2 Topology in Biology: From DNA Mechanics to Enzymology 15Fig. 2.8.Equilibrium between interwound (plectonemic) and toroidal superhelical
structures. The free energy difference between the interwound structure, that found
in free solution, and toroidal forms, such as that present in nucleosomes, is mod-
est, which suggests that the structure of negatively supercoiled DNA is dynamic.
This equilibrium could easily be perturbed by local motions of nucleosomes on a
negatively supercoiled template
these interactions may be responsible for the higher levels of organization in
the chromonema fiber [30, 31]. The modifications seem to have negligible
effects on the stability of the nucleosome, or on the 30-nm fiber alone. In
contrast, chromatin-remodeling complexes appear to act on a local level by
forming intermediate complexes with core histones, dissociating the histones
from core-particle DNA, and transferring these complexes to available binding
sites on naked DNA. The picture that therefore emerges, albeit an oversimpli-
fied one, is one in which different cellular factors operate reversibly on specific
levels of chromatin organization.
2.1.6 DNA Topology and Enzymology: Flp Site-Specific
Recombination
Site-specific recombination is a process that is functionally (but not mecha-
nistically) equivalent to a combination of restriction endonuclease and DNA
ligase activities. The recombinases that mediate these recombination events
recognize specific DNA sequences and the recombinase-bound sites interact
in a nucleoprotein intermediate calledthe synaptic complex. The synaptic