AAT Bioquest

DAPI - Blue Fluorescent DNA Stain

DAPI spectra
HeLa cell nuclei stainied with DAPI
DAPI (4'-6-diamidino-2-phenylindole) is a DNA-specific blue fluorescent dye used in many biological disciplines, including biochemistry, molecular biology, immunology, and microbiology. Because of its 20-fold fluorescence increase and high binding affinity for adenine-thymine (AT) rich regions of double-stranded DNA (dsDNA), DAPI is an excellent dye for cell counting and sorting, measuring apoptosis, and as a nuclear counterstain in fluorescence microscopy and flow cytometry. While DAPI is more sensitive for use with dsDNA, it also binds to adenine-uracil (AU) regions of RNA but with less affinity and fluorescence enhancement.



DAPI Overview

When bound to dsDNA, DAPI has an excitation/emission maxima of 359/457 nm. It is well-excited by the violet (405 nm) laser and detected through the DAPI filter. The high quantum yield (Φ = 0.92) of the DAPI/dsDNA complex enables it to emit bright blue fluorescence making DAPI an excellent counterstain in multicolor fluorescent techniques with other green (e.g., iFluor® 488, Alexa Fluor® 488, FITC, GFP) and red (e.g., iFluor® 647, Alexa Fluor® 647, Cy5, RFP) fluorophores. DAPI will also bind to RNA but at a lower affinity and emit a significantly weaker fluorescence signal, ∼20% as high as the yield of the DAPI/dsDNA complex. The DAPI/RNA complex also exhibits a longer-wavelength emission maximum at ∼500 nm.

DAPI spectra

Absorption and emission spectra for DAPI.

In most applications, cell/tissue fixation and permeabilization are done before DAPI staining since the dye is moderately cell impermeant. Increasing the DAPI concentration or incubation time may be necessary. However, this could lead to decreased cell viability. For live-cell DNA staining, Nuclear Violet™ LCS1 and Hoeschts dyes are popular alternatives. They have absorption and fluorescence emission maxima similar to DAPI and are cell-permeant. Besides labeling cell nuclei, DAPI is also used to detect mycoplasma or virus DNA in cell cultures.

Table 1. DAPI Specifications

CAS # 28718-90-3
Molecular Weight350.25
Ex Max (nm) 359
Em Max (nm) 457
Extinction Coefficient 27,000 cm-1M-1
Quantum Yield 0.58
Filter set DAPI
Laser line Violet (405 nm)


DAPI Products

FluoroQuest™ anti-fade mountant with DAPI
Fluorescence IHC of formaldehyde-fixed, paraffin-embedded human lung adenocarcinoma positive tissue. Human lung adenocarcinoma positive tissue sections were stained with rabbit anti-EpCam antibody and then incubated with polyHRP-labeled Goat anti-Rabbit IgG secondary antibody followed by iFluor® 488 Styramide™ stain, respectively. The tissue was mounted in FluoroQuest™ Anti-fading Mounting Medium with DAPI.
AAT Bioquest's portfolio of DAPI reagents includes ready-to-use formulations and FluoroQuest™ anti-fade mounting mediums fortified with DAPI. FluoroQuest™ anti-fade mountants preserve the fluorescence of tissue and cell smears for long-term storage and analysis by reducing the photobleaching rate of DAPI. FluoroQuest™ anti-fade mountants are used in in situ hybridization techniques or other methods requiring DNA staining with blue fluorescence.


Table 2. Product ordering information for DAPI reagents.

Ex (nm)
Em (nm)
Unit Size
Cat. No.
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *10 mM solution in water*3594572 mL17507
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*35945710 mg17510
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*35945725 mg17513
DAPI [4,6-Diamidino-2-phenylindole, dihydrochloride] *CAS 28718-90-3*359457100 mg17511
DAPI Dilactate35945725 mg17509
FluoroQuest™ Mounting Medium with DAPI35945750 mL20004
FluoroQuest™ Anti-fading Mounting Medium with DAPI35945720 mL20005


Nuclear LCS1™ Dyes - Alternatives to DAPI

One drawback to DAPI is its broad emission spectrum. The very long tail end in the DAPI emission overlaps considerably with green fluorophores, such as FITC and GFP, and will require spectral unmixing to remove artifacts. To address this concern, we offer a variety of different color Nuclear™ LCS1 live-cell nucleic acid stains that can be used as alternatives for DAPI. Nuclear™ LCS1 dyes readily penetrate live cells with healthy membranes and fluoresce strongly upon binding to DNA. Nuclear Violet™ LCS1 is a direct replacement for DAPI.

DAPI and FITC spectra

Emission spectra of DAPI and FITC illustrating considerable cross-talk between 475 and 600 nm.

Nuclear™ Red LCS1
Fluorescence images of HeLa cells stained with MitoLite™ Green FM (Cat No. 26695) using fluorescence microscope with a FITC filter set. Live cells were co-stained with nuclei stain Nuclear Red™ LCS1 (Cat No. 17542).

Key Features of Nuclear™ LCS1 Dyes

  • No-wash, nuclear-specific DNA dyes
  • Low toxicity for live cell imaging
  • Membrane-permeant dyes that stains nuclei of live, dead, or fixed cells
  • Nuclear Red™ LCS2 compatible with SIM, STED, or STORM
  • Choose from violet, blue, green, yellow, orange, red, or far-red fluorescence


Table 3. Product ordering information for Nuclear™ LCS1 DNA stain.

Ex (nm)
Em (nm)
Unit Size
Cat. No.
Nuclear Blue™ LCS13534560.5 mL17559
Nuclear Yellow [Hoechst S769121] *CAS 74681-68-8*[3725040.5 mL17539
Nuclear Violet™ LCS1 *5 mM DMSO Solution*4014600.5 mL17543
Nuclear Green™ LCS1 *5 mM DMSO Solution*5035270.5 mL17540
Nuclear Orange™ LCS1 *5 mM DMSO Solution*5145560.5 mL17541
Nuclear Red™ LCS1 *5 mM DMSO Solution*6226450.5 mL17542
Nuclear Red™ LCS2 *5 mM DMSO Solution*6516810.5 mL17545