counterstain

Direct Blue 1 (Pontamine sky blue), a counterstain for background autofluorescence in immunofluorescence histochemistry, structurally resembles glutamate and operates as a potent, competitive VGLUT inhibitor, not impacting plasma membrane transporters. This compound stands out as the inaugural small molecule PrP ligand to inhibit Aβ binding.

BODIPY TR methyl ester serves as a lipophilic GFP counterstain, easily permeating cell membranes to accumulate in endomembranous organelles, while exhibiting minimal localization in plasma membranes. It is a highly effective red fluorescent vital dye (Ex=568 nm, Em=625 nm) that can reveal the location and shape of cell nuclei, the morphology of cells in embryonic tissues, and the boundaries of organ-forming tissues within an entire embryo [1].

Nuclear Fast Red, an anthraquinone dye, serves primarily as a red nuclear counterstain in the presence of excess aluminum ions. Additionally, it functions as a histochemical and colorimetric reagent for calcium [1] and acts as a highly sensitive off on fluorescent probe for detecting guanine [2].

YOYO-3, a cell-impermeant dye with far-red fluorescence, is utilized as a nuclear counterstain and dead cell indicator, generating bright fluorescence upon binding to DNA.