52 A. Gabibov et al.
This scheme reflects the most probable mechanism of top II action [27, 28].
Free enzyme associates with the first segment of DNA containingnsuperturns.
As it will serve as a Gate segment at the next step of reaction we denote it as
Gn. The formation and the dissociation of thegnEcomplex are described with
association and dissociation constants (kanandkdn, respectively), which, in
general, could depend onσ. Then the second segment of DNA, the T-segment,
binds to thegnEcomplex giving two types of ternary complexes,TgnE∼and
∼TgnE (Fig. 4.4a). Since T- and G-segments practically coincide after the
formation of these complexes, effective change of the DNA linking number (by
approximately±1) takes place. These complexes have different constants of
Fig. 4.4.Analysis of the complexes of scDNA with topoisomerase II. (a)Schematic
representation of complexes formed by topoisomerase II with G and T DNA seg-
ments. A sign of the linking number depends on the superhelix symmetry of the
complex. (b) Topological transformations of scDNA catalysed by topoisomerase II.
Changes of the type of ternary complex effect on the linking number (approximately
by±1). The Gibbs energy change is characterised by factor 4Bn/RT.The kinetic
constants reflecting the transformations between (n+2) and (n−2) topoisomers
are described by exp(− 4 Bn/RT) function