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We describe a system to analyze the individual contribution of a single physical DNA end on intramolecular recombination between partially homologous sequences. We took advantage of this partial sequence divergence to measure the distance separating the DNA end from the final recombination event. We show that a single physical DNA end stimulates recombination when located in a region of homology. Recombination frequency decreases gradually with the distance from the DNA end. A recombinational hot spot is found at the end of the region of homology. A large insertion of unrelated DNA interferes asymmetrically with this process, suggesting that a recombinogenic signal propagates along the region of homology.

Intramolecular recombination between partially homologous sequences in Escherichia coli and Xenopus laevis oocytes.