Invitrogen™ Vybrant™ DiO Cell-Labeling Solution

A typical method is to label one cell line with orange fluorescent DiI C₁₈ and the other cell line with green fluorescent DiO C₁₈. These orange and green lipophilic cyanine dyes will stain the membranes of cells. Cells that fuse will then have both dyes, yielding a yellow color (when images are overlaid or cells are imaged in a dual-bandpass filter). These live cells can then be labeled with Hoechst 33342 (a cell-permeant blue DNA stain comparable in wavelength to DAPI), but only as an endpoint just before imaging (since DNA stains can interrupt DNA function).

Lipophilic cyanine dyes, such as DiI (Cat. No. D282), DiO (Cat. No. D275), DiD (Cat. No. D7757) or DiR (Cat. No. D12731), are commonly used. The longer the alkyl chain on the dye, the better the retention in lipophilic environments.

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.

Please see this Web link (http://www.thermofisher.com/us/en/home/life-science/cell-analysis/cell-tracing-tracking-and-morphology/cell-tracking.html) to help you choose the right option for your application. Start by planning how long you want to track your cells, then consider the mechanism of binding. Calcein dyes are very uniform in label and are good for short-term cell migration, but may be rapidly effluxed from some cell types. Lipophilic cyanine dyes, such as DiI, DiO, and similar dyes label cell membranes, don’t disrupt function, and can last longer, but have the potential to cross to other cells if membranes fuse. They are also lost upon permeabilization. CellTracker dyes are better for longer-term labeling, as they possess a mildly reactive chloromethyl moiety that allows covalent binding to cellular components. CFDA SE also covalently binds to cellular components. With all the reagents, their retention within cells is dependent upon the rate of cell division and the inherent properties of the cell (active efflux, membrane and protein turnover rates, etc.) and reagents that allow for covalent attachment exhibit longer retention than those that do not.

The longest-lasting and brightest options are the Qtracker reagents, which are taken up through endocytosis. These are so bright individual quantum dots can be detected, and are also robust enough to survive not only fixation and permeabilization, but even the heat and solvents used in paraffin processing.

For live-cell imaging, the CellVue and CellMask Plasma Membrane Stains are the most uniform and the slowest to be endocytosed. However, they are not the best choice if you wish to fix and permeabilize your cells, such as for antibody labeling. Wheat germ agglutinin (WGA) conjugates are also able to label live cells, or can label already formaldehyde-fixed cells. They can survive subsequent permeabilization with detergents, such as Triton X-100. If cells are already permeabilized, WGA will label internal structures as well. Thus, only an antibody against a plasma membrane protein can be used if cells are already permeabilized. Lipophilic cyanine dyes, such as DiI, will label all cell membranes in live cells, not just plasma membranes, if left on live cells for extended periods. Following page will help you choose (http://www.thermofisher.com/us/en/home/life-science/cell-analysis/cell-structure/plasma-membrane.html).