DNA double-crossover molecules containing two Holliday junctions have
been prepared and treated with endonuclease VII, the resolvase from ba
cteriophage T4. One molecule contains antiparallel double-helical doma
ins, and the other molecule contains parallel domains. The parallel do
uble-crossover model system has been made tractable by closing the fre
e ends of the molecule, to convert it to a catenane. The products resu
lting from the two substrates differ substantially. The molecule conta
ining antiparallel helical domains is cleaved three nucleotides 3' to
the crossover points, in a fashion similar to single Holliday junction
analogs. The molecule containing parallel helical domains is cleaved,
but the major points of scission are five nucleotides 5' to a branch
point on the crossover strands and six nucleotides 3' to the same bran
ch point on the non-crossover strands. The major sites of scission ref
lect features of molecular symmetry in each case, suggesting that the
resolvase recognizes structural features. The cleavage results suggest
that the antiparallel structure is the natural substrate, if the Holl
iday junction is unconstrained within the cell. It is straightforward
to reconcile antiparallel Holliday junctions with the conventional par
allel paradigm of recombination. Nevertheless, the cleavage of the par
allel molecule shows that a parallel substrate could also be cleaved s
ymmetrically by endonuclease VII (but with different products) if the
molecule were constrained to assume that conformation within the cell.