During recombination, four-way junctions are resolved by enzymes to complete the process of strand exchange between duplexes. A 63° angle is estimated from atomic force microscopy studies on arrays of such junctions ( 10). 1) and the duplexes related by ∼60° ( 6– 9).
Divalent cations and polyvalent polyamines help shield the phosphate charges ( 5), allowing the junction to adopt a more compact structure with pairs of arms coaxially stacked as duplexes (Fig. 1) to minimize electrostatic repulsion between phosphates. In the presence of monovalent cations, the four arms of the junction are extended into a square planar geometry (Fig. Studies on synthetic four-stranded complexes and DNA cruciforms show that four-way junctions can adopt either an open extended-X or the more compact stacked-X conformations (for a recent review, see ref. Interactions within this core define the conformation of the Holliday junction, including the angle relating the stacked duplexes and how the base pairs are stacked in the stable form of the junction. The 3′-C⋅G base pair of this ACC core forms direct and water-mediated hydrogen bonds to the phosphates at the crossover strands. A sequence comparison with previous B-DNA and junction crystal structures shows that an ACC trinucleotide forms the core of a stable junction in this system. The junction is in the stacked-X conformation, with two interconnected duplexes formed by coaxially stacked arms, and is crossed at an angle of 41.4° as a right-handed X. Unlike the previous crystal structures, this DNA junction has B-DNA arms with all standard Watson–Crick base pairs it therefore represents the intermediate proposed by Holliday as being involved in homologous recombination.
We present here the single-crystal structure of the inverted repeat sequence d(CCGGTACCGG) as a Holliday junction at the nominal resolution of 2.1 Å. Holliday junctions are important structural intermediates in recombination, viral integration, and DNA repair.
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