Molecular Probes™ Hoechst 34580

DAPI is considered a semi-permeant/impermeant nucleic acid stain. Staining of nucleic is dependent upon the cell line in its performance. Some cell lines will label with DAPI, others not at all, and others label inconsistenly. Instead, we recommend using either Hoechst 33342 or Hoechst 33258, which have the same wavelength and binding mode as DAPI (at the A-T minor groove) but are readily cell-permeant.

We do not recommend doing this. DAPI is considered to be a semi-permeant/impermeant nucleic acid stain. DAPI staining of live cells may be inconsistent. It is best used as a counterstain for fixed samples. Other cell permeable nucleic acid stains, such as Hoechst or the SYTO dyes may affect cellular function.

For mammalian cells, we recommend using the CellLight Nucleus transduction reagents, available in CFP, GFP and RFP. With these reagents, the cells are transduced overnight in a single labeling step and the next day the nuclei will fluoresce. The label may be retained for 3-5 days and should not affect cell function. Cytoplasmic cell tracking dyes such as the CellTracker dyes may also be used.

DAPI is a very common blue-fluorescent dye for nuclear counterstaining and gives very bright labeling on nuclei in fixed and permeabilized cells and tissues. However, it is considered to be a semi-permeant to impermeant stain and provides inconsistent staining of live cells. Hoechst 33342 dye is cell-permeant and stains with the same binding mechanism and fluorescent color; it is preferred for live-cell imaging and is just as good as DAPI for fixed cell labeling.