Search Results (479)

Mono- and bis-guanyl hydrazone-functionalized tricyclic compounds were here designed and investigated as putative G-quadruplex ligands in the context of anticancer drug development. The G-quadruplex on Controlled Pore Glass (G4-CPG) assay, a fast and easy screening method based on affinity chromatography for identifying potential G-quadruplex binders, together with biophysical techniques such as circular dichroism and fluorescence spectroscopy, demonstrated a higher selectivity of mono- with respect to disubstituted derivatives in recognizing G-quadruplexes from telomeric and oncogenic DNA regions vs. duplexes. Among the mono-substituted compounds, higher G-quadruplex selectivity was found for those containing the pyrido [3,4-b]indole and dibenzofuran scaffolds compared to the 9H-fluorene, 9H-carbazole, and dibenzothiophene ones. Molecular docking studies suggested that the investigated ligands bound the hybrid telomeric G-quadruplex model by adopting a coplanar arrangement of the core and guanyl hydrazone moieties, both stacked on the 5′-G-quartet, while in the interaction with the parallel oncogenic G-quadruplex model the guanyl hydrazone moieties pointed towards the grooves/loops. Finally, biological assays highlighted the higher potential of mono-guanyl hydrazone-derivatized tricyclic compounds as selective anticancer agents, showing higher anticancer activity and selectivity of action than the bis-guanyl hydrazone derivatives. Full article

Piperine, the principal alkaloid of Piper nigrum, has gained attention as a multifunctional dietary compound with broad effects on epigenetic and transcriptional regulation in cancer and chronic diseases. Evidence shows that piperine modulates DNA methylation (↓ DNMT3B), histone acetylation (↓ HDAC activity), and microRNA networks (↑ miR-29c, ↓ miR-383), thereby reshaping key oncogenic and tumor-suppressive pathways. Beyond canonical epigenetic control, it can also stabilize G-quadruplex structures in promoters such as c-MYC, adding an architecture-based mechanism of transcriptional repression. Its dual redox behavior—antioxidant at low doses and pro-oxidant at higher doses—confers context-dependent selectivity, enabling oxidative stress–mediated apoptosis in tumor cells. Compared with other nutriepigenetic agents (curcumin, resveratrol, EGCG), piperine stands out for its multi-target profile and preliminary evidence of activity against cancer stem cell–like phenotypes. Nonetheless, limited solubility, rapid metabolism, and scarce in vivo validation constrain clinical translation. Future efforts should focus on advanced formulations, multi-omics approaches, and cancer stem cell models to better define its therapeutic potential and safety. Full article

Non-canonical nucleic acid structures such as G-quadruplexes (G4s), i-motifs, triplexes, junctions, and structured RNA domains offer coordination environments that differ fundamentally from those of canonical duplex DNA. This review is deliberately G4-centred, because DNA G4s currently provide the most mature mechanistic and biological evidence for noble-metal recognition, while i-motifs, quadruplex–duplex hybrids, junctional structures, R-loops, Z-DNA/Z-RNA, and structured RNA remain emerging or less extensively validated target classes. The discussion addresses how platinum, gold, palladium, and silver complexes recognize these architectures through combinations of coordination chemistry, pi-stacking, electrostatics, scaffold-dependent shape complementarity, and metal-mediated base pairing. A further distinction is made between direct structural recognition, cellular target engagement, and downstream phenotypic responses, emphasizing where causality has been experimentally demonstrated and where it remains inferential. Particular emphasis is placed on G-quadruplexes in telomeric, promoter, and mitochondrial contexts, while i-motifs, junctional DNA, hybrid DNA/RNA structures, and structured RNA are treated as expanding but less mature areas of investigation. The review also critically addresses selectivity, resistance, delivery, and translational challenges, highlighting how the concept of functional architectures can help unify structural chemistry with pathway-level biology in the design of next-generation metallodrugs. Full article

G-quadruplex (DG4) is folded in guanine-rich DNA sequences and regulates DNA replication and transcription. Although bioinformatics analyses have predicted the presence of DG4 in maize, its biological functions remain largely unexplored. In this study, we treated maize seedlings with 0, 100, 200, and 300 μM TMPyP4, a DG4-stabilizing ligand, and observed that TMPyP4 inhibits radicle growth by increasing reactive oxygen species (ROS) levels and inducing DNA fragmentation in radicle cells. Transcriptomic RNA-seq revealed that TMPyP4 modulated the expression of 1614 genes in maize radicle cells, which were predominantly associated with redox reactions, membrane components, and secondary metabolic pathways. BG4-ChIP-seq analysis demonstrated that DG4 structures are evenly distributed across the ten chromosomes of the maize genome, occupying 22,449 loci and showing significant enrichment for specific DG4-binding motifs. Integrative analysis of RNA-seq data and BG4-ChIP-seq identified 944 differentially expressed genes, which were significantly enriched in pathways related to redox reactions and secondary metabolism. Collectively, these findings suggest that DG4-stabilizing ligands regulate maize radicle growth by modulating ROS homeostasis, providing critical insights into the functional roles of DG4s in maize. Full article

G-quadruplexes are guanine-rich DNA or RNA structures comprising two or more stacked guanine tetrads (G-quartet) with nucleobases in the loops linking the G-quartets. The thermal stability of the thrombin-binding aptamer G2 d(G₂T₂G₂TGTG₂T₂G₂) G-quadruplex was quantified using m-values in aqueous glycine betaine (GB), proline, TMAO, and urea solutions using UV-absorbance spectroscopy. The thermal stability of the G2 variants was also explored with nucleobase substitutions in the TGT loop (TAT, TCT, TTT, UGU, and UUU), in the T₂ loops (T₄, U₂), or in both loops (UGU and U₂, UUU and U₂). GB and TMAO strongly stabilized G2 and its variants. Urea weakly destabilized G2 and its variants, while proline acted as a weak stabilizer or destabilizer depending on G2 variant nucleobase sequence. Both the unfolding enthalpy and entropy were positively correlated with cosolute molality for all cosolute and G-quadruplex combinations. Analysis of the change in solvent-accessible surface area (ΔASA) after unfolding G2 suggested the stability of G2 and its variants in aqueous cosolute solutions was driven by favorable interaction of cosolutes with G-quartet ΔASA and net-favorable or unfavorable interactions with the loop ΔASA. Our results reinforce a general mechanism of folded DNA and RNA stability modulation in cosolute solutions. Full article

G-quadruplexes (G4s) are non-canonical nucleic acid secondary structures that help maintain genomic stability and regulate gene transcription. Although the genome contains a vast number of putative G4-forming sequences (PQSs, sequences with intrinsic in vitro G4-forming potential), only a small fraction fold stably into G4 structures within the complex chromatin environment of living cells. Existing deep learning approaches improve predictive accuracy by incorporating cell line–specific epigenetic data; however, their heavy reliance on costly, large-scale sequencing assays (e.g., ChIP-seq) limits broader application to clinical samples and newly profiled cell lines. To address this challenge, we propose iDualG4, an interpretable dual-channel deep learning framework that uses DNA sequence as the only input at inference time. By leveraging a pretrained Enformer module, iDualG4 infers epigenomic proxy features directly from DNA sequence and integrates them with local sequence features, thereby replacing the need for newly measured cell-specific epigenomic assays during prediction. Evaluations across multiple cell lines, including K562, demonstrate that iDualG4 significantly outperforms existing methods, particularly in handling imbalanced data (achieving an AUPR of 0.981 on K562). Interpretability analysis based on DeepSHAP indicates that iDualG4 provides an in vivo G4 prediction tool combining high precision and interpretability without the need for additional experimental sequencing data, and offers a novel computational framework for elucidating how sequence and the epigenetic environment jointly determine genomic G4 formation. Full article

Mercury ions (Hg²⁺), a heavy metal contaminant of strong biotoxicity, pose a serious threat to ecosystems and human health in aquatic environments. Developing highly sensitive and specific detection methods is therefore of great importance. This study presents a novel label-free fluorescent biosensor for Hg²⁺ by ingeniously coupling target-induced aptamer switching with rolling circle amplification (RCA). Upon Hg²⁺ binding, the conformational change releases a sequestered primer to initiate RCA, generating G-quadruplex-rich DNA products that produce a strong “turn-on” signal with N-methylmesoporphyrin IX (NMM). Under optimized conditions, the assay exhibits excellent linearity from 10 to 1000 nM with a detection limit of 3.2 nM, along with high selectivity over competing metal ions. Validation using spiked environmental water samples yielded accurate and reproducible recoveries in the range of 93.8% to 106.0%. With its operational simplicity, high sensitivity, and robust performance in complex matrices, this label-free strategy offers a reliable and promising platform for detecting Hg²⁺ in environmental waters. Full article

G-quadruplexes (G4s) are noncanonical nucleic acid structures involved in gene regulation and genome stability. Among them, the telomeric repeat-containing RNA (TERRA) forms biologically relevant RNA G4s (rG4s) that participate in telomere maintenance and genome stability. Although many ligands targeting DNA G4s have been reported, the recognition and modulation of RNA G4 topologies remain less explored. In this work, we investigated the interaction between TERRA and the spermine-functionalized Zn(II) porphyrin, ZnTCPPSpm4, using UV–vis absorption, fluorescence, resonance light scattering (RLS), and circular dichroism (CD) spectroscopy. In K⁺, where TERRA adopts a parallel G4 conformation, ZnTCPPSpm4 binds through a stepwise mechanism involving external end-stacking, forming discrete supramolecular complexes without altering the native topology. In contrast, under Na⁺ conditions, ZnTCPPSpm4 induces a gradual conformational rearrangement of TERRA from the antiparallel to a parallel-like G4 topology. A CD melting study showed that ZnTCPPSpm4 stabilizes the parallel RNA G4, while slightly destabilizing the antiparallel topology. Overall, our results demonstrate that ZnTCPPSpm4 is not a simple G4 binder, but a topology-selective ligand capable of remodeling TERRA G4 structures, highlighting the potential of metalloporphyrins as RNA G4-targeting scaffolds. Full article

Background: Guanine-rich DNA regions can fold into G-quadruplex (G4) structures, which are prevalent in telomeres and oncogene promoters, making them attractive targets for anticancer therapeutics. Small molecules capable of selectively stabilizing G4 DNA can disrupt telomerase activity and oncogene expression, offering a promising strategy for cancer intervention. Methods: A rationally designed series of DPPZ–anhydride-conjugated ligands (1 and 2) and their corresponding quaternized derivatives (1-q and 2-q) were synthesized to investigate the combined effects of π-extension, bromine substitution, and cationic modification on DNA recognition. The synthetic strategy relied on the incorporation of a highly planar DPPZ–anhydride scaffold to enhance π-surface area, followed by selective quaternization to introduce permanent positive charge and reinforce electrostatic interactions with the DNA backbone. All compounds were fully characterized by NMR and spectroscopic methods. The DNA-binding properties of the ligands were systematically evaluated toward duplex (ds-DNA) and G-quadruplex (G4-DNA) structures using UV–Vis absorption titration, fluorescence intercalator displacement (FID) assays, and competitive dialysis experiments. Quaternization markedly enhanced intrinsic binding constants and significantly reduced DC₅₀ values, particularly for G4-DNA. While bromine substitution increased overall binding affinity, it did not substantially improve topology selectivity. Among the series, compound 1-q exhibited the most favorable balance between affinity and G4 selectivity. Results: The interaction of the compounds with BSA was quantified using Stern–Volmer quenching constants, which demonstrated a clear trend of enhanced quenching efficiency upon modification. The binding strength followed a descending order of 1-q > 2-q > 1 > 2, highlighting the superior performance of the first series over the second. These findings indicate that the structural features of 1-q facilitate a more robust interaction within the hydrophobic pockets of the protein. Conclusions: Overall, the results demonstrate that strategic π-conjugation combined with electrostatic reinforcement provides an effective approach for the development of topology-selective DNA-binding ligands. Full article

The structural characterization of GG-rich DNA sequences in presence of metal ions provides essential insight into quadruplex stability and ion-dependent conformational specifics. We report the crystal structure of the GG-quadruplex formed by the sequence GGGGTTTTGGGG in the presence of Zn²⁺, K⁺, and Na⁺. It was deposited in the RCSB Protein Data Bank under the accession code 9FTA. The structure was determined by single-crystal X-ray diffraction at a resolution of 2.49 Å in the space group P2₁2₁2₁. It reveals a parallel-stranded, two-G-tetrad stabilized by K⁺ ions within the central channel, while Na⁺ and Zn²⁺ occupy peripheral and groove-associated sites. Zn²⁺ ions are engaged in noncanonical coordination interactions with phosphate oxygens and structured water molecules, contributing to lattice stabilization and subtle adjustments in groove dimensions. The T4 loop forms a compact, ordered motif that contributes to crystal packing rather than intramolecular G4 stabilization. The presence of mixed cations produces a sole lattice architecture mediated by ions that provides structural insight into how bivalent and monovalent metals mutually modulate G-quadruplex topology. These results suggest a basis for understanding the specific ion effects on G4 structures and may direct the design of metal open DNA architectures. Full article

The leishmaniases are a group of neglected tropical diseases caused by kinetoplastid protozoa of the genus Leishmania, transmitted by phlebotomine sandflies. In the absence of a human vaccine, current chemotherapeutic options remain suboptimal due to limited target selectivity, high cost, restricted availability in endemic low-resource regions, and escalating parasite resistance. This review highlights recent advances in rational drug design directed at the kinetoplast—a distinctive mitochondrial organelle critical for parasite viability. Different targets (e.g., kDNA, G-quadruplex, topoisomerases) and innovative approaches employing mitochondrion-targeted small molecules are discussed, as well as ligand-functionalized nanoparticle delivery systems that can transport bioactive agents to the parasite’s mitochondrial microenvironment. These strategies highlight the kinetoplast’s strong translational relevance as a selective antileishmanial target. By exploiting its unique molecular machinery, these strategies may offer improved parasite selectivity, although potential mitochondrial liabilities in host cells must be carefully evaluated. Full article

Ochratoxin A (OTA) is a highly toxic mycotoxin commonly detected in food and agricultural products, requiring sensitive analytical methods for reliable monitoring. Herein, we report an ultrasensitive turn-on electrochemical aptasensor for OTA detection based on a target-induced displacement of an aptamer–complementary DNA (cDNA) duplex assembled on an electrochemically reduced graphene oxide (ERGO)-modified glassy carbon electrode (GCE). In the absence of OTA, a methylene blue (MB)-labeled aptamer hybridized with cDNA is immobilized on the ERGO surface via π–π stacking interactions, forming a rigid duplex that suppresses electron transfer and yields a low electrochemical signal. Upon OTA binding, the aptamer undergoes a conformational transition into a G-quadruplex structure, leading to dissociation of the cDNA strand. This target-induced folding brings the MB redox tag into close proximity to the ERGO surface, markedly accelerating electron transfer and enhancing the cathodic reduction current of MB, thereby producing a pronounced signal-on response in square-wave voltammetry (SWV). The ERGO-modified electrode provides a conductive and stable interface without chemical linkers. Under optimized conditions, the aptasensor shows a linear response to OTA from 10 fM to 100 pM with an ultralow LOD of 0.67 fM, together with high selectivity, good reproducibility, and satisfactory stability. This work demonstrates a simple and effective turn-on aptasensing strategy for sensitive electrochemical detection of OTA. Full article

The objective of this study is to develop a label-free fluorescent sensor for the quantitative detection of hypochlorite ions (ClO⁻) and validate its applicability in biological samples, particularly exploring the potential of ClO⁻ as a biomarker for stress-induced hypertension (SIH). Male Sprague-Dawley rats (8 weeks old, 250–300 g) were used to establish the SIH model. A guanine-rich (G-rich) signal DNA sequence (S-DNA) was rationally designed, with a ClO⁻-responsive phosphorothioate (PS) moiety integrated into the probe architecture. In the absence of ClO⁻, the S-DNA folds into a stable G-quadruplex structure, which specifically binds to ThT and triggers a significant enhancement of the dye’s fluorescence intensity. Upon introduction of ClO⁻, the specific hydrolysis reaction between the PS moiety and ClO⁻ induces cleavage of the S-DNA into two discrete fragments, thereby abrogating G-quadruplex formation and resulting in a remarkable quenching of ThT fluorescence. This proposed method exhibits excellent anti-interference capability against other reactive oxygen species (ROS) and achieves a low detection limit of 41.2 nM for ClO⁻. Furthermore, this strategy was successfully applied to the quantitative determination of endogenous ClO⁻ in human cells and the plasma of stress-induced hypertensive (SIH) rats, highlighting its substantial potential for clinical and physiological research. Full article

G-quadruplexes (G4s) are specialized nucleic acid structures extensively formed throughout the genome, with particular enrichment in regulatory regions such as telomeres, promoters, and transcriptional enhancers. These four-stranded assemblies are involved in multiple chromosomal processes, including DNA replication, transcription, maintenance of genomic stability, and epigenetic regulation, and are closely associated with cancer biology. Due to their unusual thermodynamic stability, G4s serve as physical barriers to DNA/RNA unwinding, thereby impeding replication, transcription, and translation and compromising genome integrity. To mitigate this threat, cells have evolved dedicated helicases that can actively resolve G4 structures. In this review, we summarize recent structural advances—primarily derived from protein crystallography—regarding the mechanisms by which helicases unwind G4 quadruplexes. The insights presented herein establish a framework for elucidating the molecular basis of G4 unfolding and for the rational design of small-molecule G4 ligands and therapeutic agents. Additionally, we explore the applications of G4 helicases in nanopore sequencing, which aim to enhance sequencing accuracy, throughput, and continuity. Full article

G-quadruplex (G4) DNA structures have recently emerged as promising chiral scaffolds for enantioselective catalysis. This study investigates how thymidine loop modifications influence the catalytic performance of the telomeric G4 sequence HT21 in the asymmetric sulfoxidation of thioanisole. To this end, several singly or doubly modified HT21 derivatives were synthesized by using β-L-2′-deoxythymidine, 5-hydroxymethyl-2′-deoxyuridine, and 5-bromo-2′-deoxyuridine instead of a T residue, or β-L-2′-deoxyadonesine instead of an A residue, in specific positions within the TTA loops. The catalytic activity of these analogues was evaluated in the Cu(II)-mediated oxidation of thioanisole using hydrogen peroxide as oxidant. All modified sequences maintained complete substrate conversion, but their enantioselectivities varied markedly. Whereas the highest enantiomeric excess (84% ee) had previously been achieved with the HT21 analogue bearing a β-L-2′-deoxyadenosine in the first loop, the thymidine-based modifications, either alone or in combination, resulted in lower ee values, suggesting that loop alterations critically affect the chiral microenvironment, not all loop positions are functionally equivalent, and single substitutions within the same loop can result in different enantioselectivities. These findings highlight new insights on how individual loop residues contribute to asymmetric induction and offer further details for tuning G4-based catalytic scaffolds. Full article