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. 2005 Jan 14;88(3):1692–1701. doi: 10.1529/biophysj.104.054486

FIGURE 1.

FIGURE 1

Statistical mechanics of protein-mediated DNA looping. (A) DNA looping as a two-state system. Three free energies determine the lifetimes of the looped and unlooped states: the energy of unlooped DNA, the loop energy, and the kink energy. The loop energy includes contributions from protein-DNA interactions and DNA bending. The kink energy is associated with the deformation of DNA exterior to the loop. (B) The kink angle specifies different looping geometries. Maximum kinking occurs in the hairpin loop (θ = 0°). Parallel alignment of operators results in no kinking (θ = 180°).