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. 2014 Aug 14;42(16):10823–10831. doi: 10.1093/nar/gku756

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© The Author(s) 2014. 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 License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Charge neutralization patterns of NA duplexes by bound CoHex ions, assessed by the strength of the electric field near the NA-CoHex complex surface. (A) A-form mixed sequence RNA with CoHex counterions, which bind mostly in the major groove. (B) B-form mixed sequence DNA with CoHex ions, which are bound mostly externally. The specific snapshots are chosen to illustrate the internal (A) and external (B) binding modes from Figure 3 and reflect the actual average binding preferences; each snapshot has 15 bound (near neutralizing) CoHex ions, and is taken from the corresponding 320 ns-long all-atom MD simulation described in ‘Materials and Methods’. See Supplementary Data for a detailed visual characterization of CoHex ion distributions around these structures. The field is computed 3 Å away from the NA-CoHex complex molecular surface.