18 S.D. Levene
Fig. 2.10.Topology of products generated by recombination of circular DNA mole-
cules mediated by theλ-int superfamily of site-specific recombinases. Diagrams show
planar projections of negatively supercoiled DNA substrates undergoing intramolec-
ular recombination. Recombination sites, indicated byarrows, divide the DNA con-
tour into two domains, shown as black and outlined gray curves. Random Brownian
motion of recombination sites (left column) leads to site synapsis in DNA conforma-
tions that involve varying numbers of interdomainal supercoils (supercoils involving
separate DNA domains). Only interdomainal supercoils are trapped in the form of
knot or catenane crossings by strand-exchange steps in recombination (middle col-
umn). The resulting topologies are shown in the form of diagrams (right column)
that depict only the number and topological sign of irreducible crossings in each
knotted or catenated product, which are given to the right below each figure. These
diagrams correspond to actual products in which extraneous supercoils have been
removed by nicking of one DNA strand. (a) Inversely oriented sites. Inversion gen-
erates knotted products that are separated by intervals of +2 knot crossings; these
knots belong to the so-called “torus” class because of the property that these knots
can all be inscribed on the surface of a torus. Only three examples of knotted prod-
ucts are shown. (b) Directly oriented sites. In addition to unlinked circles, deletion
reactions generate (−) torus catenanes that also differ by steps of two crossings.
Only two examples of catenated products are shown