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

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Mathematics of DNA Structure, Function and Interactions

Part of the book series: The IMA Volumes in Mathematics and its Applications ((IMA,volume 150))

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Abstract

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.

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Author information

Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of Maryland, 20742-2021, College Park, MD, USA

    Jason D. Kahn

  2. Collagen Matrix, Inc., 509 Commerce Street, 07417, Franklin Lakes, NJ, USA

    James R. Jenssen

  3. Atlantic Equities LLP, 15 St. Helen’s Place, EC3A 6DE, London, UK

    Vasavi Vittal

Authors
  1. Jason D. Kahn
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  2. James R. Jenssen
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  3. Vasavi Vittal
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Corresponding author

Correspondence to Jason D. Kahn .

Editor information

Editors and Affiliations

  1. Dept. Pharmacology & Genome Center, University of California, Davis, E. Health Sciences Drive 451, Davis, 95616, USA

    Craig John Benham

  2. Dept. Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, 30332-0400, USA

    Stephen Harvey

  3. Dept. Chemistry & Chemical Biology, Rutgers State University of New Jersey, Taylor Rd. 610, Piscataway, 08854-8087, USA

    Wilma K. Olson

  4. Dept. Mathematics, Florida State University, Tallahassee, 32306-4510, USA

    De Witt Sumners

  5. Dept. Mathematics, University of Pittsburgh, Thackeray Hall 301, Pittsburgh, 15260, USA

    David Swigon

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Kahn, J.D., Jenssen, J.R., Vittal, V. (2009). Useful Intrusions of DNA Topology Into Experiments on Protein-DNA Geometry. In: Benham, C., Harvey, S., Olson, W., Sumners, D., Swigon, D. (eds) Mathematics of DNA Structure, Function and Interactions. The IMA Volumes in Mathematics and its Applications, vol 150. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-0670-0_8

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