Exposure of mammalian cells to ionizing radiation induces nuclear matrix proteins and their attached transcribing DNA sequences to form cross-links. To characterize the cellular and matrix components necessary for DNA-protein crosslink (DPC) formation, DPC yields have been examined in isolated nuclear matrices and in the intermediate steps during cell fractionation. It was found that, in both unirradiated and irradiated cells, all components of DPC are retained in isolated nuclei, and the formed DPC are retained as well during the cell fractionation procedure resulting in nuclear matrices. In contrast, nuclear matrices isolated from unirradiated cells are deficient in the ability to form DPC upon irradiation, indicating that elements necessary for DPC production have been disrupted or removed during the isolation procedure. When isolated nuclei were irradiated, the yield of radiation-induced DPC was about 2-fold higher than that for intact cells, presumably due to the removal of soluble cellular scavengers during the isolation procedure. Treatment of nuclei with Cu2+ to stabilize nuclear structural organization during the preparation of the nuclear matrix caused additional DNA, especially the matrix-associated newly replicated DNA, to become bound to protein. Such treatment also enhanced radiation-induced DPC production which was sensitive to OH radical scavengers. Moreover, radiation-induced DPC production in Cu(2+)-treated nuclei was more sensitive to EDTA and catalase than in untreated nuclei. It is therefore proposed that excess DPC induction in Cu(2+)-treated nuclei occurs preferentially at the sites of Cu2+ binding to chromatin where hydroxyl radicals are produced repeatedly through the Fenton reaction.