Mono- and trivalent ions around DNA: a small-angle scattering study of competition and interactions

Abstract

The presence of small numbers of multivalent ions in DNA-containing solutions results in strong attractive forces between DNA strands. Despite the biological importance of this interaction, e.g., DNA condensation, its physical origin remains elusive. We carried out a series of experiments to probe interactions between short DNA strands as small numbers of trivalent ions are included in a solution containing DNA and monovalent ions. Using resonant (anomalous) and nonresonant small angle x-ray scattering, we coordinated measurements of the number and distribution of each ion species around the DNA with the onset of attractive forces between DNA strands. DNA-DNA interactions occur as the number of trivalent ions increases. Surprisingly good agreement is found between data and size-corrected numerical Poisson-Boltzmann predictions of ion competition for non- and weakly interacting DNAs. We also obtained an estimate for the minimum number of trivalent ions needed to initiate DNA-DNA attraction.

FIGURE 1

Schematic of the CHESS C-1 beamline, configured for ASAXS.

FIGURE 2

SAXS profiles of DNA acquired near the Rb edge. The solid line shows the profile acquired at the nonresonant energy, 15.094 keV. The dashed line shows scattering close to the edge, at 15.194 keV and reflects resonant effects. The anomalous signal, derived by subtraction of the resonant from nonresonant profile, is shown in the inset.

FIGURE 3

(Co(NH₃)₆)³⁺ (dash), Sr²⁺ (dot-dash), and Rb⁺ (solid) ion ASAXS profiles, matched at low-q. The different shapes of the anomalous signals reflect differences in the spatial distribution of ions around the DNA. As the ion valence is increased, the weight of the scattering shifts to higher angle or q, indicating the tighter binding to the DNA of the more highly charged counterions.

FIGURE 4

Inter-DNA attraction assessed from nonresonant scattering profiles. (a) The dashed curve shows scattering of noninteracting DNA (28). The solid curve shows a SAXS profile of DNA in 100 mM RbCl and 0.2 mM Co(NH₃)₆Cl₃. The similarity of these profiles suggests no interaction between DNAs at this low concentration of (Co(NH₃)₆)³⁺. However, when more (Co(NH₃)₆)³⁺ is added (b and c), an “upturn” in the SAXS profiles appears at q < 0.04 Å⁻¹, indicating weak attraction between DNAs. (b) SAXS profiles acquired at the nonresonant energy associated with the Rb edge in solutions containing 0.2 mM (solid), 0.65 mM (dash), or 0.8 mM (dot-dash) Co(NH₃)₆Cl₃, monovalent ion concentration kept at 100 mM RbCl. Data taken at 0.35 mM and 0.5 mM Co(NH₃)₆Cl₃ coincide with the 0.2 mM scattering profile within error (not shown). (c) SAXS profiles acquired at the nonresonant energy associated with the Co edge in solutions containing 0.2 mM (solid) and 0.8 mM (dot-dash) Co(NH₃)₆Cl₃, monovalent at 100 mM NaCl.

FIGURE 5

Comparison of counterion competition data with the numerical solution of the PB equation. (Upper-half) DNA charge compensated by Rb⁺ ions in competition with (Co(NH₃)₆)³⁺ (circles) and spermidine³⁺ (squares) in 100 mM RbCl, 0.2 mM [DNA]. (Lower-half) DNA charge compensated by (Co(NH₃)₆)³⁺ ions in competition with 100 mM NaCl at 0.2 mM [DNA] (triangles) and in competition with 100 mM NaCl (diamonds) or RbCl (stars) at 0.6 mM [DNA]. Data without error bars have errors smaller than symbol size. The dashed lines represent APBS computations for DNA surrounded by ions with different radii. A 2 Å ion radius underestimates the fraction of monovalent ions in the atmosphere. The data are consistent with ion radii of 3 Å or greater with an upper bound of 6 Å.