We have been able to isolate as plasmids the products of recombination events occurring in mouse cell lines created by co-transferring unlinked pBR322 and Herpes Simplex Virus thymidine kinase gene (Tk) sequences into L cells deficient in thymidine kinase. The co-transferred DNAs were linked inside the eukaryotic cells and were integrated into high molecular weight cellular DNA. The plasmids were created by digesting DNA purified from the transformed cells with a restriction endonuclease and then ligating the resulting fragments under conditions favoring intra-molecular circularization. Plasmids were isolated by using the ligated DNA to transform E. coli and then selecting for ampicillin resistant colonies. Many of these "rescued" plasmids contain the pBR322 replication origin and BLA gene linked to Tk or cellular sequences or both. By using the cellular DNA sequences near the junctions as hybridization probes for genomic Southern blots we have shown that the DNA originates from unique sequence mouse DNA. Sequence analysis of the recombination junctions consistently showed that at least 15-20 BP homologies exist between the (otherwise grossly dissimilar) DNAs near the point where the linkage occurred. In addition, several palindromic and inverted repeat sequences appear to have been involved in the recombination process.