Resolution of model Holliday junctions by yeast endonuclease is dependent upon homologous DNA sequences

Holliday junctions, in which two double-stranded DNA molecules are linked by single-stranded crossovers, are thought to be central intermediates in genetic recombination. We report here the in vitro specificity of a yeast endonuclease for structures analogous to Holliday junctions. Plasmids that extrude inverted repeat sequences into cruciform junctions are cleaved by the introduction of nicks into strands of like polarity, approximately 4-8 nucleotides from the base of the junction. In all cases, cleavage occurs within homologous sequences, and with precise symmetry across the junction. In contrast, a junction containing four arms of unrelated sequence is cleaved asymmetrically. The dependence upon homology for symmetrical cleavage is not found with T4 endonuclease VII, which cleaves branched structures in vitro. Holliday junction resolution appears to occur in a concerted manner by the introduction of nicks into two homologous DNA helices held in alignment.