DiI

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
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
3D model (JSmol)
ChemSpider
PubChem CID
  • 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
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

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:

  • 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
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