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Review
. 2009 Jun;37(10):3125-33.
doi: 10.1093/nar/gkp250. Epub 2009 Apr 21.

Theoretical models of DNA topology simplification by type IIA DNA topoisomerases

Alexander Vologodskii  1
Affiliations
Review

Theoretical models of DNA topology simplification by type IIA DNA topoisomerases

Alexander Vologodskii. Nucleic Acids Res. 2009 Jun.

Abstract

It was discovered 12 years ago that type IIA topoisomerases can simplify DNA topology--the steady-state fractions of knots and links created by the enzymes are many times lower than the corresponding equilibrium fractions. Though this property of the enzymes made clear biological sense, it was not clear how small enzymes could selectively change the topology of very large DNA molecules, since topology is a global property and cannot be determined by a local DNA-protein interaction. A few models, suggested to explain the phenomenon, are analyzed in this review. We also consider experimental data that both support and contravene these models.

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Figures

Figure 1.
Figure 1.
Measured and simulated equilibrium fractions of trefoil knots for different concentrations of sodium ions [based on the data from ref. (9)]. The experiments were performed with 10-kb DNA which was cyclized in solution of different NaCl concentrations via joining the cohesive ends. Each point on the graph (gray circles) is the average of 6–20 determinations. The results of computer simulation, shown by open circles, account for the salt concentration over the effective diameter of the double helix which strongly depends on NaCl concentration (11). Only traces of more complex knots were observed in the experiment.
Figure 2.
Figure 2.
Type IIA topoisomerase, topo IV from E. coli, removes topological links from DNA to level below equilibrium (3). The reaction reached its steady state at substoichiometric values of the enzyme/DNA ratio. The equilibrium value of the knot fraction for the given conditions and DNA length, 7 kb, is shown as a reference level by the dashed line. Also shown, as a control, the fraction of knots found for topo III, type I topoisomerase from E. coli, which does not consume the energy during the catalysis and thus must shift the fraction of trefoils to the equilibrium level.
Figure 3.
Figure 3.
Typical simulated conformation of knotted (top) and unknotted (bottom) 7-kb DNA molecules. Each of the shown conformations has a segment located inside the hairpin-like G segment (red). For both conformations the potential T segment and G segment, which could interact with the enzyme, are circled by the dashed line. It seems clear from the figure that the mutual path of the segments inside the circle cannot specify topology of the entire chains. Indeed, the topology of both conformations can be easily changed outside the dashed circles. The conformations were selected from the equilibrium ensemble generated by a Metropolis Monte Carlo procedure (5).
Figure 4.
Figure 4.
The model of type IIA topoisomerase action. The enzyme (red) bends the G segment of DNA into a hairpin-like conformation. The entrance gate for the T segment of DNA is inside the hairpin. Thus, the T segment can pass through the G segment only from inside to outside the hairpin. Although it is not clear that the suggested mechanism has to provide simplification of DNA topology, the computational analysis shows that it really does (5).
Figure 5.
Figure 5.
Cartoon representation of the structure of the Topo II DNA-binding and cleavage core bound with DNA fragment [reproduced from ref. (18)]. DNA fragment, shown by orange, is bent by 150° in the complex.
Figure 6.
Figure 6.
The two-gate mechanism of the strand-passing reaction. The diagram illustrates the experiment with mutant yeast Topo II enzyme, which the C-gate was locked by disulfide links (13). The reaction substrate consisted of the large supercoiled molecule linked with small nicked circular DNA. Unlinking of circular DNA molecules accompanied by the AMPPNP driven closure of the N-gate, left the small circular molecule topologically linked with mutant Topo II. Such an outcome is possible only if a T segment enters through the N-gate of the enzyme and exits through the C-gate.
Figure 7.
Figure 7.
Diagram of a hooked juxtaposition of two DNA segments. It was suggested that such juxtapositions are typical among segment juxtaposition in linked and knotted molecules and represent a binding substrate for type IIA topoisomerases (6).
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