Locating counterions in guanosine quadruplexes: a contrast-variation neutron diffraction experiment in condensed hexagonal phase

Self-oriented anisotropic structure of G-hydrogels as a delicate balance between attractive and repulsive forces

Guanine (G) hydrogels are very attractive materials made by the supramolecular organization of G-derivatives in water. In this paper, hydrogels composed of guanosine 5'-monophosphate (GMP) and guanosine (Gua), that make long, flexible and knotted G-quadruplexes, were investigated by small- and wide-angle X-ray scattering (SAXS and WAXS) to comprehend the origin of their unique orientational properties. The SAXS intensity, analysed at a fixed scattering vector modulus Q as a function of polar angle, allowed us to derive the Maier-Saupe orientation parameter m. The strong dependence of m on hydrogel composition and temperature demonstrated that the preferred orientation is controlled by the quadruplex surface charge and flexibility. Indeed, a possible correlation between the orientation parameter m and the quadruplex-to-quadruplex lateral interactions was explored. Results confirmed that the balance between attractive and repulsive interactions plays a main role in the orientational anisotropy: quadruplex clusters lose their orientational properties when attractive interactions decrease. The key role of the number of negative charges per unit length of the G-quadruplex filaments was confirmed by Atomic Force Microscopy (AFM) observations. Indeed, directionality histograms showed that in the presence of a large amount of Gua, G-quadruplexes follow preferential orientations other than those related to the strong interactions with the K+ pattern on the mica surface. The fact that lateral quadruplex-to-quadruplex interactions, even in the presence of external (opposing) forces, can tune the hydrogel alignment in a given preferred direction provides novel possibilities for scaffold/3D printing applications.

Metallo-responsive self-assembly of lipophilic guanines in hydrocarbon solvents: a systematic SAXS structural characterization

Lipophilic guanines (LipoGs) in aprotic solvents undergo different self-assembly processes based on different H-bonded motifs. Cylindrical nanotubes made by π-π stacked guanine tetramers (G-quadruplexes) and flat, tape-like aggregates (G-ribbons) have been observed depending on the presence of alkali metal ions. To obtain information on the structural properties and stability of these LipoG aggregates, Small-Angle X-ray Scattering (SAXS) experiments have been performed in dodecane, both in the presence and in the absence of potassium ions. As a result, the occurrence of the two different metallo-responsive architectures (nanoribbons or columnar nanotubes) was confirmed and we reported here for the first time a systematic study on the dependence of the aggregate properties on composition, temperature and molecular unit structure. Even if dodecane was selected to favour LipoG solubility, a strong tendency to self-organize into ordered lyotropic phases was indeed detected.

Temperature and pressure limits of guanosine monophosphate self-assemblies

Guanosine monophosphate, among the nucleotides, has the unique property to self-associate and form nanoscale cylinders consisting of hydrogen-bonded G-quartet disks, which are stacked on top of one another. Such self-assemblies describe not only the basic structural motif of G-quadruplexes formed by, e.g., telomeric DNA sequences, but are also interesting targets for supramolecular chemistry and nanotechnology. The G-quartet stacks serve as an excellent model to understand the fundamentals of their molecular self-association and to unveil their application spectrum. However, the thermodynamic stability of such self-assemblies over an extended temperature and pressure range is largely unexplored. Here, we report a combined FTIR and NMR study on the temperature and pressure stability of G-quartet stacks formed by disodium guanosine 5′-monophosphate (Na₂5′-GMP). We found that under abyssal conditions, where temperatures as low as 5 °C and pressures up to 1 kbar are reached, the self-association of Na₂5′-GMP is most favoured. Beyond those conditions, the G-quartet stacks dissociate laterally into monomer stacks without significantly changing the longitudinal dimension. Among the tested alkali cations, K⁺ is the most efficient one to elevate the temperature as well as the pressure limits of GMP self-assembly.

Cooperative polymerization of one-patch colloids

We numerically investigate cooperative polymerization in an off-lattice model based on a pairwise additive potential using particles with a single attractive patch that covers 30% of the colloid surface. Upon cooling, these particles self-assemble into small clusters which, below a density-dependent temperature, spontaneously reorganize into long straight tubes. We evaluate the partition functions of clusters of all sizes to provide an accurate description of the chemical reaction constants governing this process. Our calculations show that, for intermediate sizes, the partition functions retain contributions from two different structures, differing in both energy and entropy. We illustrate the microscopic mechanism behind the complex polymerization process in this system and provide a detailed evaluation of its thermodynamics.

Small-angle X-ray scattering study of self-assembling lipophilic guanines in organic solvents: G-quadruplex formation and cation effects in cyclohexane

Lipophilic guanilic derivatives (lipoGs) dissolved in organic solvents can undergo different self-assembly pathways based on different H-bonded motifs, e.g., the cyclic discrete G-quartet, which forms in the presence of alkali-metal ions, and the "infinite" tape-like G-ribbon observed in the absence of ions. Using in-solution small-angle X-ray scattering, we analyzed a series of lipoGs dissolved in cyclohexane in the presence of different salts. The formation of G-quartet based supramolecular aggregates has been confirmed, evidencing the coexistence equilibrium of octamers and noncovalent molecular nanowires (the so-called G-quadruplexes). By global fitting the scattering data, the concentration of the two kinds of particles as well as the nanowire length have been derived as a function of temperature for the different compounds and salts. The thermodynamic parameters show that the self-assembly aggregation process is enthalpy driven, while the observed enthalpy-entropy compensation suggests that similar stacking interactions control the self-assembly of the different compounds. However, the strength of the stacking interactions, and then the nanowire stability, depends on the nature of templating cations and on their capacity to fill the central cavity of quadruplexes, with the order Sr(+) < Na(+) ≲ K(+).

Guanosine quadruplexes in solution: a small-angle x-ray scattering analysis of temperature effects on self-assembling of deoxyguanosine monophosphate

We investigated quadruplex formation in aqueous solutions of 2′-deoxyriboguanosine 5′-monophosphate, d(pG), which takes place in the absence of the covalent axial backbone. A series of in-solution small angle X-ray scattering experiments on d(pG) have been performed as a function of temperature in the absence of excess salt, at a concentration just above the critical one at which self-assembling occurs. A global fit approach has been used to derive composition and size distribution of the scattering particles as a function of temperature. The obtained results give thermodynamical justification for the observed phase-behavior, indicating that octamer formation is essential for quadruplex elongation. Our investigation shows that d(pG) quadruplexes are very suitable to assess the potential of G-quadruplex formation and to study the self-assembling thermodynamics.

Supramolecular structure and polymorphism of alkali metal salts of guanosine 5'-monophosphate: SEM and NMR study

Scanning electron microscopy images of the Na(+), K(+), and Rb(+) salts of guanosine 5'-monophosphate (5'-GMP) in the presence of the corresponding metal chloride have shown the formation of exceptionally large molecular aggregates. These are much larger than those previously reported in solution. Each cation system produced a solid with a different morphology. The SEM samples were prepared from concentrated aqueous (D(2)O) solutions containing various amounts of 5'-GMP and metal chloride, and they approached the limit of solubility for the 5'-GMP under these conditions. Straight or slightly curved "free standing" rods composed of bundles of parallel stacks of G-quartets were formed from solutions of 0.85-1.0 M Na(2)(5'-GMP) containing 0.25-0.50 M NaCl. The rods had varying lengths of 6000-40 000 nm and an average diameter of 2000 nm. Calculations estimate this diameter to correspond to approximately 650 parallel stacks of G-quartets. Alignment of the individual G-quartet stacks into bundles and rods occurred as a result of phosphate charge neutralization by the high concentration of Na(+) ions. The SEM image of the K(+) system showed the presence of two types of morphologies, a rodlike lattice formation interpreted to be formed of stacked G-quartets, and irregular twisting fibers of varying diameter. In conjunction with the (1)H NMR data, the latter are proposed to be composed of continuous helices of doubly hydrogen-bonded guanines having the same H-bonding motif as the planar G-quartets. The Rb(+) system had some similarities to both the Na(+) system and the K(+) system. (1)H NMR spectra were different for each cation system, corresponding to the differences observed by SEM imaging of the solids. Polymorphism has been observed in telomeric sequences but has not been extensively explored in 5'-GMP.

Small angle X-ray scattering analysis of deoxyguanosine 5'-monophosphate self-assembing in solution: nucleation and growth of G-quadruplexes

To solve details of the self-assembling process of guanosine in diluted aqueous solution and to derive a thermodynamical model for quadruplex formation, the structural behavior of deoxyguanosine 5'-monophosphate has been analyzed by in-solution small angle X-ray scattering. The experiments have been performed as a function of guanosine concentration and at fixed guanosine concentration but in the presence of varying amounts of KCl. As a result, the self-assembling process, in terms of both aggregate particle fractions and aggregate length, has been observed to be strongly dependent on composition and largely affected by excess potassium ions in the solution. In particular, the different aggregate forms have been resolved and their concentration derived as a function of sample composition. In accordance with a hierarchical aggregation process, a nucleation and elongation mechanism has been used to derive the thermodynamical parameters for self-assembling. The results show that the annealing and fragmentation steps play an important role in the aggregation process.

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

The 8-oxoguanosine derivative 1 and the 8-oxoinosine derivative 2 b, with appropriate substituents on their ribose moieties, form hexagonal lyotropic mesophases in hydrocarbon solvents. Small-angle X-ray scattering analysis of a film of 1 and of the mesophase of 2 b, and NMR and CD spectra of isotropic solutions of 2 b, indicate that in both cases the supramolecular structures adopted are continuous helices formed by a hydrogen-bond network between the heterocyclic bases. Notably, while derivative 2 b, which bears large substituents on its ribose moiety, undergoes self-assembly and mesophase formation, oxoinosine 2 a, with only decanoyl groups on its ribose moiety, does not. This may be ascribed to the reduced amphiphilic properties of the latter and the absence of aromatic groups.