Cations as Hydrogen Bond Donors: A View of Electrostatic Interactions in DNA

Supplemental Material

Supplementary Data

• Description

  Because most oligonucleotide crystals have been obtained from solutions containing Mg²⁺ and spermine, relatively little is known about the detailed structure of other divalent cations bound to DNA. Nevertheless, the few available structures indicate that such cations behave similarly to Mg²⁺. Four examples are briefly considered in Cations as Hydrogen Bond Donors: A View of Electrostatic Interactions in DNA with five additional views of the interaction of solvated ions with DNA pictured below.

  Download all Supplemental Figures as a single PDF. Figures also reproduced below.

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  Supplemental Figure 8s. Interactions of a solvated Mg²⁺ ion in A form DNA (AD0007). Waters in the first solvation shell interact directly with three bases on the major groove and with another two bases through a water molecule of the secondary solvation shell.

  

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  Supplemental Figure 9s. Magnesium as a glue. In most cases magnesium ions stabilize the crystal structure by binding together different duplexes. Three duplexes bound by a single Mg²⁺ ion (Nr 38) in BD0037 (not shown), five different Mg²⁺ ions are all involved in stabilizing the crystal. Due to the crystal symmetry, every duplex is in contact with thirteen Mg²⁺ ions (44).

  

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  Supplemental Figure 10s. The primary solvation shell of different ions: (a) Ni²⁺ (1); (b) and (c) Ca²⁺ (35). In the latter two cases the solvation shell is irregular. In (c) it has been modelled as two Ca²⁺ ions with partial occupancy.

  

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  Supplemental Figure 11s. A typical guanine N7 - ion - N7 guanine bridge found in the crystal structure of an oligonucleotide crystallized in the presense of Ni²⁺ (1). A similar bridge may be formed by Co²⁺ (78).

  

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  Supplemental Figure 12s. Examples of two Na⁺ ions clearly localized in crystals obtained with a low degree of hydration: left, dCpG (10); right, Z-DNA (48). The parallel DNA dimer crystal (10) only contains 3.5 water molecules/base pair and the Z-DNA crystal about fifteen water molecules/base pair (48). Thus these structures are significantly more dehydrated than standard A or B DNA, which contain about twenty five water molecules/base pair. In the case of dCpG, the sodium ion has an additional oxygen from cytosine lying below the square pyramidal face at a long 362 pm distance. It is not clear whether this cystosine atom should be considered part of the solvation layer of Na⁺. This ambiquity is a further example of the variable solvation of monovalent ions in general.