Incubation of isolated rat liver nuclei with ATP, NAD+, and micromolar Ca2+ concentrations of various metal ions resulted in extensive DNA hydrolysis. Half-maximal activity occurred with 1.0 microM Ca2+ added, and saturation of the process was observed with 10 microM Ca2+. The Ca2+ (10 microM)-activated DNA fragmentation was inhibited by the presence of Ca2(+)-binding protein regucalcin isolated from rat liver cytosol. The inhibitory effect of regucalcin was complete at 0.5 microM. At 25 microM Ca2+ added, such an effect of regucalcin (1.0 microM) was not seen. Regucalcin also inhibited Ca2(+)-activated DNA fragmentation in the presence of calmodulin (10 and 20 micrograms). The results show that regucalcin can inhibit the Ca2(+)-activated DNA fragmentation due to binding the metal, suggesting a role in regulation of liver nuclear functions.