Locating Counterions in Guanosine Quadruplexes:  A Contrast-Variation Neutron Diffraction Experiment in Condensed Hexagonal Phase

Abstract

Guanosine, one of the primary components of nucleic acids, self-associates in water to form G-quadruplexes, four-stranded helicoidal aggregates, made by stacked planar tetramers, consisting of four planar guanine molecules. Essential for the stability of these supramolecular aggregates is the presence of monovalent cations. As G-quadruplexes show a lyotropic polymorphism, neutron diffraction, in combination with the H2O/D2O contrast variation technique, has been applied to study the cation structural features of quadruplexes in hexagonal phase at different hydrations and counterion concentrations. The guanosine 5'-monophosphate, dipotassium salt, was considered and G-quadruplexes in hexagonal phase were prepared in the different experimental conditions (contrast, hydration and KCl solution concentration) by using the osmotic stress technique. The calculated scattering length density distribution maps show that counterions fill the helix inner cavity and that atmospheric cations are bound to a second site, close to the external phosphate groups. The site occupancy turned out to be very high: we found on the inner site 0.87 K ions per tetramer in G-quadruplexes prepared in pure water and 0.97 K ions per tetramer in G-quadruplexes prepared in KCl 0.5 M, while in all cases 6 ions per unit cell were detected to occupy the outer sites, partially neutralizing the two formal negative charges per phosphate group. The very large K ions concentration difference between the binding sites and the bulk solution demonstrates that counterions are structurally involved in the formation and in the stabilization of the helices.

Guanosine Quadruplexes in Solution: A Small‐Angle X‐Ray Scattering Analysis of Temperature Effects on Self‐Assembling of Deoxyguanosine Monophosphate

“…Moreover, all the other common parameters are in very good agreement with previous reported structural data [17–19, 21, 24, 25, 27]. As expected, the main structural parameters of G-quadruplexes do not depend on the experimental conditions.…”

“…X-ray and neutron diffraction experiments showed that d(pG) quartets are stacked on the top of each other at the van der Waals distance of 3.4 Å and rotated with respect to each other by an angle of about 30° [ 14 – 16 ]. The presence of monovalent cations was observed to be essential for the stability of these supramolecular aggregates: the cation, located between two G-quartets, stabilizes the hydrogen-bonded quartets by cation-dipole interactions with the O6 ketone groups of eight separate molecules of guanine, enhancing base-stacking interactions [ 17 ].…”

Temperature and pressure limits of guanosine monophosphate self-assemblies

“…The Na + ion has a diameter of 1.9 Å and a volume of 3.6 Å 3 . As the central channel formed by G-quartet stacks is only occupied by dehydrated cations and very few water molecules (diameter d = 2.75 Å) 69 , it is reasonable to assume that a significant number of water-inaccessible voids is present in the G-quartet stacks. Those voids will disappear upon dissociation of the G-quartet structure.…”

The Supramolecular Helical Architecture of 8‐Oxoinosine and 8‐Oxoguanosine Derivatives

“…The two-dimensional electron-density profile can thus be obtained by calculating the two-dimensional Fourier distribution [Eq. (3)]: [11,12] 1ðx,yÞ…”

“…The correct sign of the Fourier coefficients F h,k has been obtained by considering a geometrical model of the helix. [12] For the sake of simplicity, this model was assumed to be cylindrically symmetric. The unit cell was split into four regions: the central cavity, the 8-oxoguanine region, the sugar residue region, and the hydrocarbon region in which the lipophilic substituents (and possibly also the hydrocarbon solvent) are located, as shown in Figure 5.…”