We analyzed the der(11) and der(4) genomic breakpoint junctions of a t(4;11) in the leukemia of a patient previously administered etoposide and dactinomycin by molecular and biochemical approaches to gain insights about the translocation mechanism and the relevant drug exposure. The genomic breakpoint junctions were amplified by PCR. Cleavage of DNA substrates containing the normal homologues of the MLL and AF-4 translocation breakpoints was examined in vitro upon incubation with human DNA topoisomerase II␣ and etoposide, etoposide catechol, etoposide quinone, or dactinomycin. The der(11) and der(4) genomic breakpoint junctions both involved MLL intron 6 and AF-4 intron 3. Recombination was precise at the sequence level except for the overall gain of a single templated nucleotide. The translocation breakpoints in MLL and AF-4 were DNA topoisomerase II cleavage sites. Etoposide and its metabolites, but not dactinomycin, enhanced cleavage at these sites. Assuming that DNA topoisomerase II was the mediator of the breakage, processing of the staggered nicks induced by DNA topoisomerase II, including exonucleolytic deletion and templatedirected polymerization, would have been required before ligation of the ends to generate the observed genomic breakpoint junctions. These data are inconsistent with a translocation mechanism involving interchromosomal recombination by simple exchange of DNA topoisomerase II subunits and DNA-strand transfer; however, consistent with reciprocal DNA topoisomerase II cleavage events in MLL and AF-4 in which both breaks became stable, the DNA ends were processed and underwent ligation. Etoposide and͞or its metabolites, but not dactinomycin, likely were the relevant exposures in this patient. L eukemia has become an increasingly common complication of effective chemotherapy (reviewed in ref. 1). Two classes of chemotherapy are associated with leukemia-alkylating agents and DNA topoisomerase II inhibitors (reviewed in refs. 1-3). The hallmarks of leukemias associated with DNA topoisomerase II inhibitors are balanced chromosomal translocations, many of which involve the MLL gene at chromosome band 11q23 (reviewed in refs. 2, 4, and 5). It has been suggested that the MLL translocation mechanism may involve DNA topoisomerase IImediated chromosomal breakage and formation of the translocations when the breakage is repaired (2, 4, 5).DNA topoisomerase II catalyzes the relaxation of supercoiled DNA by transiently cleaving and religating both strands of the double helix (6). The DNA topoisomerase II homodimer introduces four-base staggered nicks in DNA as each subunit covalently binds and cleaves one strand (6). In the presence of ATP, the DNA open gate allows passage of a second DNA helix through the cleaved strands (6). Next, the cleaved DNA strands are religated, and after ATP hydrolysis, the enzyme homodimer attains its original conformational state to catalyze another cycle (6). DNA topoisomerase II has been implicated in MLL translocations, because several anticancer drugs interfere with its c...