Crossing over by homologous recombination between monomeric circular chromosomes generates dimeric circular chromosomes that cannot be segregated to daughter cells during cell division. In Escherichia coli, homologous recombination is biased so that most homologous recombination events generate noncrossover monomeric circular chromosomes. This bias is lost in ruv mutants. A novel protein, RarA, which is highly conserved in eubacteria and eukaryotes and is related to the RuvB and the DnaX proteins, ␥ and , may influence the formation of crossover recombinants. Those dimeric chromosomes that do form are converted to monomers by Xer site-specific recombination at the recombination site dif, located in the replication terminus region of the E. coli chromosome. The septum-located FtsK protein, which coordinates cell division with chromosome segregation, is required for a complete Xer recombination reaction at dif. Only correctly positioned dif sites present in a chromosomal dimer are able to access septum-located FtsK. FtsK acts by facilitating a conformational change in the Xer recombination Holliday junction intermediate formed by XerC recombinase. This change provides a substrate for XerD, which then completes the recombination reaction.homologous recombination ͉ Ruv͞Xer recombination ͉ dimer resolution ͉ FtsK B arbara McClintock, during her work on ring chromosomes in maize, inferred in 1932 that whereas crossing over between rod-shaped (linear) chromosomes does not alter their topology, crossing over between ring (circular) chromosomes generates larger ring chromosomes (circular dimers) that cannot be segregated normally at cell division (1). This topological complication arising from crossing over between circular chromosomes was largely ignored until the 1980s, when it was demonstrated that site-specific recombination systems act to convert dimeric plasmid molecules, formed by homologous recombination, to monomers, and thereby facilitate stable plasmid inheritance (2, 3). Subsequently, it was shown that one of these site-specific recombination systems, XerCD site-specific recombination, also functions in the conversion of dimeric Escherichia coli chromosomes to monomers (4-6). Xer recombination uses two related recombinases, XerC and XerD, belonging to the tyrosine recombinase family, each recombinase catalyzing the exchange of one pair of strands in a reaction that proceeds through a Holliday junction (HJ) intermediate (7)(8)(9). XerCD act at the recombination site dif, located in the replication terminus region of the E. coli chromosome and at related sites in multicopy plasmids, for example, psi in plasmid pSC101 and cer in ColE1 (3, 10).Here we outline the processes that limit dimer formation by homologous crossing over in E. coli. We also discuss the mechanism that restricts Xer recombination at chromosomal dif to converting dimers to monomers by making a part of the recombination machine only accessible to dif sites when they are present in chromosomal dimers at the time of cell division.Homologous recom...