Cations Form Sequence Selective Motifs within DNA Grooves via a Combination of Cation-Pi and Ion-Dipole/Hydrogen Bond Interactions

Abstract

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.

Exploring the effect of additives on polyamide membrane surface for seawater desalination using density functional tools

“…It is clear that the cation-π interactions between the MPD π-cloud and each metal ion is significant and increases the binding energy by 5-7 kcal mol −1 . The distance between the metal ions and the π-cloud is calculated to be in the range of 2.6-3.2 Å, which is in excellent agreement with the values reported in the literature for similar molecules [56]. Among the four cations, the divalent Mg 2+ ion shows stronger binding than the rest of the ions with K + being the least binding cation.…”

“…5). The distance between the metal ion and the TRP π-cloud is 2.7 Å, which is close to that identified in the literature for cation-π interactions in amino acids [56].…”

Multivalent ions and biomolecules: Attempting a comprehensive perspective

“…[361] In addition to electrostatic interactions between the RNA phosphate backbone and cations, both mono-and divalent cations have also been shown to interact with DNA bases through cation-π interactions as well as through the first hydration shell water molecules of the cations. [362] These types of interactions can lead to an enhanced stabilisation of certain DNA binding motifs, thus playing a role in cellular processes relying on, e. g., protein-DNA binding. [362] Because of its crucial role in cell proliferation, DNA is an obvious target for cancer treatment.…”

“…[362] These types of interactions can lead to an enhanced stabilisation of certain DNA binding motifs, thus playing a role in cellular processes relying on, e. g., protein-DNA binding. [362] Because of its crucial role in cell proliferation, DNA is an obvious target for cancer treatment. In the context of this review, the chemotherapeutic cisplatin needs to be emphasised.…”

Bioremediation potential of Cd by transgenic yeast expressing a metallothionein gene from Populus trichocarpa

“…This interaction is essentially electrostatic, in which a cation is attracted to the negatively charged cloud of electrons from aromatic groups (π systems), and is considered one of the strongest noncovalent interactions (Ma and Dougherty, 1997;Mahadevi and Sastry, 2013). Although mostly reported for monovalent cations, cation-π can also happen with divalent metal ions, such as seen with Mg 2+ (Stewart et al, 2013).…”