The structure of DNA four-way junctions

The stereochemical conformation of the four-way helical junction in DNA (the Holliday junction; the putative central intermediate of genetic recombination) has been analyzed, using molecular mechanical computer modelling. A version of the AMBER program package was employed, that had been modified to include the influence of counterions and a nonlocal optimisation procedure. The problem of local minima can be reduced considerably by searching a subspace of relevant conformations. The choice of relevant subspace depends solely on the problem under study. The Bremermann routine has been used for nonlocal optimisation within the subspace. This method has been applied to the structure of a DNA four-way junction. As a result three distinct structures (and their intermediates) have been found. One structure is closely related to a square-planar cross, in which there is no stacking interaction between the four double helical stems. This structure is probably closely similar to that observed experimentally in the absence of cations. The remaining two structures are based on related, yet distinct, conformations, in which there is pairwise coaxial stacking of neighbouring stems. In these structures, the four DNA stems adopt the form of two quasi-continuous helices, in which base stacking is very similar to that found in standard B-DNA geometry. The two stacked helices so formed are not aligned parallel to each other, but subtend an angle of approximately 60°