Useful Intrusions of DNA Topology Into Experiments on Protein-DNA Geometry

  • Jason D. KahnEmail author
  • James R. Jenssen
  • Vasavi Vittal
Conference paper
Part of the The IMA Volumes in Mathematics and its Applications book series (IMA, volume 150)


Small DNA minicircles are useful for characterizing protein-induced DNA bending and twisting, because obfuscating effects of DNA flexibility are less important than in larger DNA. Our work on DNA geometry and flexibility in protein-DNA complexes has employed T4 ligase-mediated DNA cyclization to make minicircles. Experiments can be carried out as forward ligations, or equivalently protein binding to minicircles can be characterized. In every case we have studied, topological characterization of minicircle synthesis or properties has led to unexpected geometric or mechanistic conclusions. Examples concerning the catabolite activator protein, E. coli RNA polymerase, the Lac repressor, and the TATA-box binding protein are discussed. Topological results have the experimental advantages that they are qualitatively unmistakable and internally controlled: new topoisomers are readily identified even in small amounts, and they are formed in the same reaction as relaxed products. Simulations of topoisomer distributions are quite sensitive to geometrical and flexibility parameters, which helps set stringent constraints on possible structural/dynamic models. However, the disadvantage of a topological measurement is it is consistent with any combination of writhe and twist that sums to the observed ΔLK, so it is difficult to be confident that a structural/dynamic model is a unique solution.

Key words

Minicircle DNA bending DNA cyclization RNA polymerase TBP Lac repressor CAP 


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Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Jason D. Kahn
    • 1
    Email author
  • James R. Jenssen
    • 2
  • Vasavi Vittal
    • 3
  1. 1.Department of Chemistry and BiochemistryUniversity of MarylandCollege ParkUSA
  2. 2.Collagen Matrix, Inc.Franklin LakesUSA
  3. 3.Atlantic Equities LLPLondonUK

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