The experiments reported here begin to define the molecular nature of the Cre-loxP interaction. It is instructive to compare some of the features of this system with the two other well-characterized site-specific recombination systems of phage lambda and transposon Tn3. In terms of the DNA required for a functional recombining site, the Cre-loxP system appears to be the simplest of the three, requiring only 34 bp of sequence to bind the recombinase. In contrast, both lambda and Tn3 systems have multiple binding sites for their respective recombinases (Hsu et al. 1980; Grindley et al. 1982). It is believed that these additional binding sites, although not the sites of cleavage and strand exchange, are somehow important in bringing the DNA into a suitable configuration necessary for recombination (Better et al. 1982; Grindley et al. 1982; Pollock and Nash 1983). DNA conformation, i.e., whether the DNA substrate is supercoiled or linear, also appears to play a more important role in both of these systems, whereas the Cre-loxP system works efficiently, irrespective of the DNA conformation. All of the recombinases mentioned above create staggered cuts in the DNA during the process of strand exchange and form a covalent attachment to the DNA at the site of cleavage (Reed and Grindley 1981; Craig and Nash 1983b; R.H. Hoess and K. Abremski, in prep.). It should be pointed out that covalent attachment to the DNA is a general feature that these recombinases share with topoisomerases (Gellert 1981). The nature of the cuts made in the DNA is more similar for Int and Cre than for Tn3 resolvase.(ABSTRACT TRUNCATED AT 250 WORDS)