Site-specific recombination between molecules of bacteriophage P1 DNA occurs at sites called loxP and requires the action of a protein that is the product of the P1 cre gene. Although recombination between two loxP sites is very efficient, recombination between loxP and a unique site in the bacterial chromosome (loxB) is inefficient and generates two hybrid lox sites called loxR and lozL. We present here the nucleotide sequences of all four lox sites. Analysis of these sequences indicates that (i) a region of extensive homology is not present at the loxP x loxB crossover point, in contrast to the 15-base pair common-core sequence in the bacteriophage A aft sites, and (ii) the sites contain a region ofdyad symmetry with 8-to 13-base pair inverted repeats separated by an 8-to 9-base pair sequence. The loxP X loB crossover point falls in the sequence that separates the inverted repeats, and deletions that remove either the left or the right inverted repeat of loxP inactivate the site. These two observations are consistent with the conclusion that the region of dyad symmetry is important in lox recombination. We have shown further that the loxP X loxP crossover point occurs in a 63-base pair sequence containing the loxP x loxB crossover point, suggesting that, despite the great difference in efficiencies of the two reactions, the crossover points may occur at the same place in both. Explanations for the different recombination properties of the various lox sites are discussed.Bacteriophage P1 is a temperate virus that has both lytic and lysogenic phases in its life cycle. In contrast to other temperate phages, such as A, P2, and P22, phage P1 rarely integrates into the chromosome of its host in its lysogenic mode but maintains itself as an autonomous unit-copy plasmid (1). Recently, the existence ofa site-specific recombination system in P1 has been demonstrated (2), and a number offunctions have been ascribed to it. Among these are the cyclization ofphage P1 DNA injected into a recA host and the rare integration ofP1 into the bacterial chromosome. Perhaps the most important role for this recombination, however, is to ensure proper segregation of P1 plasmid molecules to daughter cells at cell division (3). We have postulated that dimer plasmid molecules formed by homologous recombination between monomers interfere with orderly segregation ofthe products ofplasmid replication to daughter cells. P1 has overcome this problem by being able to resolve dimeric molecules rapidly into monomers by means of its site-specific recombination system.The site-specific recombination system of P1 consists of two elements, a site on the DNA called lox (for locus of crossingover) and a phage-encoded protein, the product of the P1 cre gene (4). The site on P1 DNA is termed loxP, and the site on the bacterial chromosome into which the P1 plasmid integrates with low efficiency is called loxB. On integration of P1 DNA The publication costs ofthis article were defrayed in part by page charge payment. This article must therefore be...

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