The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling

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Abstract
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 〈(ΔLk)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 〈(ΔLk)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 γ in mixed NaCl/MgCl2 solutions. Both γ 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.