An endonuclease has been isolated from human B lymphoblastoid cells that copurifies with an exonucleolytic activity and has been shown to produce double-strand breaks and a high proportion of single-strandedness in phage X DNA in vitro. The data are consistent with a model in which single-strand cuts are made by the endonucleolytic activity, possibly in A+T-rich regions of the DNA, followed by creation of single-stranded regions (gaps) precessing from the site of a cut. Generation of overlapping gaps on opposite strands or of a gap opposite a nick would lead to the creation of the banding patterns that we have seen on electrophoretic gels. This endonucleolytic activity copurifies with other enzymes induced by Epstein-Barr virus that relate to the process of viral DNA replication in productively infected cells. However, a more general role is proposed for this class of eukaryotic endonuclease activities. A marked degree of single-strandedness has been found in the replicating DNAs of many eukaryotes, and these gaps could be generated by endonucleases with associated exonucleolytic activity such as that reported here. This EpsteinBarr virus-induced nuclease activity has been shown to resemble the recBC nuclease isolated from the prokaryote Escherichia coli and also the endonuclease isolated from the eukaryote Chlamydomonas.Our laboratory has recently reported that human B lymphoblastoid cell lines that are productively infected with Epstein-Barr virus (EBV) contain EBV-induced DNA polymerase (1) and DNase (2) activities. We have shown that the DNase is separable from the polymerase after several stages of purification and that it digests both native and denatured DNA, used as substrate, to mononucleotides (2). We report here that this EBV-induced exonuclease is inseparable through multiple purification steps from an endonucleolytic activity that also is EBV-induced and acts in a selective manner on phage X DNA used as substrate. This EBV-induced endonuclease reduces X DNA to a discontinuous series of large fragments that are then very sensitive to the action of S1 endonuclease. However, DNA fragments of similar length, generated from the large X genome, result from this endonucleolytic reaction only in the presence of concentrations of salt sufficient to inhibit the active exonucleolytic activity (160-180 mM KCI).The EBV-induced endonuclease reported here resembles in many important respects an enzymatic activity isolated from the eukaryote Chlamydomonas by Burton et al. (3). The Chlamydomonas endonuclease has been postulated to cut at specific sites on one strand and to then digest one of the two strands of the substrate DNA. The gel electrophoretic pattern of fragments generated by treatment of DNA with various concentrations of the Chlamydomas enzyme resembles the pattern of digests shown in the present report that result from the action of the EBV-induced endonuclease on phage X DNA.We also suggest that this class of eukaryotic nuclease resembles the prokaryotic nuclease recBC isolated from Escherichi...