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 (Alexa Fluor® 488, FITC, GFP) and red (Alexa Fluor® 594, rhodamine, 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


DAPI products

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

Learn more here:

DAPI stain

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

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

Alternative to fluoresceinBPAE cells fixed and permeabilized using the Image-iT® Fixation/Permeabilization Kit. Nuclei were stained using NucBlue® Live Cell Stain.


Molecular Probes® Handbook

Molecular Probes HandbookThe 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.


Antifade reagents

Antifade reagentsAntifade reagents suppress photobleaching and preserve the signals of your fluorescently labeled target molecules. They offer excellent compatibility with DAPI and a multitude of dyes across the spectrum, making them especially valuable tools for multicolor applications.


Cell stain tool

Cell stain toolStain 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.


Fluorescence SpectraViewer

Fluorescence SpectraviewerPlot and compare spectra and check the spectral compatibility for common fluorophores including all the Molecular Probes® fluorescent probes. The Fluorescence SpectraViewer tool is formatted for both microscope imaging and flow cytometry applications.