The lox-Cre site-specific recombination system of bacteriophage P1 is comprised of a site on the DNA where recombination occurs called loxP, and a protein, Cre, which mediates the reaction. The loxP site is 34 base pairs (bp) in length and consists of two 13 bp inverted repeats separated by an 8 bp spacer region. Previously it has been shown that the cleavage and strand exchange of recombining loxP sites occurs within this spacer region. We report here an analysis of various base substitution mutations within the spacer region of loxP, and conclude the following: Homology is a requirement for efficient recombination between recombining loxP sites. There is at least one position within the spacer where a base change drastically reduces recombination even when there is homology between the two recombining loxP sites. When two loxP sites containing symmetric spacer regions undergo Cre-mediated recombination in vitro, the DNA between the sites undergoes both excision and inversion with equal frequency.

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Cre, the site-specific recombinase from bacteriophage P1, catalyzes a recombination reaction between specific DNA sequences designated as lox sites. The breakage and rejoining of partners during this recombination process must be highly concerted because it has not been possible to detect intermediates ofthe reaction with wild-type Cre. Several mutant Cre proteins have been isolated that produce significant amounts of a possible intermediate product of the recombination reaction. The product has been identified as a Holliday structure in which one set of the DNA strands of the recombining partners has been exchanged. Wild-type Cre protein is capable of acting on this structure to form recombinant products, which is consistent with this being an intermediate in the recombination reaction. Characterization of the Holliday structure indicated that one set of strands in the recombiming partners was always exchanged preferentially before the other set. In addition, it has been found that certain Cre mutants that are unable to carry out recombination in vitro are able to resolve the intermediate. This suggests that these mutants are defective in a step in the reaction that precedes the formation of the Holliday intermediate.Genetic recombination requires the physical exchange of DNA strands among partners in the reaction. The development of well-defined in vitro recombination systems has offered the possibility of biochemically dissecting this complex reaction (reviewed in refs. 1 and 2). Of considerable importance in understanding the mechanism of recombination is the identification and isolation of intermediates in the reaction. Because of its relative simplicity, we have chosen the Cre lox site-specific recombination system of bacteriophage P1 as a model to study this reaction. The system consists of a single protein, Cre, which mediates the recombination process between two 34-base-pair (bp) sequences designated as lox sites (3). Each lox site is comprised of two 13-bp inverted repeats separated by an 8-bp spacer region (4). Upon binding to the inverted repeats, Cre cleaves the DNA in the spacer region to initiate strand exchange with an equivalent partner in the reaction (5).Early concepts of genetic recombination involved a simple breakage and rejoining mechanism, in which double-stranded breaks were formed and all partners in the reaction were exchanged at once. The discovery of gene conversion in fungi, which could not be adequately explained by simple breakage and rejoining, stimulated the formulation of an alternative model (6). This model proposed that recombination took place by sequential exchange, with first one set of strands being cleaved and exchanged followed by similar reactions with the second set of strands. The model predicts that between those two events a cross-stranded structure or Holliday intermediate will be formed (6). A large body ofboth genetic and physical evidence has implicated the Holliday structure as an intermediate in recombination. Perhaps most convincing are the direct o...