Energetics of superhelicity and of B-Z transitions in superhelical DNA |
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Authors: | Craig J Benham |
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Institution: | (1) Mathematics Department, University of Kentucky, 40506 Lexington, KY |
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Abstract: | The linking difference, α, imposed upon a superhelically constrained DNA molecule must be partitioned between twisting and
bending deformations. Transitions to alternative secondary structures can occur at susceptible sites, altering the local molecular
twist by an amount ΔTw
trans. That part of the linking difference not accommodated in this way, the residual linking difference αres, must be manifested as smooth torsional and flexural deformations of secondary structure. The competition among the alternative
ways of accommodating the imposed linking difference α determines a stressed equilibrium state. The superhelical free energy,G(α), is the excess free energy of the equilibrium state at linking difference α above that of the relaxed state under identical
conditions. In this paper a method is described by which the free energies associated both to linking,G(α), and to residual linking differences can be determined from data on superhelical conformational transitions. The application
of this approach to previously published experimental data on the B-Z transition suggests that the free energy associated
with αres is about 30% larger at substantial superhelicities than it is near the relaxed state. At the onset of transition the functional
form ofG(α) is shown to change in a manner dependent upon the length of the Z-susceptible site. |
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Keywords: | Supercoiled DNA conformational energetics B-Z transitions |
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