Cyclopentenone prostaglandins (PGs) such as PGA2 and delta 12-PGJ2 (9-deoxy-delta 9,12-PGD2) are taken up by cultured cells and exert growth inhibition. Within cells they are transferred to and accumulate in nuclei by a temperature-dependent process. In this study, the authors analyzed and compared subnuclear distribution and binding of these PGs. Nuclei accumulating either [3H]PGA2 or [3H] delta 12-PGJ2 were extracted successively with a hypotonic solution and with a 1% Triton X-100 solution, and the radioactivities in the two extracts (fractions of nucleoplasm and nuclear membrane, respectively) and the remaining residues (a fraction of chromatin and nuclear matrix) were determined. About three-fourths of PGA2-derived nuclear radioactivity was found in the extracts, and only 20% in the residues. Most of the radioactivity in the extracts was recovered in ethyl acetate under acidic conditions and identified as intact PGA2, suggesting that the majority of PGA2 in nuclei was present as free molecules. On the other hand, more than 70% of delta 12-PGJ2-derived nuclear radioactivity was associated with the residues and resistant to extraction with acidic ethyl acetate. This radioactivity, however, became extractable after brief alkali treatment and was identified as intact delta 12-PGJ2. In order to identify nuclear component binding of this PG, the authors digested the residues with either DNases or proteases. The radioactivity in the residues was almost completely released by digestion with proteases and clearly separated from DNA by ethanol precipitation. These results suggested that most of nuclear delta 12-PGJ2 bound covalently to protein(s) of chromatin and nuclear matrix.(ABSTRACT TRUNCATED AT 250 WORDS)