ROLE OF PARTNER HOMOLOGY IN DNA RECOMBINATION - COMPLEMENTARY BASE-PAIRING ORIENTS THE 5'-HYDROXYL FOR STRAND JOINING DURING FLP SITE-SPECIFIC RECOMBINATION

Absolute homology between partner substrates within the strand exchang e region is an essential requirement for recombination mediated by the yeast site-specific recombinase Flp. Using combinations of specially designed half- and full-site Flp substrates, we demonstrate that the s trand joining step of recombination is exquisitely sensitive to spacer homology. At each exchange point, 2-3 spacer nucleotides adjacent to the nick within the cleaved strand of one substrate must base pair wit h the corresponding segment of the un-nicked strand from the second su bstrate for efficient strand joining in the recombinant mode. In accor dance with the ''cis-activation/trans-nucleophilic attack'' model for each of the two transesterification steps of Flp recombination (strand cleavage and strand joining), we propose that the limited strand pair ing orients the DNA-nucleophile (5'-hydroxyl) for attack on its target diester (3'-phosphotyrosyl-Flp). During one round of recombination, 4 -6 terminal base pairs of the spacer (2-3 base pairs at each spacer en d) must unpair, following strand cleavage, within a DNA substrate and pair with the partner substrate prior to strand union. In this model, the extent of branch migration of the covalently closed Holliday inter mediate is limited to the central core of the spacer. The templated po sitioning of reactive nucleic acid groups (which is central to the mod el) may be utilized by other recombination systems and by RNA splicing reactions.