We show that recombination between directly repeated sequences in plasmids occurs via both recA-independent and recA-dependent mechanisms in Escherichia coli. They are differentially affected by two factors, the distance separating the homologies and the size of the homology. Recombination between tandem duplications up to 300 base-pairs shows virtually no recA dependence. Increasing the size of the duplications beyond 309 base-pairs gradually increases the recA dependence. Furthermore, insertion of a sizable DNA sequence in between the duplications, substantially increases the recA dependence. We conclude that increasing the distance separating the homologous regions preferentially inhibits the recA-independent recombination. On the other hand, shortening of the homology preferentially inhibits recA-dependent recombination. Consequently, recombination between short tandem duplications is totally recA-independent.
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