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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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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.
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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.

Mentions: Of course, both experimental and theoretical approaches of determining the values of fieq must produce the same results, and, as shown, they do (Figure 1). Remarkably, the measured and calculated fractions of the trefoil knots are in agreement over a wide range of ionic conditions in which they change by more than the order of the value (due to the change of the electrostatic repulsion between the DNA segments). If we take into account that the theoretical calculation has no adjustable parameters, the results presented in the figure should be considered solid proof that we know how to obtain the values of fieq for different topological states.Figure 1.


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

Vologodskii A - Nucleic Acids Res. (2009)

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

License
Show All Figures
getmorefigures.php?uid=PMC2691845&req=5

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.
Mentions: Of course, both experimental and theoretical approaches of determining the values of fieq must produce the same results, and, as shown, they do (Figure 1). Remarkably, the measured and calculated fractions of the trefoil knots are in agreement over a wide range of ionic conditions in which they change by more than the order of the value (due to the change of the electrostatic repulsion between the DNA segments). If we take into account that the theoretical calculation has no adjustable parameters, the results presented in the figure should be considered solid proof that we know how to obtain the values of fieq for different topological states.Figure 1.

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