A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast.

HO nuclease is a site-specific double-strand endonuclease present in haploid Saccharomyces cerevisiae undergoing mating type interconversion. HO nuclease initiates mating type interconversion by making a double-strand break within the MAT locus. To define the recognition site for the enzyme in vitro, we have constructed a number of point mutations and deletions within or adjacent to the HO recognition site. Digestion of these substrates with HO in vitro reveals that the minimal recognition site is 18 base pairs long, although several shorter substrates and substrates containing point mutations are cleaved at low levels in vitro. A 24-base-pair HO recognition site stimulates homologous recombination when present in a region unrelated to MAT. Recombinants arise from both gene conversion and crossover events. The identification of the HO recognition site provides a way of introducing a defined initiation site for recombination.