4 Dynamics of DNA Supercoiling 55〈σ〉
Fig. 4.6.Kinetic analysis of the scDNA transformations catalysed by topoisomerase
II. (a) Computer simulations of the distribution of topoisomers of pTM plasmid
induced by topoisomerase II. The following parameters were taken:kdis=1s−^1 ,
kass =1,000 s−^1 ,kt=5s−^1. DNA Hooks constantB=1, 150 RT.(b)〈σ〉vs
time dependence calculated according to formula (4.16). (c)ρvs time dependence
calculated according to formula (4.17)
actually caused by DNA relaxation. During the reaction, the amplitude ofσ
shifts exactly corresponded to the difference between LD of the relaxed and
supercoiled plasmids. In serial experiments (under sodium chloride concentra-
tions exceeding 100 mM), the signal growth obeys the first-order kinetics. In
contrast to the case of pTM, in the experiments with the BlueScript plasmid
no change of LD signal was detected during the reaction course,although in
accordance with the electrophoresis assay data the plasmid actually changes
its linking number during the enzyme-mediated reaction. Actually, under any
experimental conditions (e.g. under different enzyme-substrate ratio and dif-
ferent ionic strength), the BlueScript plasmid relaxation cannot be detected