DNA junctions, antijunctions, and mesojunctions.

Antijunctions and mesojunctions are new classes of multistranded DNA complexes. They represent a generalization of DNA branched junction complexes, such as the Holliday recombination intermediate. Each strand of a conventional branched junction participates in two different double helices, and this is also true for mesojunctions and antijunctions. The helix axes of conventional branched junction complexes may be drawn to converge at a point, but this convergence occurs for lines drawn perpendicular to the helix axes of antijunctions. Mesojunctions are complexes that mix these features of junctions and antijunctions. Antijunction complexes require an even number of strands. We have synthesized the mesojunction containing three strands, the two mesojunctions containing four strands, and the antijunction containing four strands; we compare them with branched junctions containing three and four strands, derived by permutations of the same sequences. Each double helix is designed to contain 1.5 turns of DNA. A tendency to oligomerize makes it difficult to capture antijunctions and mesojunctions in stable discrete complexes, in contrast to conventional branched junctions. For both three-strand and four-strand complexes, Tm is highest for conventional branched junctions. Ferguson analysis indicates similarities in the occluded surface area of junctions, antijunctions, and one four-strand mesojunction, but the other four-strand mesojunction has a much lower apparent surface area. Hydroxyl radical cleavage patterns suggest that the four-strand antijunction and the low-surface-area four-strand mesojunction form stacking domains, analogous to the behavior of conventional branched junctions. These new structures are related to replicational and recombinational intermediates and to single-stranded nucleic acid knots.