All change at Holliday junction

In the absence of added metal ions, the four-way junction is extended with an open central region (3, 4). However, upon addition of magnesium or other metal ions the junction folds by pairwise coaxial stacking of helices into the stacked X-structure (reviewed in refs. 5 and 6) (Fig. 1). This structure is a substrate for a variety of junction-selective enzymes, most of which alter the global structure on binding (reviewed in ref. 7). In free solution, the DNA junction folds to create an antiparallel structure, probably governed by the favorable juxtaposition of backbones and grooves when the small angle is approximately 60°. The lowering of symmetry on formation of the stacked X-structure creates two inequivalent kinds of strands; the two continuous strands turn about the pseudo-continuous axes that pass through the stacked helical pairs, while the exchanging strands pass between the stacked helices at the crossover. The general features of the stacked X-structure have been confirmed by a variety of experimental methods (3, 8–11 …