Metallo-responsive switching between hexadecameric and octameric supramolecular G-quadruplexes

Synthesis of microporous hydrogen-bonded supramolecular organic frameworks through guanosine self-assembly

Extending the structural hierarchy and complexity through small-molecular self-assembly is a powerful way to obtain large discrete, functional molecular architecture. A hydrogen-bonded supramolecular organic framework (H_SOF) with nanometer-size pores is constructed in a solid state with simple guanosine-monomer self-assembly. To extend the hierarchy of the G-quartet self-assembly to a higher order thanthatofthetraditionalG-quadruplex,H-bondacceptorsontheC-8 position of guanosine are introduced to establish inter-quadruplex linkage via H bonding to N(2)-H_B from the neighboring G-quartet. After screening different C-8 substitution groups and various synthesis conditions, H_SOF-G1a' is obtained by solvent evaporation under diluted condition. Single-crystal X-ray structure reveals that cubic repeating units formed by G₈ are the supermolecule secondary building block (SBU) with large pores (d=34A). To our knowledge, this is the first G-quartet self-assembly with an organized structure beyond cylindrical G-quadruplexes.

Elucidating Noncovalent Reaction Mechanisms: G-Quartet as an Intermediate in G-Quadruplex Assembly

In analogy to covalent reactions, the understanding of noncovalent association pathways is fundamental to influence and control any supramolecular process. Following an approach that is reminiscent of covalent methodologies, we study here, for the first time, the mechanism of G-quadruplex formation in organic solvents. Our results support a reaction pathway in which the cation shifts the equilibrium towards a G-quartet transient intermediate, which then acts as a template in the formation of the G-quadruplex product.

Construction of a cross-layer linked G-octamer via conformational control: a stable G-quadruplex in H-bond competitive solvents

Methanol soluble and stable guanosine octamers were successfully achieved via H-bond self-assembly. Through structural conformational design, we developed a new class of guanosine derivatives with modification on guanine (8-aryl) and ribose (2',3'-isopropylidene). This unique design led to the formation of the first discrete G8-octamer with its structure characterized by single crystal X-ray diffraction, MS and NMR spectroscopy. The G8-octamer showed unique cation recognition properties, including the formation of a stable Rb+ templated G-quadruplex. Based on this observation, further modification on the 8-aryl moiety was performed to incorporate a cross-layer H-bond or covalent linkage. Similar G-octamers were obtained in both cases with structures confirmed by single crystal X-ray diffraction. Furthermore, the covalently linked G-quadruplex exhibited excellent stability even in MeOH and DMSO, suggesting a promising future for this new H-bond self-assembly system in biological and material applications.

G-Quadruplex based hydrogels stabilized by a cationic polymer as an efficient adsorbent of picric acid

Hydrogels based on G-quadruplexes (G-hydrogels) were prepared using guanosine 5′-monophosphate disodium salt, GMP, with a hyperbranched poly(ethylenimine), PEI, containing abundant –NH₂ groups.

Tracking the formation of supramolecular G-quadruplexes via self-assembly enhanced emission

We report the synthesis and self-assembly of two lipophilic 2'-deoxyguanosine (G) derivatives whose fluorescence intensity is modulated by self-assembly into supramolecular G-quadruplexes (SGQs). Whereas both derivatives self-assemble isostructurally, one shows up to 100% emission enhancement while the other shows an initial enhancement, followed by 10% quenching. Thus, the rotational restrictions resulting from self-assembly are enough to induce significant changes in emission, but it is critical to consider the specific interactions between fluorophores since they will determine the ultimate emission signature. These findings could open the door to the development of luminescent supramolecular sensors and probes.

Probing the Limits of Supramolecular G-Quadruplexes Using Atomistic Molecular Dynamics Simulations

Guanosine and related derivatives self-assemble in the presence of cations like potassium into supramolecular G-quadruplexes (SGQs), where four guanine moieties form planar tetrads (T) that coaxially stack into columnar aggregates with broad size distributions. However, SGQs made from 8-aryl-2'-deoxyguanosine derivatives (8ArGs), form mostly octamers, or two-tetrad (2T)-SGQs, while some form dodecamers (3T-SGQs), or hexadecamers (4T-SGQs), and none reported to date form higher assemblies. A theoretical model that addresses the configurational space available for the multiple pathways available for 8ArGs to self-assemble into SGQs is used to frame a series of molecular dynamics simulations (MDS) with selected SGQs. Some key insights from this work include: (a) The predicted entropic costs are not significantly higher for SGQs with more subunits due to their hierarchical assembly pathways; (b) The multiple isomeric SGQs vary in the interfacial contacts between consecutive tetrads, due to their two distinct sides (head, h; tail, t), with the MDS supporting the predicted order of stability of hh > ht > tt for octamers. (c) Such order also applies to dodecamers and hexadecamers, but with context-dependent exceptions due to strong allosteric effects. (d) The main factor disfavoring the tt interface is the repulsive dipolar interactions between the O4' from ribose moieties on adjacent tetrads. (e) SGQs with 5 or more tetrads are disfavored because the attractive interactions are not large or strong enough to overcome the many repulsive forces resulting from the addition of further tetrads. We expect these findings provide some guidelines to enable the further development of SGQs into functional materials.

Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery

G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.

Co-existence of Distinct Supramolecular Assemblies in Solution and in the Solid State

The formation of distinct supramolecular assemblies, including a metastable species, is revealed for a lipophilic guanosine (G) derivative in solution and in the solid state. Structurally different G‐quartet‐based assemblies are formed in chloroform depending on the nature of the cation, anion and the salt concentration, as characterized by circular dichroism and time course diffusion‐ordered NMR spectroscopy data. Intriguingly, even the presence of potassium ions that stabilize G‐quartets in chloroform was insufficient to exclusively retain such assemblies in the solid state, leading to the formation of mixed quartet and ribbon‐like assemblies as revealed by fast magic‐angle spinning (MAS) NMR spectroscopy. Distinct N−H⋅⋅⋅N and N−H⋅⋅⋅O intermolecular hydrogen bonding interactions drive quartet and ribbon‐like self‐assembly resulting in markedly different 2D ¹H solid‐state NMR spectra, thus facilitating a direct identification of mixed assemblies. A dissolution NMR experiment confirmed that the quartet and ribbon interconversion is reversible–further demonstrating the changes that occur in the self‐assembly process of a lipophilic nucleoside upon a solid‐state to solution‐state transition and vice versa. A systematic study for complexation with different cations (K⁺, Sr²⁺) and anions (picrate, ethanoate and iodide) emphasizes that the existence of a stable solution or solid‐state structure may not reflect the stability of the same supramolecular entity in another phase.

Structural Studies of Supramolecular G-Quadruplexes Formed from 8-Aryl-2'-deoxyguanosine Derivatives

Self-assembly is a powerful tool for the construction of complex nanostructures. Despite advances in the field, the development of precise self-assembled structures remains a challenge. We have shown that, in the presence of suitably sized cations like K(+), 8-aryl-2'-deoxyguanosine (8ArG) derivatives self-assemble into sets of coaxially stacked planar tetramers, which we term supramolecular G-quadruplexes (SGQs). Previously, we reported that, when the 8-aryl group is a phenyl ring with a meta-carbonyl group, the resulting supramolecule is a hexadecamer, which is remarkably robust as illustrated by its isostructural assembly in both organic and aqueous environments. We report here a detailed three-dimensional structure of the SGQs formed by lipophilic, and hydrophilic, 8ArG derivatives with either 8-(meta-acetylphenyl), 8-(para-acetylphenyl), or 8-(meta-ethoxycarbonylphenyl) groups. The chirality and close contacts between the subunits impose different levels of steric and electrostatic constraints on opposite sides of the tetrads, which determine their preferred relative orientation. The balance between attractive noncovalent interactions juxtaposed with repulsive steric and electrostatic interactions explains the high cooperativity, fidelity, and stability of these SGQs. These structural studies, together with titration experiments and molecular dynamics simulations, provide insight into the mechanism of formation of these SGQs.

Quadruplex Turncoats: Cation-Dependent Folding and Stability of Quadruplex-DNA Double Switches

Quadruplex (G4) nucleic acids, a family of secondary structures formed by guanine-rich sequences, exhibit an important structural polymorphism. We demonstrate here that G-rich DNA sequences may function as a double switch based on different triggers, provided that their quadruplex structures and stability display a high dependence on cation nature and concentration. A first switch is based on a remarkable antiparallel-to-parallel conversion, taking place in a few seconds at room temperature by addition of low KCl amounts to a sodium-rich sample. The second switch involves the conversion of alternative antiparallel quadruplex structures binding only one cation, formed in the presence of sub-millimolar potassium or strontium concentrations, to parallel structures by increasing the cation concentration. Incidentally, extremely low K(+) or Sr(2+) concentrations (≤5 equiv) are sufficient to induce G4 formation in a buffer devoid of other G4-promoting cations, and we suggest that the alternative structures observed contain only two tetrads. Such DNA systems are biological relevant targets, can be used in nanotechnology applications, and are valuable methodological tools for understanding DNA quadruplex folding, notably at low cation concentrations. We demonstrate that this behavior is not restricted to a narrow set of sequences but can also be found for other G-quadruplex-forming motifs, arguing for widespread applications.

G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch

Nucleic acid based molecular device is a developing research field which attracts great interests in material for building machinelike nanodevices. G-quadruplex, as a new type of DNA secondary structures, can be harnessed to construct molecular device owing to its rich structural polymorphism. Herein, we developed a switching system based on G-quadruplexes and methylazacalix[6]pyridine (MACP6). The induced circular dichroism (CD) signal of MACP6 was used to monitor the switch controlled by temperature or pH value. Furthermore, the CD titration, Job-plot, variable temperature CD and ¹H-NMR experiments not only confirmed the binding mode between MACP6 and G-quadruplex, but also explained the difference switching effect of MACP6 and various G-quadruplexes. The established strategy has the potential to be used as the chiral probe for specific G-quadruplex recognition.

Tuning supramolecular G-quadruplexes with mono- and divalent cations

Supramolecular G-quadruplexes (SGQs) are formed via the cation promoted self-assembly of guanine derivatives into stacks of planar hydrogen-bonded tetramers. Here, we present results on the formation of SGQs made from the 8-(m-acetylphenyl)-2'-deoxyguanosine (mAGi) derivative in the presence of various mono- and divalent cations. NMR and HR ESI-MS data indicate that varying the cation can efficiently tune the molecularity, the fidelity and stability (thermal and kinetic) of the resulting SGQs. The results show that, parallel to the previously reported potassium-templated hexadecamer (mAGi₁₆·3K⁺), Na⁺, Rb⁺ and [Formula: see text] also promote the formation of similar supramolecules with high fidelity and molecularity. In contrast, the divalent cations Pb²⁺, Sr²⁺ and Ba²⁺ template the formation of octamers (mAGi₈), with the latter two inducing higher thermal stabilities. Molecular dynamics simulations for the hexadecamers containing monovalent cations enabled critical insights that help explain the experimental observations.

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.

Guanosine and isoguanosine derivatives for supramolecular devices

Guanosine (G) and isoguanosine (isoG) derivatives can self-assemble, yielding supramolecules that have found broad applications in diverse fields.

A photoresponsive supramolecular G-quadruplex

Photoirradiation of a hexadecameric supramolecular G-quadruplex leads to a diastereoselective [2 + 2] cyclodimerization of half of its constituent subunits, which in turn shifts the equilibrium toward the formation of a precise heteromeric octamer.