DAPI
IUPAC name	2-(4-amidinophenyl)-1H -indole-6-carboxamidine
Identifiers
CAS number	28718-90-3
PubChem	2954
SMILES	NC(=N)c1ccc(cc1)c2[nH]c3cc(ccc3c2)C(N)=N
ChemSpider ID	2848
Properties
Molecular formula	C16H15N5
Molar mass	277.324
Except where noted otherwise, data are given for materials in their standard state (at 25 °C, 100 kPa)
Infobox references

DAPI or 4',6-diamidino-2-phenylindole is a fluorescent stain that binds strongly to DNA. It is used extensively in fluorescence microscopy. Since DAPI will pass through an intact cell membrane, it may be used to stain both live and fixed cells, though it passes through the membrane less efficiently in live cells and therefore doesn't stain as well.

For fluorescence microscopy, DAPI is excited with ultraviolet light. When bound to double-stranded DNA its absorption maximum is at 358 nm and its emission maximum is at 461 nm. (This emission is fairly broad, and appears blue/cyan.)^[1] DAPI will also bind to RNA, though it is not as strongly fluorescent. Its emission shifts to around 500 nm when bound to RNA. ^[2]

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 fluorescence overlap between DAPI and green-fluorescent molecules like fluorescein and green fluorescent protein (GFP), or red-fluorescent stains like Texas Red, but using spectral unmixing or taking images sequentially can get around this.

Apart from labelling cell nuclei, the most popular application of DAPI is in detection of mycoplasma or virus DNA in cell cultures.

Because DAPI easily enters live cells and binds tightly to DNA, it is toxic and mutagenic, though such mutagenicity may be disputed ^[3]. Care should be taken in its handling and disposal.

Bovine Pulmonary Artery Endothelial cell nuclei stained with DAPI and imaged on a fluorescent microscope.

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.

[edit] References

1. ^ Invitrogen, DAPI Nucleic Acid Stain. accessed 2009-12-08.
2. ^ Scott Prahl, DAPI. accessed 2009-12-08.
3. ^ Ohta T, Tokishita S, Yamagata H. (2001). "Ethidium bromide and SYBR Green I enhance the genotoxicity of UV-irradiation and chemical mutagens in E. coli.". Mutat Res. 492 (1-2): 91-7. PMID 11377248.