I stained my cells with a lipophilic cyanine dye, like DiI, but the signal was lost when I tried to follow up with antibody labeling. Why?
Since these dyes insert into lipid membranes, any disruption of the membranes leads to loss of the dye. This includes permeabilization with detergents like Triton X-100 or organic solvents like methanol. Permeabilization is necessary for intracellular antibody labeling, leading to loss of the dye. Instead, a reactive dye such as CFDA SE should be used to allow for covalent attachment to cellular components, thus providing for better retention upon fixation and permeabilization.
Find additional tips, troubleshooting help, and resources within our Cell Analysis Support Center.
How long does it take for lipophlic tracers to transport along the membrane? How much faster are the FAST lipophilic dyes?
The transport is fairly slow, around 6 mm/day in live tissue and slower in fixed tissue, so diffusion of lipophilic carbocyanine tracers from the point of their application to the terminus of a neuron can take several days to weeks The FAST DiO and DiI analogs (which have unsaturated alkyl tails) can improve transport rate by around 50%.
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Which form of the lipophilic tracers (DiO, DiI, DiD, etc) should I use?
Select the dye that is compatible with your available excitation source(s) and emission filter set/channels. The solid, paste and crystal forms can be applied directly to neurons in tissues. For labeling cells in culture or microinjection, the lipophilic dyes in solution or solid form can be used.
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I want to label two cell populations and then perform a cell fusion assay. Which reagents are best for imaging this?
Lipophilic cyanine dyes are preferred for this sort of assay, since they insert into cellular membranes and then, upon fusion, are shared by the fused cells as the membranes are shared. For example, one cell population can be labeled with DiI (orange-red) and another cell population can be labeled with DiO (green), and when the cells fuse, the combined color appears yellow (when imaged with a dual-bandpass filter set).
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I want to track my cells with a nucleic acid stain, like DAPI or Hoechst dye. Do you recommend this?
This is not recommended. When these stains bind to DNA and RNA, they may affect the normal function of the nucleic acids, disrupting transcription, as well as replication. Other reagents, such as CellTracker dyes or Qtracker reagents are more optimized for tracking without disrupting normal activity. If a nuclear label is still desired, though, and the cells are mammalian and non-hematopoietic, CellLight nuclear reagents can transiently transfect cells to express GFP or RFP on a nuclear-expressing protein for up to several days without affecting function.
Find additional tips, troubleshooting help, and resources within our Cell Tracing and Tracking Support Center.
