Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study

Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca²⁺, Sr²⁺ and Ba²⁺). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca²⁺ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.

Water-Mediated Interactions Enhance Alkaline Earth Cation Chelation in Neighboring Cavities of a Cytosine Quartet in the DNA Quadruplex

Larger Coulombic repulsion between divalent cations compared to the monovalent counterparts dictates the cation-cation distance in the central ion channel of quadruplexes. In this work, density functional theory and a continuum solvation model were employed to study bond energies of alkaline earth cations in adjacent cavities of the central ion channel. Four crystallized tetramolecular quadruplexes with various geometric constraints and structural motifs available in the Protein Data Bank were examined in order to understand how the cation binding affinities could be increased in aqueous solution. A cytosine quartet sandwiched between guanine quartets has a larger bond energy of the second alkaline earth cation in comparison with guanine and uracil quartets. Four highly conserved hydrogen-bonded water molecules in the center of the cytosine quartet are responsible for a higher electrostatic interaction with the cations in comparison with guanines' carbonyl groups. The reported findings are valuable for the design of synthetic quadruplexes templated with divalent cations for optoelectronic applications.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

A new approach to construct and modulate G-quadruplex by cationic surfactant

HYPOTHESIS

G-quadruplex structure has raised increasing attention in supramolecular chemistry as an effective template for ordered functional materials. Thus, it is of practical significance to advance our understanding regarding G-quadruplex structures. Typically, G-quadruplex structures are formed in the presence of suitable metal ions. New methods to construct such structures need to be explored.

EXPERIMENTS

The supramolecular assembly between CTAB and a guanosine derivative at different molar ratios was systematically studied, including assembly mechanisms, morphology, and macroscopic properties. Cationic surfactants with different alkyl chains were studied as control experiments.

FINDINGS

A novel strategy to construct G-quadruplex with the promotion of the cationic surfactant CTAB is presented in this work. The structure-property relationships of G-quadruplex gels are characterized by rheology and shrinkage ratio experiments. MacKintosh's theory was used to rationalize the relationship between gel elasticity and water content. The transition of G-quadruplex structures could be easily enabled by modulating CTAB concentration, which promotes the phase transition from gel/sol biphase to homogeneous sol phase. This work will provide a new viewpoint for the construction and modulation of G-quadruplex structures.

Metal ions confinement defines the architecture of G-quartet, G-quadruplex fibrils and their assembly into nematic tactoids

G-quadruplex, assembled from a square array of guanine (G) molecules, is an important structure with crucial biological roles in vivo but also a versatile template for ordered functional materials. Although the understanding of G-quadruplex structures is the focus of numerous studies, little is known regarding the control of G-quartet stacking modes and the spontaneous orientation of G-quadruplex fibrils. Here, the effects of different metal ions and their concentrations on stacking modes of G-quartets are elucidated. Monovalent cations (typically K+) facilitate the formation of G-quadruplex hydrogels with both heteropolar and homopolar stacking modes, showing weak mechanical strength. In contrast, divalent metal ions (Ca2+, Sr2+, and Ba2+) at given concentrations can control G-quartet stacking modes and increase the mechanical rigidity of the resulting hydrogels through ionic bridge effects between divalent ions and borate. We show that for Ca2+ and Ba2+ at suitable concentrations, the assembly of G-quadruplexes results in the establishment of a mesoscopic chirality of the fibrils with a regular left-handed twist. Finally, we report the discovery of nematic tactoids self-assembled from G-quadruplex fibrils characterized by homeotropic fibril alignment with respect to the interface. We use the Frank-Oseen elastic energy and the Rapini-Papoular anisotropic surface energy to rationalize two different configurations of the tactoids. These results deepen our understanding of G-quadruplex structures and G-quadruplex fibrils, paving the way for their use in self-assembly and biomaterials.

Polarity inversion sensitized G-quadruplex metal sensors with K+ tolerance

Due to the high abundance of K⁺ in environments and K⁺-induced high stability of G-quadruplex (G4), developing a selective G4-based fluorescent sensor for other metal ions with K⁺ tolerance is a great challenge. Herein, we found that even in the presence of 15000-fold excess of K⁺, Ba²⁺ exhibits a highly specific binding with a human telomeric G4 (htG4) in comparison with other G4-binding metal ions such as Pb²⁺ and Sr²⁺. This specific binding event can be recognized by a natural fluorophore of hypericin with a lighting-up fluorescence response. Interestingly, inverting the polarity of the most 3' G in htG4 can sensitize the Ba²⁺ response with the retaining Ba²⁺ specificity and K⁺ tolerance. This polarity inversion of htG4 causes a G4 conformation change in K⁺ and the polarity-inverted htG4 tends to favorably dimerize in response to the Ba²⁺ specific binding. To our knowledge, this is the first report that polarity inversion of G4 can be applied to construct a selective metal sensor with K⁺ tolerance. Our findings will open a new way to conveniently regulate the G4 conformation and stability by polarity inversion towards developing high-performance sensors.

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.

Effects of pH on the Shape of Alginate Particles and Its Release Behavior

A vast majority of alginate particles exist as spheres in most practical uses, and both the particle shape and size are the key factors dominating the applications and performance of alginate gels. Therefore, it becomes an issue of great interest to investigate the aspheric alginate particles. As the first step, various shaped alginate particles were formed due to various pH values in gelation solutions. It was experimentally demonstrated that a low pH brought about an oblate shape, and particularly lower concentrations of both alginate and divalent cations resulted in a flattened oblate shape. Ba2+acting as a cross-linker had a less impact on the particle shape than Ca2+due to a higher affinity in alginate intermolecular cross-linking. With a larger surface area, an oblate particle offered a higher release rate than a spheric one.

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

We report the metallo-responsive high fidelity switching between hexadecameric and octameric supramolecular G-quadruplexes triggered by a change in the metal cation promoter from potassium to strontium, respectively.