DAPI is usually used to stain fixed/permeabilized cells whereas Hoechst stain can be used to stain live cells also.
Both DAPI and Hoechst are cell permeable. The main difference is that the DAPI is more toxic so if you stain live cells they will not be alive for long.
Unfortunately both require UV (or near UV) excitation so in any case they are not the best choice if you would like to image them in living cells. I think there are new nuclear marker cell permeable that have a fluorescence in the red channel, they are clearly a better choice…
It is depend on the lypophilicity of these dyes, thats mean Hoechst is more lipophilic copmare to the DAPI, therefore more able tto cross the plasma membrane.
But if the DAPI concentration is too high live cells are stained too
Some hoechst dna intercalators are esterified dyes. They pass cell membranes as esters and cellular esterases create the hydrophilic dye that stays within the cells. In this way they stain all live cells ecen at low concentration
Both DAPI and Hoechst are cell permeable. The main difference is that the DAPI is more toxic so if you stain live cells they will not be alive for long.
Unfortunately both require UV (or near UV) excitation so in any case they are not the best choice if you would like to image them in living cells. I think there are new nuclear marker cell permeable that have a fluorescence in the red channel, they are clearly a better choice…
Molecular Probes call DAPI semi-permeable it depense on concentration
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