We have studied several features of the mechanism of site-specific genetic recombination, focusing on the reaction that inserts the DNA of bacteriophage lambda into the chromosome of its E. coli host. The role of supercoiling has been explored by probing for the melting of DNA around the site of recombination crossover. The sequence features that determine the interaction of a recombination protein, IHF, with its target have been studied by chemically synthesizing variants of the normal site and biosynthetically incorporating them into substrates for recombination. These oligonucleotide mutagenesis studies confirm the features deduced from comparison of naturally occurring DNA binding sites for IHF and indicate some unexpected flexibility in the protein-DNA interaction. The relationship between the recombination that integrates lambda DNA and that which reverses the integration process (excision) has been explored. Artificial substrates show that both recombinations show the same demand for homology in a short region around the crossover site; in this region at least one strand from each parent must be identical. The result implies that both recombinations, although they have different protein requirements, use similar mechanisms.
