Biophys J, July 2000, p. 116-136, Vol. 79, No. 1

DNA Rings with Multiple Energy Minima

Patrick B. Furrer,^* Robert S. Manning, and John H. Maddocks^*

 ^*Département de Mathématiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland, and  Mathematics Department, Haverford College, Haverford, Pennsylvania 19041 USA

Within the context of DNA rings, we analyze the relationship between intrinsic shape and the existence of multiple stable equilibria, either nicked or cyclized with the same link. A simple test, based on a perturbation expansion of symmetry breaking within a continuum elastic rod model, provides good predictions of the occurrence of such multiple equilibria. The reliability of these predictions is verified by direct computation of nicked and cyclized equilibria for several thousand DNA minicircles with lengths of 200 and 900 bp. Furthermore, our computations of equilibria for nicked rings predict properties of the equilibrium distribution of link, as calculated by much more computationally intensive Monte Carlo simulations.

Biophys J, July 2000, p. 116-136, Vol. 79, No. 1
© 2000 by the Biophysical Society   0006-3495/00/07/116/21  $2.00

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