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. 2009 Jun 24;37(15):5126–5137. doi: 10.1093/nar/gkp530

Figure 5.

Figure 5.

The free energy of DNA supercoiling increases with the extent of DNA catenation. (A) Profiles of the free energy of DNA supercoiling i.e. the energy that would be liberated upon nicking of the catenated DNA with various levels of catenation (Ca) and various extent of supercoiling (ΔLk) for modelled DNA molecules of ∼4400 bp. Notice that the free energy of catenation is not included in the graph since we are not considering here the energy that would be liberated upon progressive decatenation of modelled catenanes by Topo IV. (B) Free energy costs that DNA gyrase would need to overcome to perform sequential supercoiling cycles in catenated DNA molecules with ∼4400 bp that have different catenation numbers. Notice that during each catalytic cycle DNA gyrase reduces the linking number by two, notice also that each sequential cycle requires more energy and that in more complex catenanes this increase is more rapid than in less complex ones. The dashed line indicates the estimated level to which DNA gyrase would be able to supercoil protein-free DNA rings with different extents of catenation.