Counterion Distribution around DNA Probed by Solution X-Ray Scattering

Counterion atmospheres condensed onto charged biopolymers strongly affect their physical properties and biological functions, but have been difficult to quantify experimentally. Here, monovalent and divalent counterion atmospheres around DNA double helices in solution are probed using small-angle x-ray scattering techniques. Modulation of the ion scattering factors by anomalous (resonant) x-ray scattering and by interchanging ion identities yields direct measurements of the scattering signal due to the spatial correlation of surrounding ions to the DNA. The quality of the data permit, for the first time, quantitative tests of extended counterion distributions calculated from atomic-scale models of biologically relevant molecules.

Figure 1

X-ray scattering profiles for DNA, in the presence of 0.4 M ${\mathrm{N}\mathrm{a}}^{+}$ (triangles), ${\mathrm{M}\mathrm{g}}^{2+}$ (diamonds), ${\mathrm{R}\mathrm{b}}^{+}$ (squares), and ${\mathrm{S}\mathrm{r}}^{2+}$ (circles) counterions. Actual curves (bottom) are shown, as well as offset curves (top), to aid visual comparison with calculations for DNA without modeled counterions (dashed line, arbitrary normalization) and with NLPB ion atmospheres (solid lines). To the right is shown a 25-base-pair DNA double helix in the presence of divalent cations (black spheres), distributed according to an NLPB calculation.

Figure 2

Direct evidence for counterion condensation onto DNA. Scattering in the presence of ${\mathrm{S}\mathrm{r}}^{2+}$ counterions probed with x-ray energies off (solid circles) and on (open circles) the Sr anomalous edge; and “control” measurements on DNA with ${\mathrm{M}\mathrm{g}}^{2+}$ counterions probed off and on the Sr edge (solid and open diamonds, indistinguishable). Inset: Magnification of curves, each divided by the off-edge ${\mathrm{S}\mathrm{r}}^{2+}$ profile to aid visual comparison. Error bars are smaller than symbols.

Figure 3

DNA-counterion correlation signals. Differences between profiles taken off and on anomalous edge for DNA with ${\mathrm{R}\mathrm{b}}^{+}$ (open squares) and ${\mathrm{S}\mathrm{r}}^{2+}$ (open circles), compared to the following: NLPB predictions for monovalent and divalent ion atmospheres (lines); ${\mathrm{R}\mathrm{b}}^{+}–{\mathrm{N}\mathrm{a}}^{+}$ difference curve (solid squares); and ${\mathrm{S}\mathrm{r}}^{2+}–{\mathrm{M}\mathrm{g}}^{2+}$ difference curve (solid circles). Inset: Shape comparison (log scale) of same NLPB, ${\mathrm{R}\mathrm{b}}^{+}–{\mathrm{N}\mathrm{a}}^{+}$, and ${\mathrm{S}\mathrm{r}}^{2+}–{\mathrm{M}\mathrm{g}}^{2+}$ curves, now renormalized by the intensity extrapolated to zero scattering angle with a Porod fit [$\log (sI/I_0)\propto -s^2$] of the data at $s=0.01–0.02{\AA }^{-1}$ [14].