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

Nanoscale Interaction of Endonuclease APE1 with DNA

Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA-APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed.

Machine-Learning-Driven G-Quartet-Based Circularly Polarized Luminescence Materials

Circularly polarized luminescence (CPL) materials have garnered significant interest due to their potential applications in chiral functional devices. Synthesizing CPL materials with a high dissymmetry factor (glum ) remains a significant challenge. Inspired by efficient machine learning (ML) applications in scientific research, this work demonstrates ML-based techniques for the first time to guide the synthesis of G-quartet-based CPL gels with high glum values and multiple chiral regulation strategies. Employing an "experiment-prediction-verification" approach, this work devises a ML classification and regression model for the solvothermal synthesis of G-quartet gels in deep eutectic solvents. This process illustrates the relationship between various synthesis parameters and the glum value. The decision tree algorithm demonstrates superior performance across six ML models, with model accuracy and determination coefficients amounting to 0.97 and 0.96, respectively. The screened CPL gels exhibiting a glum value up to 0.15 are obtained through combined ML guidance and experimental verification, among the highest ones reported till now for biomolecule-based CPL systems. These findings indicate that ML can streamline the rational design of chiral nanomaterials, thereby expediting their further development.

Synthesis and Structural Studies of Nucleobase Functionalized Hydrogels for Controlled Release of Vitamins

The development of biomolecule-derived biocompatible scaffolds for drug delivery applications is an emerging research area. Herein, we have synthesized a series of nucleobase guanine (G) functionalized amino acid conjugates having different chain lengths to study their molecular self-assembly in the hydrogel state. The gelation properties have been induced by the correct choice of chain lengths of fatty acids present in nucleobase functionalized molecules. The effect of alkali metal cations, pH, and the concentration of nucleobase functionalized amino acid conjugates in the molecular self-assembly process has been explored. The presence of Hoogsteen hydrogen bonding interaction drives the formation of a G-quadruplex functionalized hydrogel. The DOSY nuclear magnetic resonance is also performed to evaluate the self-assembling behavior of the newly formed nucleobase functionalized hydrogel. The nanofibrillar morphology is responsible for the formation of a hydrogel, which has been confirmed by various microscopic experiments. The mechanical behaviors of the hydrogel were evaluated by rheological experiments. The in vitro biostability of the synthesized nucleobase amino acid conjugate is also investigated in the presence of hydrolytic enzymes proteinase K and chymotrypsin. Finally, the nucleobase functionalized hydrogel has been used as a drug delivery platform for the control and sustained pH-responsive release of vitamins B2 and B12. This synthesized nucleobase functionalized hydrogel also exhibits noncytotoxic behavior, which has been evaluated by their in vitro cell viability experiment using HEK 293 and MCF-7 cell lines.

Twisted Structures in Natural and Bioinspired Molecules: Self-Assembly and Propagation of Chirality Across Multiple Length Scales

Several biomolecules can form dynamic aggregates in water, whose nanometric structures often reflect the chirality of the monomers in unexpected ways. Their twisted organization can be further propagated to the mesoscale, in chiral liquid crystalline phases, and even to the macroscale, where chiral, layered architectures contribute to the chromatic and mechanical properties of various plant, insect, and animal tissues. At all scales, the resulting organization is determined by a subtle balance among chiral and nonchiral interactions, whose understanding and fine-tuning is fundamental also for applications. We present recent advances in the chiral self-assembly and mesoscale ordering of biological and bioinspired molecules in water, focusing on systems based on nucleic acids or related aromatic molecules, oligopeptides, and their hybrid stuctures. We highlight the common features and key mechanisms governing this wide range of phenomena, together with novel characterization approaches.

Analysis of G-Quadruplex-Forming Sequences in Drought Stress-Responsive Genes, and Synthesis Genes of Phenolic Compounds in Arabidopsis thaliana

Sequences of nucleic acids with the potential to form four-stranded G-quadruplex structures are intensively studied mainly in the context of human diseases, pathogens, or extremophile organisms; nonetheless, the knowledge about their occurrence and putative role in plants is still limited. This work is focused on G-quadruplex-forming sites in two gene sets of interest: drought stress-responsive genes, and genes related to the production/biosynthesis of phenolic compounds in the model plant organism Arabidopsis thaliana. In addition, 20 housekeeping genes were analyzed as well, where the constitutive gene expression was expected (with no need for precise regulation depending on internal or external factors). The results have shown that none of the tested gene sets differed significantly in the content of G-quadruplex-forming sites, however, the highest frequency of G-quadruplex-forming sites was found in the 5'-UTR regions of phenolic compounds' biosynthesis genes, which indicates the possibility of their regulation at the mRNA level. In addition, mainly within the introns and 1000 bp flanks downstream gene regions, G-quadruplex-forming sites were highly underrepresented. Finally, cluster analysis allowed us to observe similarities between particular genes in terms of their PQS characteristics. We believe that the original approach used in this study may become useful for further and more comprehensive bioinformatic studies in the field of G-quadruplex genomics.

Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses

Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.

Tracking Topological and Electronic Effects on the Folding and Stability of Guanine-Deficient RNA G-Quadruplexes, Engineered with a New Computational Tool for De Novo Quadruplex Folding

The initial aim of this work was to elucidate the mutual influence of different single-stranded segments (loops and caps) on the thermodynamic stability of RNA G-quadruplexes. To this end, we used a new NAB-GQ-builder software program, to construct dozens of two-tetrad G-quadruplex topologies, based on a designed library of sequences. Then, to probe the sequence–morphology–stability relationships of the designed topologies, we performed molecular dynamics simulations. Their results provide guidance for the design of G-quadruplexes with balanced structures, and in turn programmable physicochemical properties for applications as biomaterials. Moreover, by comparative examinations of the single-stranded segments of three oncogene promoter G-quadruplexes, we assess their druggability potential for future therapeutic strategies. Finally, on the basis of a thorough analysis at the quantum mechanical level of theory on a series of guanine assemblies, we demonstrate how a valence tautomerism, triggered by a coordination of cations, initiates the process of G-quadruplex folding, and we propose a sequential folding mechanism, otherwise dictated by the cancellation of the dipole moments on guanines.

Guanine Analogue-Based Assemblies: Construction and Luminescence Functions

As one of the natural nucleobases, guanine has attracted increasing interest in molecular self-assembly science because of its abundant interaction sites and high electron cloud density. Guanines, guanine derivatives, and guanine-rich DNA sequence are able to self-assemble into versatile aggregate structures by the means of hydrogen bonds and π-π, ion-dipole, solvophobic, and electrostatic interactions. Recent advances have shown that many guanine analogue-based (G-based) luminescent aggregates exhibit promising applications for fluorescent and chemiluminescent sensing and circularly polarized luminescence (CPL). This perspective summarizes the state-of-art strategies for constructing G-based assemblies and presents representative examples for luminescence functions. Finally, the inspirations are provided for exploiting unique G-based systems and luminescent G-based assemblies.

Feedback-controlled topological reconfiguration of molecular assemblies for programming supramolecular structures

In biology, nonequilibrium assembly is characterized by fuel-driven switching between associating and nonassociating states of biomolecules. This dynamic assembly model has been used routinely to describe the nonequilibrium processes in synthetic systems. Here, we present a G-quartet-based nonequilibrium system based on fuel-driven co-assembly of guanosine 5'-monophosphate disodium salt hydrate and urease. Addition of lanthanum(III) ions to the system caused macroscopic dynamic switching between precipitates and hydrogels. Interestingly, combined analyses of the nonequilibrium systems demonstrated that molecules could switch between two distinct associating states without undergoing a nonassociating state. This finding suggested a nonequilibrium assembly mechanism of topological reconfiguration of molecular assemblies. We detailed quantitatively the nonequilibrium assembly mechanism to precisely control the phase behaviors of the active materials; thus, we were able to use the materials for transient-gel-templated polymerization and transient circuit connection. This work presents a new nonequilibrium system with unusual phase behaviors, and the resultant active hydrogels hold promise in applications such as fluid confinements and transient electronics.

Guanine-Based G-Quadruplexes Templated by Various Cations toward Potential Use as Single-Ion Conductors

Inspired by the atomic-sized, shape-regulated features of G-quadruplexes comprising guanine motifs with a monovalent metal cation, the G-quadruplex-forming ability, and properties of a guanine-based π-conjugated Y2 molecule containing bithiophene and peripheral dodecyl chain units in the presence of various cation salts (Li⁺ , Na⁺ , K⁺ , and Mg²⁺ ) were exploited. A series of structural characterization revealed that Y2 yielded desirable G-quadruplexes with all the tested cations as a consequence of the combination of a hydrogen-bonded cyclic G-quartet, π-stacking, and cation-dipole interactions. The radius and nature of the coordinating cations crucially affected the structural characteristics of G-quadruplexes, leading to variations in the ion migration ability inside the cavity of the G-quadruplex (Li⁺ >Na⁺ >K⁺ >Mg²⁺ ), as characterized through theoretical and experimental investigations. These results not only improve the understanding of G-quadruplex self-assemblies based on guanine but also provide an impetus for their diverse potential applications, especially in the field of Li batteries.

Structural DNA nanotechnology: Immobile Holliday junctions to artificial robots

DNA nanotechnology marvels the scientific world with its capabilities to design, engineer, and demonstrate nanoscale shapes. This review is a condensed version walking the reader through the structural developments in the field over the past 40 years starting from the basic design rules of the double-stranded building block to the most recent advancements in self-assembled hierarchically achieved structures to date. It builds off from the fundamental motivation of building 3-dimensional (3D) lattice structures of tunable cavities going all the way up to artificial nanorobots fighting cancer. The review starts by covering the most important developments from the fundamental bottom-up approach of building structures, which is the 'tile' based approach covering 1D, 2D, and 3D building blocks, after which, the top-down approach using DNA origami and DNA bricks is also covered. Thereafter, DNA nanostructures assembled using not so commonly used (yet promising) techniques like i-motifs, quadruplexes, and kissing loops are covered. Highlights from the field of dynamic DNA nanostructures have been covered as well, walking the reader through the various approaches used within the field to achieve movement. The article finally concludes by giving the authors a view of what the future of the field might look like while suggesting in parallel new directions that fellow/future DNA nanotechnologists could think about.

Multistimuli-Responsive and Antifreeze Aggregation-Induced Emission-Active Gels Based on CuNCs

Multistimuli-responsive fluorescent gelsbased small molecular gelator by supramolecular assembly, possessing excellent dynamic and reversible characteristic, have caused much concern. In this article, aggregation-induced emission-active fluorescence gels (AIE-gels) with chirality were developed by combining Cu nanoclusters (CuNCs) and natural amino acids, l-tryptophan (l-Trp) or d-Tryptophan (d-Trp). In DMSO/H₂O mixed solvents, CuNCs can self-assemble to form intertwined fibersbased nanoparticles with numerous pores by introducing Zn²⁺. Fibers as second networks of heteronetwork structures are characterized with the participation of l-Trp or d-Trp for cross-linking to reinforce mechanical strength and chiral regulation of gel networks. Aggregation-induced emission enhancement (AIEE) of CuNCs endows the gels with excellent fluorescent properties by introducing solvents and gelation process. The fluorescent gels exhibit sufficient fluorescence intensity (FI) at -20 °C to -80 °C and possess sensitive responsibility including gel-sol transition and fluorescence behavior for stimuli of mechanical force, heating, pH, H₂O₂, and ethylene diamine tetraacetic acid (EDTA).

Stimuli-Responsive and Reversible Nanoassemblies of G-Triplexes

G-triplex (G3) structures formed with three consecutive G-tracts have recently been identified as a new emerging guanine-rich DNA fold. There could likely be a wide range of biological functions for G3s as occurring for G-quadruplex (G4) structures formed with four consecutive G-tracts. However, in comparison to the many reports on G4 nanoassemblies that organize monomers together in a controllable manner, G3-favored nanoassemblies have yet to be explored. In this work, we found that a natural alkaloid of sanguinarine can serve as a dynamic ligand glue to reversibly switch the dimeric nanoassemblies of the thrombin binding aptamer G3 (TBA-G3). The glue planarity was considered to be a crucial factor for realizing this switching. More importantly, external stimuli including pH, sulfite, O₂ and H₂ O₂ can be employed as common regulators to easily modulate the glue's adhesivity for constructing and destructing the G3 nanoassemblies as a result of the ligand converting between isoforms. However, this assembly behavior does not occur with the counterpart TBA-G4. Our work demonstrates that higher-order G3 nanoassemblies can be reversibly operated by manipulating ligand adhesivity. This provides an alternative understanding of the unique behavior of guanine-rich sequences and focuses attention on the G3 fold since the nanoassembly event investigated herein might occur in living cells.

How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes

The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺), and (post‐)transition metal (Zn²⁺, Cd²⁺, Hg²⁺, and Pb²⁺) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K⁺). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.

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.

G-Quadruplex in Gene Encoding Large Subunit of Plant RNA Polymerase II: A Billion-Year-Old Story

G-quadruplexes have long been perceived as rare and physiologically unimportant nucleic acid structures. However, several studies have revealed their importance in molecular processes, suggesting their possible role in replication and gene expression regulation. Pathways involving G-quadruplexes are intensively studied, especially in the context of human diseases, while their involvement in gene expression regulation in plants remains largely unexplored. Here, we conducted a bioinformatic study and performed a complex circular dichroism measurement to identify a stable G-quadruplex in the gene RPB1, coding for the RNA polymerase II large subunit. We found that this G-quadruplex-forming locus is highly evolutionarily conserved amongst plants sensu lato (Archaeplastida) that share a common ancestor more than one billion years old. Finally, we discussed a new hypothesis regarding G-quadruplexes interacting with UV light in plants to potentially form an additional layer of the regulatory network.

Frontiers in G-Quadruplex Therapeutics in Cancer: Selection of Small Molecules, Peptides and Aptamers

G-quadruplex, a unique secondary structure in nucleic acids found throughout human genome, elicited widespread interest in the field of therapeutic research. Being present in key regulatory regions of oncogenes, RNAs and telomere, G-quadruplex structure regulates transcription, translation, splicing etc. Changes in its structure and stability leads to differential expression of oncogenes causing cancer. Thus, targeting G-Quadruplex structures with small molecules/other biologics has shown elevated research interest. Covering previous reports, in this review we try to enlighten the facts on the structural diversity in G-quadruplex ligands aiming to provide newer insights to design first-in-class drugs for the next generation cancer treatment.

An intensive and glow-type chemiluminescence of luminol-embedded, guanosine-derived hydrogel

In this paper, an intensive and glow-type chemiluminescence (CL) hydrogel was prepared by simultaneous incorporation of chemiluminescence reagent (luminol) and catalytic cofactor (hemin) into the scaffold of guanosine-derived hydrogel. The self-assembled hydrogel consisted of K⁺ stabilized hemin/G-quartet structures, showing significant enzyme-like activity to H₂O₂-mediated oxidation of luminol. After adding H₂O₂ into the hydrogel, blue light visible to naked eyes would come into being and last for over 8 h. The lasting-time CL emission of hydrogel was achieved due to a mechanism of slow-diffusion-controlled heterogeneous catalysis. Moreover, this self-assembled hydrogel performed a good response to H₂O₂ and the CL emission images could be recorded by smartphone. The hydrogel could remain excellent lifetime stability for months and the stable, enhanced and glow-type CL emission could improve the reliability and precision of CL detection, which has a promising application in cold light source and H₂O₂ detection of real biological samples.

Self-assembled guanosine-hydrogels for drug-delivery application: Structural and mechanical characterization, methylene blue loading and controlled release

It is known that guanosine derivatives (G) self-assemble in water forming long, flexible, and interacting aggregates (the so-called G-quadruplexes): by modulating the quadruplex charges, e.g. simply using a mixture of guanosine 5'-monophosphate (GMP) and guanosine (Gua), multi-responsive, self-healing hydrogels can be obtained. In this paper, the potential application of G-hydrogels as drug delivery systems has been assessed. Hydrogels were prepared at different Gua:GMP molar ratios. The photosensitizer Methylene Blue and the pro-apoptotic protein cytochrome C were used as cargo molecules. Small angle x-ray scattering and atomic force microscopy experiments confirmed the presence of G-quadruplexes disposed in swollen matrices with different mesh-sizes. Rheology measurements showed that the Gua:GMP molar ratio leads to specific drug release mechanisms, as the gel strength is finely tuned by electrostatic repulsion and van der Waals attraction between G-quadruplexes. Noteworthy, the gel cohesion and the drug release were pH responsive. Swelling, self-healing and cell viability features were also investigated: the results qualify the Gua:GMP hydrogel as an excellent biomaterial that can entrap and deliver key biomolecules in a sustained and responsive release manner.

Enzyme-Regulated Healable Polymeric Hydrogels

The enzyme-regulated healable polymeric hydrogels are a kind of emerging soft material capable of repairing the structural defects and recovering the hydrogel properties, wherein their fabrication, self-healing, or degradation is mediated by enzymatic reactions. Despite achievements that have been made in controllable cross-linking and de-cross-linking of hydrogels by utilizing enzyme-catalyzed reactions in the past few years, this substrate-specific strategy for regulating healable polymeric hydrogels remains in its infancy, because both the intelligence and practicality of current man-made enzyme-regulated healable materials are far below the levels of living organisms. A systematic summary of current achievements and a reasonable prospect at this point can play positive roles for the future development in this field. This Outlook focuses on the emerging and rapidly developing research area of bioinspired enzyme-regulated self-healing polymeric hydrogel systems. The enzymatic fabrication and degradation of healable polymeric hydrogels, as well as the enzymatically regulated self-healing of polymeric hydrogels, are reviewed. The functions and applications of the enzyme-regulated healable polymeric hydrogels are discussed.

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.