Part I: DNA Topology and Geometry/DNA Elasticity

Saturday, September 15, 2007 - 1:30pm - 2:30pm
EE/CS 3-180
David Swigon (University of Pittsburgh)

DNA topology and geometry

  • Linking number, writhe, twist

  • The theorem of Calugareanu and White, DNA supercoiling

  • Methods for calculating and estimating writhe

  • Surface linking number, linking number paradox

  • DNA knots and catenanes, topoisomerases, recombination

DNA elasticity

  • Idealized elastic rod model, equilibrium configurations,
    supercoiling of rings, bifurcations

  • Elastic rod models with intrinsic curvature, kinetoplast

  • Higher order continuum models, kinkable DNA

  • Base-pair level models, sequence-dependence of DNA

  • elasticity
  • DNA looping, role of looping in transcription regulation

  • Electrostatic effects