DiI

DiI
Names
	IUPAC name (2Z)-2-[(E)-3-(3,3-dimethyl-1-octadecylindol-1-ium-2-yl)prop-2-enylidene]-3,3-dimethyl-1-octadecylindole; perchlorate
	Other names 3H-Indolium, 2-[3-(1,3-dihydro-3,3-di-methyl-1-octadecyl-2H-indol-2-ylidene)-1-propenyl]-3,3-dimethyl-1-octadecyl, perchlorate; 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate; D 282; DiI; DiIC18(3)
Identifiers
CAS Number	41085-99-8;
3D model (JSmol)	Interactive image;
ChemSpider	4646069;
PubChem CID	5706735;
CompTox Dashboard (EPA)	DTXSID601336591 ;
	InChI InChI=1S/C59H97N2.ClHO4/c1-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-41-50-60-54-46-39-37-44-52(54)58(3,4)56(60)48-43-49-57-59(5,6)53-45-38-40-47-55(53)61(57)51-42-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-2;2-1(3,4)5/h37-40,43-49H,7-36,41-42,50-51H2,1-6H3;(H,2,3,4,5)/q+1;/p-1 Key: JVXZRNYCRFIEGV-UHFFFAOYSA-M; InChI=1/C59H97N2.ClHO4/c1-7-9-11-13-15-17-19-21-23-25-27-29-31-33-35-41-50-60-54-46-39-37-44-52(54)58(3,4)56(60)48-43-49-57-59(5,6)53-45-38-40-47-55(53)61(57)51-42-36-34-32-30-28-26-24-22-20-18-16-14-12-10-8-2;2-1(3,4)5/h37-40,43-49H,7-36,41-42,50-51H2,1-6H3;(H,2,3,4,5)/q+1;/p-1 Key: JVXZRNYCRFIEGV-REWHXWOFAW;
	SMILES CC1(C)C(/C=C/C=C2N(CCCCCCCCCCCCCCCCC)C(C=CC=C3)=C3C\2(C)C)=[N+](CCCCCCCCCCCCCCCCC)C4=C1C=CC=C4.O=Cl(=O)([O-])=O;
Properties
Chemical formula	C59H97ClN2O4
Molar mass	933.89 g·mol−1
Melting point	68 °C (154 °F; 341 K) (decomposes)
Solubility	Soluble in ethanol, methanol, DMF, DMSO
	Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references

Cultured embryonal carcinoma were stained with either DiI (red) or DiO (green). The image was captured by scanning confocal microscopy.

DiI, pronounced like Dye Aye, also known as DiIC₁₈(3), is a fluorescent lipophilic cationic indocarbocyanine dye and indolium compound, which is usually made as a perchlorate salt. It is used for scientific staining purposes such as single molecule imaging, fate mapping, electrode marking and neuronal tracing (as DiI is retained in the lipid bilayers).

DiI is manufactured by Invitrogen, which has a series of long-chain lipophilic carbocyanine dyes, of which DiI is one of the most well researched members. Some prominent members of the series includes: DiI, also called DiIC₁₈(3); DiO, also called DiOC₁₈(3); DiD, also called DiIC₁₈(5); and DiR, also called DiIC₁₈(7), which exhibit distinct orange, green, red and infrared fluorescence, respectively, and all have the following useful properties, according to the manufacturer:^[1]^[2]

Diffuse laterally to stain the entire cell
Fluoresce weakly in water but highly fluorescent and quite photostable when incorporated into membranes
Possess very bright signals with high extinction coefficients
Are well retained in cell membranes
Demonstrate very little transfer to other cells

[1] Invitrogen Molecular probes Handbook

[2] tailed data from invitrogen on this series of lipophilic dyes

[1]

[2]