruses. Nature 253:461-2.
  6. Hammarton, T.C., et al. (2003). Stage-specific differences in cell cycle control in Trypanosoma brucei revealed by RNA interference of a mitotic cyclin. J. Biol. Chem. 278(25):22877-86.
  7. Lai, J., et al. (2003). Loss of HSulf-1 up-regulates heparin-binding growth factor signaling in cancer. J. Biol. Chem. 278(25):23107-17.
  8. Soto, P., et al. (2003). SMAD2 and SMAD7 Involvement in the post-translational regulation of Muc4 via the transforming growth factor-β and interferon-γ pathways in rat mammary epithelial cells. J. Biol. Chem. 278(22):20338-44.
  9. Nairn, R.S., et al. (1982). Comparison of ethidium bromide and 4', 6'-diamidino-2-phenylindole as quantitative fluorescent stains for DNA in agarose gels. J. Biochem. Biophys. Meth. 6:95-103.
  10. Tijssen, J.P.F., et al. (1982). Localization of polyphosphates in Saccharomyces fragilis, as revealed by 4', 6-diamidino-2-phenylindole fluorescence. Biochem. Biophys. Acta 721:394-8.
  11. Allan, R.A. and Miller, J.J. (1980). Influence of S-adenosylmethionine on 4', 6-diamidino-2-phenylindole dihydrochloride (DAPI)-induced fluorescence of polyphosphate in the yeast vacuole. Can. J. Micro. 26:912-20.
  12. Kapuscinski, J. and Skoczylas, B. (1978). Fluorescent complexes of DNA with DAPI (4',6-diamidine-2-phenyl indole dihydrochloride) or DCI (4',6- dicarboxyamide-2-phenyl indole). Nucl. Acids Res. 5:3775-99.

Related Resources:

Immunohistochemistry (IHC) technical guide
IHC counterstains technical guide

Related Products:

DyLight Reactive Fluors
All Fluorescent Labeling Reagents – including AMCA, FITC, and TRITC
Immunohistochemistry Reagents – including ABC and DAB staining kits
Cellular Imaging and Analysis Reagents (formerly Cellomics Products)

Ordering Information
Product # Description Pkg. Size Instructions MSDS CofA Price
62247 DAPI
Formulation: 4',6-Diamidino-2-phenylindole, dihydrochloride; powder
Sufficient For: 10mL of typical 1000X stock solution (10L of 1X staining solution)
10mg Product Instructions for product #62247 DAPI MSDS for product #62247 DAPI $138.00

Now available on lifetechnologies.com
62248 DAPI Solution
Formulation: 4',6-Diamidino-2-phenylindole, dihydrochloride; 1mg/mL aqueous solution
Sufficient For: 1L of typical 1X staining solution
1mL Product Instructions for product #62248 DAPI Solution MSDS for product #62248 DAPI Solution $115.00

Now available on lifetechnologies.com

Instructions | MSDS | CofA
Product Instructions | MSDS | CofA  

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