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Updated: Jul 3, 2026
06:48
CD Spectroscopy to Study DNA-Protein Interactions
Published on: February 10, 2022
DNA supercoiling inhibits DNA knotting.
Yannis Burnier1, Julien Dorier, Andrzej Stasiak
1Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne, Switzerland.
Nucleic Acids Research
|July 29, 2008
Summary
DNA topoisomerases prevent DNA knotting in cells. This study reveals that DNA supercoiling, common in bacteria, also opposes knot formation, complementing enzyme activity to maintain DNA integrity.
Area of Science:
- Biochemistry
- Molecular Biology
- Computational Biology
Background:
- DNA molecules in cells are long, crowded, and rarely knotted.
- DNA knotting can disrupt cellular functions.
- Molecular mechanisms exist to maintain low DNA knotting and catenation levels.
Purpose of the Study:
- To identify mechanisms by which DNA topoisomerases maintain low DNA knotting levels.
- To investigate the role of DNA supercoiling in preventing DNA knot formation.
Main Methods:
- Numerical simulations of DNA molecules.
- Analysis of free-energy changes associated with DNA knotting and unknotting.
Main Results:
- Type II DNA topoisomerases use ATP hydrolysis to favor unknotting over knot formation.
- DNA supercoiling in bacterial cells creates an energetic barrier against knotting.
- Intramolecular passages leading to knotting are opposed by free-energy changes in supercoiled DNA.
Conclusions:
- DNA topoisomerases and DNA supercoiling together maintain low DNA knotting levels in cells.
- Supercoiling acts as a passive mechanism to reduce knot formation, complementing active enzymatic processes.
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Topoisomerases are divided into two main types. Type I...
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