The structural changes which occur in chromatin DNA after ischemic brain injury are poorly understood. This study examined the appearance of double-strand DNA breaks and the temporal profile of DNA degradation following focal ischemic injury in rat brain. Focal cerebral ischemia was produced by tandem occlusion of the common carotid and proximal middle cerebral arteries. The effects of decapitation ischemia were also studied by DNA analysis. DNA was extracted by standard methods from the ischemic brain tissues and electrophoresed on a 1.5% agarose gel. With decapitation ischemia, random DNA cleavage was observed as a dense "smear" on the gel electrophoresis beginning 6 h after the ischemic insult, and increasing in amount thereafter. Focal ischemia provided DNA fragmentation, which is specific DNA cleavage at the internucleosomal linker regions, particularly in the caudoputamen. Coexisting random degradation and specific fragmentation of DNA was observed in the cortex following focal ischemia. To determine whether an endonuclease responsible for DNA fragmentation was present, nuclear proteins were extracted from normal brain nuclei and the endonuclease activity was determined using plasmid DNA and a nuclear incubation system. This demonstrated that brain nuclear proteins have Ca(2+)-dependent endonuclease activity which is related to DNA fragmentation. Ischemic injury causes both random and specific DNA cleavage in the brain, which is probably mediated by Ca(2+)-dependent endonuclease.