Nucleic Acids Research, Vol 25, Issue 7 1412-1418, Copyright © 1997 by Oxford University Press
VV Rybenkov, AV Vologodskii and NR Cozzarelli
We determined the free energy of DNA supercoiling as a function of the
concentration of magnesium and sodium chloride in solution by measuring the
variance of the equilibrium distribution of DNA linking
number,<(DeltaLk)2>. We found that the free energy of supercoiling
changed >1.5-fold over the range of ionic conditions studied. Comparison
of the experimental results with those of computer simulations showed that
the ionic condition dependence of<(DeltaLk)2>is due mostly to the
change in DNA effective diameter, d, a parameter characterizing the
electrostatic interaction of DNA segments. To make this comparison we
determined values of d under all ionic conditions studied by measuring the
probability of knot formation during random cyclization of linear DNA
molecules. From the topoisomer distributions we could also determine the
changes in DNA helical repeat, gamma, in mixed NaCl/MgCl2 solutions. Both
gamma and d exhibited a complex pattern of changes with changing ionic
conditions, which can be described in terms of competition between
magnesium and sodium ions for binding to DNA.
ARTICLES
The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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