Inter-DNA Attraction Mediated by Divalent Counterions

Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating attraction between short DNA strands mediated by ${\mathrm{Mg}}^{2+}$ ions. Solution small angle x-ray scattering data collected as a function of DNA concentration enable model independent extraction of the second virial coefficient. As the [${\mathrm{Mg}}^{2+}$] increases, this coefficient turns from positive to negative reflecting the transition from repulsive to attractive inter-DNA interaction. This surprising observation is corroborated by independent light scattering experiments. The dependence of the observed attraction on experimental parameters including DNA length provides valuable clues to its origin.

Figure 1

Experimental $I(Q)$’s from 25 bp DNA strands as a function of [DNA] are shown in each panel at a given [${\mathrm{Mg}}^{2+}$]. Each curve has been normalized by [DNA] to enable direct comparisons. The appearance of either a downturn (a),(b) or upturn (c),(d) at the lowest scattering angle indicates repulsion or attraction between DNA strands.

Figure 2

As in Fig. 1, experimental $I(Q)$’s as a function of [DNA] are shown in each panel for 25 bp (a)–(d), 16 bp (e), and 8 bp (f) DNA strands. No attraction is observed at any measured [${\mathrm{Na}}^{+}$] for 25 bp DNA, while weak attraction is indicated for 16 bp and 8 bp DNA strands at [${\mathrm{Mg}}^{2+}$] of $10\mathrm{m}M$.

Figure 3

Interactions between DNA strands are reflected by changes in the $y$ intercept of $I(Q)$ [$\propto S(c,Q=0)$]. Here $1/S(c,Q=0)$ (symbols) is shown as a function of [DNA] (a) at different [${\mathrm{Na}}^{+}$], (b) at different [${\mathrm{Mg}}^{2+}$], and (c) as a function of DNA length at $10\mathrm{m}M$ ${\mathrm{Mg}}^{2+}$. The second virial coefficient can be derived from these data according to Eq. (1). The variation of $A_2$ as a function of ionic strength is shown in (d). Both repulsion ($A_2>0$) and attraction ($A_2<0$) are observed as [${\mathrm{Mg}}^{2+}$] increases; however, only repulsion is observed in the presence of monovalent ions. The data for 25 bp DNA in ${\mathrm{Mg}}^{2+}$ are multiplied by a factor of 3 for clarity. Most error bars have sizes comparable to symbols.

Figure 4

The structure factor $S(Q)$ can be extracted from the measured $I(Q)$ using models (see text). Panel (a) shows measured $I(Q)$’s of 25 bp DNA ($\sim 0.7\mathrm{m}M$) (symbols) and the fits (lines). Panel (b) shows the corresponding $S(Q)$’s only with the same color annotation as in (a).