An extensive analysis of the fate and structure of polyomavirus-plasmid recombinant molecules transfected into Rat-1 cells has revealed that the DNA often becomes integrated within transformed cell DNA in a head-to-tail tandem arrangement. This occurs independently of the replicative capacity of the transforming DNA and is facilitated by the use of large quantities of DNA during transfection. These observations have led us to suggest that head-to-tail tandems are formed by homologous recombination between transfected DNAs either before or after integration within cellular DNA. To test this hypothesis, we have measured the transforming activity of pairs of mutant, nontransforming, recombinant plasmid DNAs that carry different lesions in the transforming gene of polyomavirus. The results show that, although the individual mutant DNAs are incapable of transformation, transfection with pairs of mutant DNAs leads to the formation of transformed cells at high frequency. Moreover, there is a direct relationship between the distance between the lesions in pairs of mutant DNAs and their transforming activity. Finally, analyses of-the structures of integrated recombinant plasmid DNAs and the viral proteins within independent transformed cells prove that recombination occurs between the mutant genomes to generate a wild-type transforming gene.Polyomavirus, one member of the papovaviruses, is a small double-stranded DNA tumor virus that is capable of replicating in mouse cells and transforming other rodent cells in culture. The transforming potential of the virus resides in the early transcription unit which encodes three tumor antigens, large, middle, and small T antigen (28). Large T antigen facilitates the initiation of transformation (8, 9, 12), whereas middle T antigen is required to maintain the transformed phenotype (3,10,14,16,20,22,23,25,27,29). The role of small T antigen in transformation is not known. Stable cellular transformation is achieved by the integration of the viral sequences within cellular DNA. Recombination between the cellular and viral genomes does not appear to involve specific sites, nor are regions of extensive homology required (15). One distinguishing characteristic of polyomavirus-transformed cells, especially transformed rat cells, is the arrangement of the integrated viral sequences within transformed cell DNA in a headto-tail tandem array (1, 2,4,13,19). This arrangement of integrated viral sequences is not only unique to polyomavirus-transformed cells but also occurs in simian virus 40-transformed cells (5, 18) and in cells transformed with viral recombinant DNA (24). The formation of tandemly arranged, integrated viral DNA may be stimulated by large T antigen (7), perhaps indirectly, but is not absolutely dependent on the activity of this protein (24). We have suggested that tandemly integrated sequences are formed by recombination between transforming DNAs (24), and have now formally tested this possibility.To determine whether homologous recombination can occur after transfection of ma...