Cruciform (Holliday Junction(
 
 A key intermediate in DNA recombination is the Holliday junction that involves the joining of four homologous DNA strands into a cruciform arrangement, as visualized by electron microscopy some years ago. Supercoiling also can induce the formation of the cruciform for inverted repeat sequences. Detailed structural analysis of the cruciform DNA structure became possible when specific sequences were designed to form a so-called immobile junction. Studies on those molecules using gel electrophoresis and fluorescence indicated that the structure has a stacked X shape (ie, not tetrahedral) in the presence of metal ions (eg, Mg⁺ or CO(NH₃)₆³⁺  ). Models of the detailed structure at the junctions have been proposed. One such model involves a right-handed, antiparallel X structure, with two stacked helices crossing over each other with a crossover angle of ~ 60° (or 120°). Within each helix of the X structure, the two arms are collinear and the junction site is folded. A number of B-DNA structures determined by X-ray crystallography showed helix–helix packing contacts in the crystal lattice that are remarkably similar to the X structure. Recently the crystal structures of two proteins that are involved in the recombination process have been solved in the presence of their DNA substrate. The crystal structure at 2.4 Å resolution of Cre recombinase bound to a loxP DNA substrate showed that four recombinases and two loxP sites form a synapsed structure in which the bound DNA adopts a conformation similar to the four-way Holliday junction (1). The synapse assembly has a pseudofourfold symmetry, and the junction core is less compact than that proposed for the “free” Holliday junction.
References
1. F. Guo, D. N. Gopaul, and G. D. Van Duyyne (1997) Nature 389, 40–46.