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. 2015 Aug 24;43(17):8405–8415. doi: 10.1093/nar/gkv830

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 4. — The effect of cation size on spatial distribution functions. (Left) Cylindrical radial distribution functions of cations from 3D-RISM calculations where both the background (Na⁺) and competing (Li⁺, K⁺ and Rb⁺) cation have the same bulk concentration (50 mM). The normalized running integral of the difference between the background and competing cation densities, (Equation 8), is shown in black and its corresponding scale is shown on the right. The most competitive cations bring an excess of density located mainly in the vicinity of the DNA, particularly in the region of the phosphate binding, whereas for radii greater than ∼15 Å the densities of both cations are the same. (Right) Difference between 2D-untwisted ion densities () where X⁺ = Li⁺, K⁺ and Rb⁺. Untwisted densities for each cation are presented in Supplementary Figure S6.

Inline graphic — The effect of cation size on spatial distribution functions. (Left) Cylindrical radial distribution functions of cations from 3D-RISM calculations where both the background (Na⁺) and competing (Li⁺, K⁺ and Rb⁺) cation have the same bulk concentration (50 mM). The normalized running integral of the difference between the background and competing cation densities, (Equation 8), is shown in black and its corresponding scale is shown on the right. The most competitive cations bring an excess of density located mainly in the vicinity of the DNA, particularly in the region of the phosphate binding, whereas for radii greater than ∼15 Å the densities of both cations are the same. (Right) Difference between 2D-untwisted ion densities () where X⁺ = Li⁺, K⁺ and Rb⁺. Untwisted densities for each cation are presented in Supplementary Figure S6.