DAPI (4′,6-diamidino-2-phenylindole)

DAPI (4′,6-diamidino-2-phenylindole) is a blue-fluorescent DNA stain that exhibits ~20-fold enhancement of fluorescence upon binding to AT regions of dsDNA. It is excited by the violet (405 nm) laser line and is commonly used as a nuclear counterstain in fluorescence microscopy, flow cytometry, and chromosome staining.

DAPI’s spectral properties make it ideal for use with green (Invitrogen Alexa Fluor 488, FITC, GFP) and red (Invitrogen Alexa Fluor 594, rhodamine, Invitrogen Texas Red, mCherry, mKate-2) fluorophores in multicolor experiments.

Because of its high affinity for DNA, it is also frequently used for counting cells, measuring apoptosis, sorting cells based on DNA content, and as a nuclear segmentation tool in high-content imaging analysis.

DAPI is generally used to stain fixed cells since the dye is cell impermeant, although the stain will enter live cells when used at higher concentrations. For live-cell staining, Hoechst 33342 dye is a popular cell-permeant nuclear counterstain.

DAPI dashboard

Initial brightness

DAPI serves as an ideal nuclear counterstain for fixed cells where its relative brightness is well matched to the abundance of nuclear DNA.  

Photostability in buffer


Photostability in antifade



Human iPSC staining using Mouse Anti Beta-Tubulin Monoclonal Antibody. Nuclei (blue) were labeled with Invitrogen NucBlue Fixed Cell ReadyProbes Reagent (Ready-to-use liquid DAPI formulation).

DAPI products

We offer a broad range of DAPI products including Invitrogen ReadyProbes ready-to-use stain formulations and antifade mountants.

Learn more here:

BPAE cells fixed and permeabilized using the
Invitrogen Image-iT Fixation/Permeabilization
Kit. Nuclei were stained using Invitrogen 
NucBlue Live Cell Stain.

Alternatives to DAPI

We offer a number of nucleic acid stains—with various emission wavelengths—that can be used as alternatives to DAPI for imaging live cells.

Nuclear counterstaining in live cells

For live-cell staining, Hoechst 33342 dye is a popular cell-permeant nuclear counterstain.

A special formulation of Hoechst 33342 dye, NucBlue Live ReadyProbes nucleic acid stain is supplied ready to use in a dropper bottle.

Additional probes for nucleic acid staining


Molecular Probes Handbook

Cell stain tool

The significantly revised 11th Edition is the most complete fluorescence labeling and detection reference available. The Molecular Probes Handbook can help you achieve the best experimental results for your fluorescence labeling and detection experiments. View the handbook online or order your own copy.

Go to the Handbook online
Order your copy of the Handbook

Antifade reagents

Cell stain tool

Antifade reagents suppress photobleaching and preserve the signals of your fluorescently labeled target molecules. They offer excellent compatibility with a multitude of dyes across the spectrum, making them especially valuable tools for multicolor applications. For added convenience, some formulations include the nuclear counterstain DAPI, eliminating the need for a separate counterstaining step.

See the performance of this dye in SlowFade Antifade reagents
See the performance of this dye in ProLong Antifade reagents

Cell stain tool

Cell stain tool

Stain your own cell by using our simulation tool to develop reproducible results with many of our signature fluorescent dyes. Develop your multiplexing strategy for antibody probes, reactive dyes, and counterstains to create your perfectly labeled fluorescent cell.

Go to the cell stain tool

Fluorescence SpectraViewer


Plot and compare spectra and check the spectral compatibility for common fluorophores including all of the fluorescent probes from Thermo Fisher Scientific. The Fluorescence SpectraViewer tool is formatted for both microscope imaging and flow cytometry applications.

Go to the Fluorescence SpectraViewer

Not for resale. Super Bright Polymer Dyes are sold under license from Becton, Dickinson and Company.