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

K vs. Na Effects on the Self-Assembly of Guanosine 5'-Monophosphate: A Solution SAXS Structural Study+. NANOMATERIALS (BASEL, SWITZERLAND) 2020;10:E629. [PMID: 32231081 PMCID: PMC7221663 DOI: 10.3390/nano10040629]

The hierarchical process of guanosine (G) self-assembly, leading in aqueous solution and in the presence of metal cations to the formation of G-quadruplexes, represents an intriguing topic both for the biological correlation with telomerase activity and for the nano-technological applications, as demonstrated by the current measured in a quadruplex wire 100 nm long. Similar to G-rich DNA sequences and G-oligonucleotides, the guanosine 5'-monophosphate (GMP) self-aggregates in water to form quadruplexes. However, due to the absence of a covalent axial backbone, this system can be very useful to understand the chemical-physical conditions that govern the guanosine supramolecular aggregation. We have then investigated by in-solution Synchrotron Small Angle X-ray Scattering technique the role of different cations in promoting the quadruplex formation as a function of concentration and temperature. Results show how potassium, with its peculiar biological traits, favours the G-quadruplex elongation process in respect to other cations (Na + , but also NH 4 + and Li + ), determining the longest particles in solution. Moreover, the formation and the elongation of G-quadruplexes have been demonstrated to be controlled by both GMP concentration and excess cation content, even if they specifically contribute to these processes in different ways. The occurrence of condensed liquid crystalline phases was also detected, proving that excess cations play also unspecific effects on the effective charges on the G-quadruplex surface.

Playing supramolecular dominoes with light: building and breaking a photoreversible G-quadruplex made from guanosine, boric acid and an azobenzene

Addition of azobenzene-derivative 1 in its E configuration to an aqueous solution containing various guanosine borate esters induces a helical G-quartet based self-organization, stabilized by intercalation of the dye. The process is driven, in a domino fashion, by the initial host-guest interaction between the dye and a specific guanosine borate diester, whose structure can be thus assigned. This inclusion complex templates the formation of G-quartets. The quartets, in turn, pile up to form a supramolecular G-quadruplex structure, in which other G species present in solution are progressively included. The G-quadruplex can be reversibly broken and reformed by photoisomerization of the dye. This hierarchical and photosensitive self-assembly is unprecedented for simple guanosine derivatives.

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.

On the structural stability of guanosine-based supramolecular hydrogels

Supramolecular hydrogels formed from the self-assembly of low molecular weight derivatives are very attractive systems, because of their potential applications in nano- and bio-technology. In this paper, the stable and transparent hydrogels observed in binary mixtures of guanosine derivatives (G), namely guanosine 5'-monophosphate (GMP) and guanosine (Gua), dissolved in water (at volume fractions larger than 0.95), were investigated by microscopy techniques and Small Angle X-ray Scattering (SAXS). The results confirm the presence of G-quadruplexes, chiral cylindrical rods obtained by the regular stacking of self-assembled planar cyclic guanosine quartets. However, the addition of Gua determines the formation of very stable hydrogels able to trap large amounts of water (up to a volume fraction of 0.99) and characterised by an unusual anisotropic order. A modified lateral helix-to-helix interaction pattern, tuned by Gua, is suggested to be responsible for the supramolecular gelation and the stability of the hydrogels during swelling.

Thermodynamics of host-guest interactions between fullerenes and a buckycatcher

¹H NMR and isothermal titration calorimetry (ITC) experiments were employed to obtain reliable thermodynamic data for the formation of the 1:1 inclusion complexes of fullerenes C₆₀ and C₇₀ with the buckycatcher (C₆₀H₂₈). NMR measurements were done in toluene-d₈ and chlorobenzene-d₅ at 288, 298, and 308 K, while the ITC titrations were performed in toluene, chlorobenzene, o-dichlorobenzene, anisole, and 1,1,2,2-tetrachloroethane at temperatures from 278 to 323 K. The association constants, K_a, obtained with both techniques are in very good agreement. The thermodynamic data obtained by ITC indicate that generally the host–guest association is enthalpy-driven. Interestingly, the entropy contributions are, with rare exceptions, slightly stabilizing or close to zero. Neither ΔH nor ΔS is constant over the temperature range studied, and these thermodynamic functions exhibit classical enthalpy/entropy compensation. The ΔC_p values calculated from the temperature dependence of the calorimetric ΔH values are negative for the association of both fullerenes with the buckycatcher in toluene. The negative ΔC_p values are consistent with some desolvation of the host-cavity and the guest in the inclusion complexes, C₆₀@C₆₀H₂₈ and C₇₀@C₆₀H₂₈.

A lipophilic "fully-anti" dodecamer from a (5'S)-5',8-cyclo-2'-deoxyguanosine

The self-assembly of a lipophilic derivative of (5'S)-5',8-cyclo-2'-deoxyguanosine, a mutagenic product formed by hydroxyl radical attack against DNA, has been investigated. This derivative forms, with high fidelity, a dodecameric complex composed of three stacked G-quartets in the presence of strontium picrate. This is the first example of a fully-anti lipophilic G-quadruplex.

GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro-molecules in solution

Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.

Folding and structural polymorphism of G-quadruplex formed from a long telomeric sequence containing six GGG tracts

A long telomeric sequence preferentially forms a thermodynamically stable G-quadruplex at the 3′ end rather than at the 5′ end or at internal positions.