Topology in Molecular Biology

2 Topology in Biology: From DNA Mechanics to Enzymology 19

Fig. 2.11.(a) Linear DNA recombination substrates consisting of minimal FRT
sites present in a specific orientation and in the indicated location. In the presence
of Flp these molecules can synapse to form either parallel or antiparallel intermediate
complexes. (b) Synaptic complexes formed on 1048 bp FRT1-L fragments visualized
by electron microscopy and corresponding digital tracings of DNA contours in the
micrographs. Thearrowindicates the position of the FLP synaptosome. Both com-
plexes were scored as parallel. The distribution of parallel and antiparallel complexes
is also shown, based on an analysis of 146 synaptic complexes. For details, see [42]

There are two distinct scenarios for DNA duplex juxtaposition in the Flp
synaptic intermediate. As shown in Fig. 2.11, synapsis of two DNA segments
in which the target site is located close to one end of the molecule could align
so that identical pairs of short and long DNA segments that flank the target
site are present on either side of the complex. This structure would imply that
the global alignment of target sites is roughly parallel. Alternatively, pairing
of segments that are dissimilar in size implies the formation of a globally
antiparallel synapse. Analysis of over 100 synaptic complexes shows a strong
preference for globally parallel alignment of the recombination sites, as shown
in the examples in Fig. 2.10.
The observed preference for globally parallel alignment of recombination
sites stands in contrast to the expected antiparallel alignment of sites based
on the geometry of immobile Holliday-junction analogs. It is possible that
this difference is due to dramatic differences in the geometry of the four-
way junction intermediate in the bound-Flp state; alternatively, there may