DiI (DiIC18(3); 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine) is a widely used lipophilic carbocyanine dye that labels cell membranes by inserting its two long (C18) hydrocarbon chains into the lipid bilayer. It has been extensively used for the antero- and retro-grade labeling of neurons.
Neuro-DiI (also available as a ready-to-use staining solution, CellBrite™ Green) was developed by Biotium as an alternative to DiI. It has two additional t-butyl groups (one on each side of the dye) attached to the dye chromophore which introduce structural flexibility in the dye making it much more soluble in both organic solvents and in cell membranes. Improved dye solubility in the membranes enables rapid dispersion of the dye molecules, away from each other much more rapidly than regular DiI which has a relatively flat structure that promotes dye aggregation, and slows down dispersion of dye molecules. Neuro-DiI therefore results in more uniform, rapid and stable staining as compared to DiI.
FAST™ DiI uses a different strategy to solubilize the dye. Replacing the saturated C18 lipophilic chain of regular DiI with unsaturated linoleyl chains gives the dye molecules a bent structure, making them less likely to aggregate and thus disperse faster in the membrane.
Both Neuro-DiI and FAST™ DiI would diffuse faster than regular DiI in membranes, but a comparison of the relative diffusion rate between the two dyes has not been made. Neuro-DiI may have a potential advantage over FAST™ DiI. The t-butyl groups of Neuro-DiI render it more hydrophobic than FAST™ DiI, likely resulting in more stable membrane staining and make dye transfer between cells less likely.