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Theoretical models of DNA topology simplification by type IIA DNA topoisomerases.

Vologodskii A - Nucleic Acids Res. (2009)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA. alex.vologodskii@nyu.edu

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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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.
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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.

Mentions: A very important result, supporting the model, was obtained at the end of 2007 by Dong and Berger who published the X-ray structure of a complex between the DNA binding and cleavage core of yeast Topo II and a gate DNA segment (18). The DNA segment was sharply bent at about 150° (Figure 5). Complemented by the earlier biochemical studies, the structure showed that the directionality of a T segment passage relative to the bent G segment corresponds to one required by the model.Figure 5.


Theoretical models of DNA topology simplification by type IIA DNA topoisomerases.

Vologodskii A - Nucleic Acids Res. (2009)

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.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2691845&req=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.
Mentions: A very important result, supporting the model, was obtained at the end of 2007 by Dong and Berger who published the X-ray structure of a complex between the DNA binding and cleavage core of yeast Topo II and a gate DNA segment (18). The DNA segment was sharply bent at about 150° (Figure 5). Complemented by the earlier biochemical studies, the structure showed that the directionality of a T segment passage relative to the bent G segment corresponds to one required by the model.Figure 5.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA. alex.vologodskii@nyu.edu

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.

Show MeSH
Related in: MedlinePlus