1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate

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)
3D model (JSmol)
  • 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
  • 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
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).
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]

Name and Chemical Structure[]

The "Di" possibly stands for the di-alkyl nature and the "I" of DiI possibly stands for the "indocarbocyanine" group (which it shares with D383, D384, D3886, D3899, D3911, D7756, D7776, D7777, D12730, N22880). The full chemical name of this major member of the group is 1,1'-dioctadecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate, the chemical formula is C59H97ClN2O4 It has 18-carbon-long straight alkyl hydrocarbon tails on each on the nitrogen (Position 1) of the two indoline rings, a conjugated 3-carbon bridge connecting the 2nd positions (Carbon) on the rings symmetrically, and two methyl groups each on each of the 3rd positions (carbon) of the two rings. The longer names e.g. DiIC18(3) mention the length of the alkyl chain (e.g. 18) and the length of the conjugated bridge between the aromatic rings e.g. 3.

Derivatives and Analogs[]

DiI has several derivatives and analogs in use:[3]

Physical Properties[]

The dye (DiIC18(3)) is a violet crystal that is soluble in ethanol, methanol, dimethylformamide, and dimethylsulfoxide.[8] The crystal form of the dye has melting point of 68 °C (at which it decomposes). The dye had an absorption maximum at 549 nm and an emission maximum 565 nm[8] similar to tetramethyl rhodamine. It is mildly fluorescent in aqueous suspension, but becomes bright when bound to cell membrane.[9] Once bound to a membrane it diffuses laterally in 2 dimensions; if there is no diffusion barrier, DiI generally stains the whole leaflet (one surface) of a biological membrane rapidly, but does not readily flip across to the other leaflet.

See also[]


  1. ^ Invitrogen Molecular probes Handbook
  2. ^ detailed data from invitrogen on this series of lipophilic dyes
  3. ^ Probes Chapter 14 — Fluorescent Tracers of Cell Morphology and Fluid Flow
  4. ^ "Catalog of Cell Biology Products - Carbocyanine Membrane Dyes for Neuronal Tracing". Archived from the original on 2013-06-19. Retrieved 2013-06-16.
  5. ^ Jensen, Kristian H. R.; Berg, Rune W. (2016-09-06). "CLARITY-compatible lipophilic dyes for electrode marking and neuronal tracing". Scientific Reports. 6: 32674. Bibcode:2016NatSR...632674J. doi:10.1038/srep32674. ISSN 2045-2322. PMC 5011694. PMID 27597115.
  6. ^ molecular probes 2001 product information
  7. ^ Shan, L. (2004). "Near-infrared fluorescence 1,1-dioctadecyl-3,3,3,3-tetramethylindotricarbocyanine iodide (DiR)-labeled macrophages for cell imaging". Molecular Imaging and Contrast Agent Database (MICAD). National Center for Biotechnology Information (US). PMID 20641730.
  8. ^ a b R. W. Sabnis (2010). Handbook of Biological Dyes and Stains: Synthesis and Industrial Applications. John Wiley & Sons. ISBN 9780470586235.
  9. ^ "Dil Stain (1,1'-Dioctadecyl-3,3,3',3'-Tetramethylindocarbocyanine Perchlorate ('DiI'; DiIC18(3)))".