DAPI

DAPI

Names
IUPAC name 2-(4-Amidinophenyl)-1H-indole-6-carboxamidine
Other names 4',6-Diamidino-2-phenylindole
Identifiers
CAS Number	28718-90-3 Y
3D model (Jmol)	Interactive image Interactive image
ChEBI	CHEBI:51231 Y
ChemSpider	2848 Y
ECHA InfoCard	100.044.700
PubChem CID	2954
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	277.33 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
Y  (what is YN ?)
Infobox references

DAPI (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. As DAPI can pass through an intact cell membrane, 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.

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 bound. This led to its use in identifying 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.

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.