Figure 4.

Preferential binding of Mg²⁺, Ba²⁺ and Ca²⁺ in the minor groove promotes condensation of triple-stranded but not double-stranded DNA. (A) Free energy of pair interaction per one molecule calculated for 10 mM divalent ion concentrations in 10 mM Tris, 1 mM EDTA, assuming that 60% of bound divalent counterions are located in the middle of the minor groove with the rest located at random sites on DNA surface. The ionic strength of the Tris/EDTA buffer has only a small effect on the interaction energy. The values of θ were calculated from the Onsager-Manning theory for divalent ions, $\theta =1-l_c/2l_{\text{B}}$, yielding θ ≈ 0.88 for double-stranded DNA (l_c ≈ 1.7 Å) and θ ≈ 0.92 for triple-stranded DNA (l_c ≈ 1.1 Å). The curve for tsDNA calculated at the value of θ expected for dsDNA is shown to demonstrate the relative contribution of the phosphate charge pattern in tsDNA condensation, but for practical purposes only the dashed and bold lines should be compared. (B) Free energy per molecule in hexagonal, columnar aggregates calculated at the same conditions as in panel A.