Differences Between Positively and Negatively Supercoiled DNA that Topoisomerases May Distinguish

  • Jonathan M. Fogg
  • Daniel J. CataneseJr
  • Graham L. Randall
  • Michelle C. Swick
  • Lynn ZechiedrichEmail author
Conference paper
Part of the The IMA Volumes in Mathematics and its Applications book series (IMA, volume 150)


In all living cells, DNA is homeostatically underwound relative to its lowest energy conformation, resulting in egative supercoiling. This underwinding of DNA is critical to the metabolism of DNA and, thus, is vital to cell survival. Enzymes called topoisomerases regulate and maintain the supercoiled state of DNA and are critical to the successful replication of the genome. These enzymes are major targets for drugs used in the treatment of bacterial infections and cancer. One puzzling phenomenon of the topoisomerase mechanism is how these enzymes, orders of magnitude smaller than their substrate, can search, recognize and act at a local level to affect global DNA topology. While the homeostatic state of DNA supercoiling in cells is negative, both positive and negative supercoils exist transiently. Because of the right-handed nature of the DNA helix, the positive and negative supercoils are not equivalent. Several computational and theoretical models have been developed in an effort to describe the features of both positively and negatively supercoiled DNA. These models have accurately predicted some of the phenomena observed in vivo. However, the over-simplifying assumptions cannot account for the different biological activities of positively and negatively supercoiled DNA. This review will discuss the models in place and the mathematical and energetic properties of this elegant molecule and the “machines that push it around.”


Torsional Rigidity Reverse Gyrase Negative Supercoiling Positive Supercoiling Intercalate Ethidium Bromide 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jonathan M. Fogg
    • 1
  • Daniel J. CataneseJr
    • 1
  • Graham L. Randall
    • 2
  • Michelle C. Swick
    • 2
    • 3
  • Lynn Zechiedrich
    • 1
    • 2
    • 3
    • 4
    Email author
  1. 1.Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonUSA
  2. 2.Institutional Program in Structural and Computational Biology and Molecular Bio-physicsBaylor College of MedicineHoustonUSA
  3. 3.Interdepartmental Program in Cell and Molecular BiologyBaylor College of MedicineHoustonUSA
  4. 4.LZ: Funded by NIH Grant RO1 A1054830HoustonUSA

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