Dynamics of Supercoiled DNA

We use Brownian dynamic simulations to directly investigate large scale supercoiled DNA dynamics. One interesting question is related to DNA site juxtaposition -- the process bringing sites distant in DNA sequence together in space.
  • At physiological conditions, DNA has a regular interwound superhelical structure.

    • In unbranched structure, slithering of the opposite segments of the superhelix dominates the process.

      These snapshots are taken from a BD simulation of 3000 bp DNA with superhelicity at -0.06 and salt concentration at 0.2 M. The simulation time interval between each two snapshots is 0.1 ms. In this time scale, we usually can observe such bidirectional movements of opposite strands while the unbranched superhelical structure does not change.

    • In branched structure, the branch creation/deletion as well as the slithering through branch junctions accelerates the global dynamics.

      The snapshots are taken from the a BD simulation at the same condition as the last one. In this branched structure, the local slithering on each branch correlates with the change of joint position. The creating/deleting of branches occur at millisecond time scale, one to two orders longer than the local slithering.

  • At lower salt concentration and/or at lower DNA supercoiling, global reshaping of interwound superhelical structure plays a more significant role.

    Examples shown are for a 3000 bp DNA with -0.02 superhelicity and low salt (0.01 M). DNA structure is more irregular. Dynamicly, it quickly undergoes global distortions of superhelix with creating/deleting branches rather than slithering.

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Last modified Sept 18, 2000.