Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA

We show that recombinases form joint molecules over very short regions of homology. When these molecules are deproteinized the three strands are in a structure that is surprisingly resistant to dissociation by branch migration, even at elevated temperatures. The joint molecules dissociate at temperatures comparable to those required to melt DNA duplexes of the same length and sequence. We also show that nonenzymatically formed structures of the same length and sequence, which have a free third strand ready to branch migrate, dissociate at much lower temperatures. These results provide compelling evidence that the three DNA strands in the region of pairing are hydrogen bonded to each other. Our observations suggest that such a novel three-stranded DNA molecule, or a structure very similar to it, may be the intermediate in general recombination that is used in the recognition of sequence homology. We discuss some of the structural features implicit in this molecule containing any base sequence and compare them with those manifest in true DNA triple helices containing special sequence motifs.