DAPI

DAPI

Names
IUPAC name 2-(4-amidinophenyl)-1H -indole-6-carboxamidine
Identifiers
CAS Number	28718-90-3
3D model (JSmol)	Interactive image Interactive image
ChEMBL	ChEMBL48217 Y
ChemSpider	2848 Y
PubChem CID	2954
CompTox Dashboard (EPA)	DTXSID50963757
InChI InChI=1S/C16H15N5/c17-15(18)10-3-1-9(2-4-10)13-7-11-5-6-12(16(19)20)8-14(11)21-13/h1-8,21H,(H3,17,18)(H3,19,20) Y Key: FWBHETKCLVMNFS-UHFFFAOYSA-N Y InChI=1/C16H15N5/c17-15(18)10-3-1-9(2-4-10)13-7-11-5-6-12(16(19)20)8-14(11)21-13/h1-8,21H,(H3,17,18)(H3,19,20) Key: FWBHETKCLVMNFS-UHFFFAOYAH
SMILES [N@H]=C(N)c3ccc(c2cc1ccc(cc1n2)C(=[N@H])N)cc3 [H]/N=C(/c1ccc(cc1)c2cc3ccc(cc3[nH]2)/C(=N/[H])/N)\N
Properties
Chemical formula	C16H15N5
Molar mass	277.324
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Y verify (what is YN ?) Infobox references

DAPI or 4',6-diamidino-2-phenylindole is a fluorescent stain that binds strongly to A-T rich regions in DNA. It is used extensively in fluorescence microscopy. DAPI can pass through an intact cell membrane therefore it can be used to stain both live and fixed cells, though it passes through the membrane less efficiently in live cells and therefore the effectiveness of the stain is lower.

History

DAPI was first synthesised in 1971 in the laboratory of Otto Dann as part of a search for drugs to treat trypanosomiasis although it was unsuccessful as a drug. Further investigation indicated it bound strongly to DNA and became more fluorescent when it did so. This led to its use in identifying mitochondrial DNA in ultracentrifugation in 1975, the first recorded use of DAPI as a fluorescent DNA stain.

Strong fluorescence when bound to DNA led to the rapid adoption of DAPI for fluorescent staining of DNA for fluorescence microscopy. Its use for detecting DNA in plant, metazoa and bacteria cells and virus particles was demonstrated in the late 1970s, and quantitative staining of DNA inside cells was demonstrated in 1977. Use of DAPI as a DNA stain for flow cytometry was also demonstrated around this time.

Fluorescence properties

When bound to double-stranded DNA DAPI has an absorption maximum at a wavelength of 358 nm (ultraviolet) and its emission maximum is at 461 nm (blue). Therefore for fluorescence microscopy DAPI is excited with ultraviolet light and is detected through a blue/cyan filter. The emission peak is fairly broad DAPI will also bind to RNA, though it is not as strongly fluorescent. Its emission shifts to around 500 nm when bound to RNA.

DAPI (magenta) bound to the minor groove of DNA (green and blue). From PDB: 1D30​.

DAPI's blue emission is convenient for microscopists who wish to use multiple fluorescent stains in a single sample. There is some fluorescence overlap between DAPI and green-fluorescent molecules like fluorescein and green fluorescent protein (GFP) but the effect of this is small. Use of spectral unmixing can account for this effect if extremely precise image analysis is required.

Outside of analytical fluorescence light microscopy DAPI is also popular for labeling of cell cultures to detect the DNA of contaminating mycoplasma or virus. The labelled mycoplasma or virus particles in the growth medium fluoresce once stained by DAPI making them easy to detect.

Live cells and toxicity

DAPI can be used for both fixed and live cell staining, though the concentration of DAPI needed for live cell staining is generally much higher than for fixed cells. It is labeled non-toxic in its MSDS and though was not shown to have mutagenicity to E. coli, it is labelled as a known mutagen in manufacturer information. As it is a DNA binding compound it is likely to have some low level mutagenic properties and care should be taken in its handling and disposal.

Alternatives

Epithelial cells stained with DAPI (blue) and two antibodies via immunofluorescence (green and red)

The Hoechst stains are similar to DAPI in that they are also blue-fluorescent DNA stains which are compatible with both live- and fixed-cell applications.