The Holliday junction is a topologically symmetrical structure. A few simple manipulations of it, which
involve no breaking of covalent or hydrogen bonds, results in two possible fates, namely recombination or
strand swapping (Figure 6.38). Enzymes which recognise and cleave Holliday junctions are known, such
as bacteriophage T4 endonuclease 7. So if a Holliday junction is formed, it is a plausible substrate for
recombination. The choice between which bonds are cleaved in Figure 6.38 determines whether a strand
swap or a recombination event occurs. This choice may be influenced by the DNA sequence at the junc-
tion, both because the enzymes may display sequence specificity for cleavage and also because the three
dimensional structure of the junction is not a simple tetrahedron but is distorted by the sequence.
Genes and Genomes 241
Figure 6.38 The Holliday junction can yield recombination or strand swapping. Endonucleolytic cleavage at A or
B yields a recombination event or a strand swap, respectively