Many antitumor and antibacterial drugs inhibit DNA topoisomerases by trapping covalent enzyme-DNA cleavage complexes. Formation of cleavage complexes is important for cytotoxicity, but evidence suggests that cleavage complexes themselves are not sufficient to cause cell death. Rather, active cellular processes such as transcription and/or replication are probably necessary to transform cleavage complexes into cytotoxic lesions. Using defined plasmid substrates and two-dimensional agarose gel analysis, we examined the collision of an active replication fork with an antitumor drug-trapped cleavage complex. Discrete DNA molecules accumulated on the simple Y arc, with branch points very close to the topoisomerase cleavage site. Accumulation of the Y-form DNA required the presence of a topoisomerase cleavage site, the antitumor drug, the type II topoisomerase, and a T4 replication origin on the plasmid. Furthermore, all three arms of the Y-form DNA were replicated, arguing strongly that these are trapped replication intermediates. The Y-form DNA appeared even in the absence of two important phage recombination proteins, implying that Y-form DNA is the result of replication rather than recombination. This is the first direct evidence that a drug-induced topoisomerase cleavage complex blocks the replication fork in vivo. Surprisingly, these blocked replication forks do not contain DNA breaks at the topoisomerase cleavage site, implying that the replication complex was inactivated (at least temporarily) and that topoisomerase resealed the drug-induced DNA breaks. The replication fork may behave similarly at other types of DNA lesions, and thus cleavage complexes could represent a useful (site-specific) model for chemical-and radiation-induced DNA damage.Type II DNA topoisomerases are involved in diverse cellular processes such as replication, transcription, recombination, chromosome condensation, and the maintenance of genome stability. These enzymes transform the topological state of DNA by a strand passage reaction (for reviews, see references 6, 65, and 66). After binding to one segment of duplex DNA, a type II topoisomerase cleaves the duplex with a four-base stagger while covalently attaching to both 5Ј ends via phosphotyrosine linkages. This reaction intermediate, with the enzyme covalently linked to broken DNA, is referred to as the cleavage complex. After passage of a second duplex segment through the break, the topoisomerase reverses the phosphotyrosine linkages and rejoins the cleaved DNA ends.Mammalian type II topoisomerases are targets of many important antitumor drug classes, including aminoacridines, anthracenediones, anthracyclines, ellipticines, and epipodophyllotoxins (for reviews, see references 10, 13, and 55). In addition, bacterial type II topoisomerases are targets of clinically important antibacterial agents (quinolones and flouroquinolones) (17, 28). Remarkably, all these antitumor and antibacterial agents inhibit the enzyme by trapping the cleavage complex. The simplest model is that the drug, l...