Topology in Molecular Biology

2 Topology in Biology: From DNA Mechanics to Enzymology 17

Fig. 2.9.Two representations of the structure of a DNA Holliday junction. (a)
Diagram showing the alignment of DNA sequences within an immobile Holliday-
junction analog. The absence of symmetry abolishes the ability of this junction
to undergo branch migration, which would permit relocation of the branch point
along the DNA sequence. (b) Composite three-dimensional structure of the immobile
junction shown in (a) based on detailed biophysical studies from several laboratories.
The junction assumes a roughly fourfold symmetric structure in which the non-
exchanging DNA strands are oriented in an antiparallel fashion

Because of its importance as a recombination intermediate, substantial ef-
fort has been focused on elucidating the structure of Holliday junctions. Hol-
liday junctions that are generated by recombination normally have at least
twofold DNA-sequence symmetry and thus can undergo isomerization via a
process calledbranch migration[41]. Most available data on the structure of
four-way DNA junctions has been derived from studies of immobile junctions,
which lack the symmetry required for branch migration. Nevertheless, the pic-
ture that has emerged from these efforts has been extremely informative and
provided a framework for addressing the more complex problem of Holliday-
junction intermediates bound to recombination and other junction-recognizing
proteins.
One question that we have investigated in our laboratory is that of the
geometry of duplex DNA segments in the Flp synaptic intermediate [42]. In
particular, we have sought to determine the average relative alignment of
duplex recombination sites in the intermediate Flp-DNA complex because
biases in relative orientation influence the overall topology of circular Flp-
recombination products and the interpretation of topology in terms of re-
combination mechanism. This is a question that is best addressed by directly
imaging intermediate complexes, which we have done by using transmission
electron microscopy.