Mouse thymocytes readily undergo apoptosis-associated DNA degradation upon exposure to glucocorticoids or ionizing radiation. It has been previously shown that flow cytometric cell cycle analysis of propidium iodide-stained apoptotic thymocytes results in the appearance of a distinct cell cycle region (the A, region) below the GdGl region. Cells in this region were shown to be undergoing apoptosis, and determination of apoptosis by flow cytometric analysis was proposed as a superior method for evaluating thymocyte apoptosis. In this study, a variety of DNA binding dyes with diverse primary binding mechanisms were evaluated for their ability to detect glucocorticoid and ionizing radiation-induced apoptosis in mouse thymocytes. Apoptotic thymocytes stained with DNA binding dyes from the phenanthridinium, acridine, actinomycin, chromomycinone, anthracycline, and bisbenzimidazole groups all demonstrated clearly defined A, , regions with percentages comparable to those obtained for propidium iodide. These results indicate that the appearance of the A, region is not dependent on a particular dye binding characteristic and may be the consequence of extensive changes in chromatin structure resulting in a significant degree of dye exclusion.Key terms: Programmed cell death, phenanthridinium, acridine, chromomycinone, anthracycline, bisbenzimidazole Apoptosis, or programmed cell death, is a well-documented phenomenon in many cellular systems (31). Apoptosis is characterized by a number of structural changes in the cell, including the degradation of nuclear chromatin into internucleosomal fragments, presumably by the activation of an endogenous endonuclease (32). Glucocorticoid-(5,32) and ionizing radiation-(28) induced apoptosis in mouse thymocytes has been particularly well characterized in this regard. Internucleosomal DNA fragmentation has formed the basis for the majority of assay systems used to detect apoptosis, including electrophoresis of internucleosoma1 DNA fragments (32) and the separation of small internucleosomal DNA fragments by high-speed centrifugation (33). As previously described, assay systems of this type are by their very nature inadequate since they fail to evaluate apoptosis on a cell by cell basis (27).In a previous paper we described a method by which glucocorticoid-induced apoptosis could be detected in individual, intact mouse thymocytes by reduced fluorescence of the DNA binding dye propidium iodide in the apoptotic subpopulation (27). The apoptotic subpopulation manifested itself as a discrete peak displaying reduced fluorescence with respect to the G$G, cell cycle region. Reduced DNA binding dye fluorescence in apoptotic cells has also been observed using acridine orange (6,12,20), mithramycidethidium bromide (11, and the Hoechst dyes (13,171 in several systems. The apparent ability of DNA binding dyes to distinguish apoptotic cells based on reduced fluorescence by an as yet unclear mechanism has the potential to be an important means of studying programmed cell death,