Search Results (23)

The escalating demand for high-performance dielectric energy storage materials in pulse-power systems and portable electronics calls for polymer film capacitors with high discharged energy density and breakdown strength. Conventional polymers, however, suffer severe performance degradation under concurrent thermal and electrical stress, and existing reinforcement strategies—involving inorganic nanofillers or chemical crosslinking—often compromise flexibility, introduce interfacial defects, or involve complex processing. Herein, we demonstrate that incorporating a rigid mechanically interlocked molecule, specifically an octacationic homo[2]catenane, into a polyimide matrix yields robust, crosslink-like networks through strong [π∙∙∙π] electrostatic interaction between electron-rich aromatic units of polyimide and electron-deficient homo[2]catenane. This supramolecular network simultaneously enhances breakdown strength via densified chain packing and suppresses conduction loss by forming deep electron traps derived from the high electron affinity of homo[2]catenane. The optimized PI–HC⁸⁺ composite achieves a high discharged energy density of 7.86 J/cm³ with an efficiency > 80% and sustains stable performance over 10⁵ charge–discharge cycles at 150 °C. This research establishes mechanically interlocked molecules as a new class of functional fillers for high-performance polymer dielectrics, opening an unexplored avenue in the design of next-generation capacitive energy-storage materials. Full article

The design, construction, and operation of devices and machines at the molecular scale using the bottom-up approach captivates a lot of interest in nanoscience. Particularly intriguing are interlocked molecular architectures, which are ideal candidates for these aims. [n]Pseudorotaxanes, [n]rotaxanes, and [n]catenanes serve as versatile prototypes for constructing molecular machines because they can be engineered to execute a diverse range of functions, including mechanical-like movements in response to chemical, photochemical, or electrochemical stimuli. The study explores the synthesis and characterization of a two-station two-gate calix[6]arene-based [2]catenane. Building on prior work with calix[6]arene-based Mechanically Interlocked Molecules (MIMs), this research integrates two functional gates—an azobenzene unit and a stilbene unit —into a two-station “track” ring. The synthesis employed threading and capping strategies to prepare the precursor [2]rotaxane isomers 12(azo-up) and 12(azo-down). Challenges in the deprotection of TBS groups led to the adoption of a supramolecular-assisted approach for the direct synthesis of the desired pseudorotaxane. The final catenation reaction, using a trans-stilbene-based bisacyl chloride as the “clipping unit”, afforded the [2]catenane C3(azo-down) in 25% yield after purification. Mass spectrometry and NMR spectroscopy confirmed the successful synthesis and orientation of C3(azo-down). Full article

The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, “bubbles”, R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the “B-Z-topoII hypothesis” and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments (“Z-flipons”) as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover “conformase” activity on given G(ate) B-DNA segments (“Z-flipins”), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural–functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents. Full article

A review of heteroditopic interlocked molecules and their application as receptors for simple inorganic ion pair species. The review details the design and ion recognition properties of the rotaxane and catenane receptors, as well as highlighting some of the experimental challenges; hence, it provides insight into possible future avenues of research in this youthful field. Full article

Polyynes are alternations of single and triple bonds between carbon atoms, while cumulenes are successions of double bonds. Since the triple bond is the strongest bond between two carbon atoms, recent preoccupations included synthesizing and condensing cyclic polyynes and cumulenes and their clusters. Density functional theory calculations predicted stable monocyclic rings formation for a number of C atoms equal to or higher than 16. Alternative to the series of Carbon atoms are alternations of Boron and Nitrogen. Large rings (such as those of 24 atoms) can be crossed and thus small clusters can be formed. Patterns of three crosses seem to further stabilize the atomic ensemble. Clusters of $4C_{24}$ and $4B_{12}{N}_{12}$ (96 atoms) as well as $4C_{26}$ (104 atoms) have been designed, and their conformation has been studied here. Full article

Endometrial carcinoma (EC) is the most common type of gynecologic malignant epithelial tumor, with the death rate from this disease doubling over the past 20 years. Mitochondria provide cancer cells with necessary anabolic building blocks such as amino acids, lipids, and nucleotides, and EC samples have been shown to increase mitochondrial biogenesis. In cancer, mitochondrial DNA (mtDNA) heteroplasmy studies suggest that heteroplasmic variants encode predicted pathogenic proteins. We investigated the mtDNA genotypes within peri-normal and tumor specimens obtained from three individuals diagnosed with EC. DNA extracts from peri-normal and tumor tissues were used for mtDNA-specific next-generation sequencing and analyses of mtDNA content and topoisomers. The three tumors harbor heteroplasmic somatic mutations, and at least one mutation in each carcinoma is predicted to deleteriously alter a mtDNA-encoded protein. Somatic heteroplasmy linked to two mtDNA tRNA genes was found in separate tumors, and two heteroplasmic non-coding variants were identified in a single EC tumor. While two tumors had altered mtDNA content, all three displayed increased mtDNA catenanes. Our findings support that EC cells require wild-type mtDNA, but heteroplasmic mutations may alter mitochondrial metabolism to help promote cancer cell growth and proliferation. Full article

DNA topoisomerase II (TOPII) plays a very important role in DNA topology and in different biological processes such as DNA replication, transcription, repair, and chromosome condensation in higher eukaryotes. TOPII has been found to interact directly with a protein called topoisomerase II binding protein 1 (TopBP1) which also seems to have important roles in DNA replication and repair. In this study, we conducted different experiments to assess the roles of TopBP1 in DNA repair, mitosis, and meiosis, exploring the relationship between TOPII activity and TopBP1. We found that topbp1 mutant seedlings of Arabidopsis thaliana were hypersensitive to cisplatin treatment and the inhibition of TOPII with etoposide produced similar hypersensitivity levels. Furthermore, we recognised that there were no significant differences between the WT and topbp1 seedlings treated with cisplatin and etoposide together, suggesting that the hypersensitivity to cisplatin in the topbp1 mutant could be related to the functional interaction between TOPII and TopBP1. Somatic and meiotic anaphase bridges appeared in the topbp1 mutant at similar frequencies to those when TOPII was inhibited with merbarone, etoposide, or ICFR-187. The effects on meiosis of TOPII inhibition were produced at S phase/G2 stage, suggesting that catenanes could be produced at the onset of meiosis. Thus, if the processing of the catenanes is impaired, some anaphase bridges can be formed. Also, the appearance of anaphase bridges at first and second division is discussed. Full article

DNA topoisomerases are the enzymes that regulate DNA topology in all living cells. Since the discovery and purification of ω (omega), when the first were topoisomerase identified, the function of many topoisomerases has been examined. However, their ability to relax supercoiling and unlink the pre-catenanes of partially replicated molecules has received little attention. Here, we used two-dimensional agarose gel electrophoresis to test the function of three type II DNA topoisomerases in vitro: the prokaryotic DNA gyrase, topoisomerase IV and the human topoisomerase 2α. We examined the proficiency of these topoisomerases on a partially replicated bacterial plasmid: pBR-TerE@AatII, with an unidirectional replicating fork, stalled when approximately half of the plasmid had been replicated in vivo. DNA was isolated from two strains of Escherichia coli: DH5αF’ and parE10. These experiments allowed us to assess, for the first time, the efficiency of the topoisomerases examined to resolve supercoiling and pre-catenanes in partially replicated molecules and fully replicated catenanes formed in vivo. The results obtained revealed the preferential functions and also some redundancy in the abilities of these DNA topoisomerases in vitro. Full article

More than three decades of research efforts have yielded powerful methodologies based on transition metal template-directed syntheses for the assembly of a huge number of interlocked systems, molecular knots, machines and synthesizers. Such template techniques have been applied in the preparation of mechanically linked electron donor–acceptor artificial photosynthetic models. Consequently, synthetic challenging photoactive rotaxanes and catenanes have been reported, in which the chromophores are not covalently linked but are still associated with undergoing sequential energy (EnT) and electron transfer (ET) processes upon photoexcitation. Many interlocked photosynthetic models produce highly energetic, but still long-living charge separated states (CSS). The present work describes in a historical perspective some key advances in the field of photoactive interlocked systems assembled by transition metal template techniques, which illustrate the usefulness of rotaxanes and catenanes as molecular scaffolds to organize electron donor–acceptor groups. The effects of molecular dynamics, molecular topology, as well as the role of the transition metal ion used as template species, on the thermodynamic and kinetic parameters of the photoinduced energy and electron transfer processes in the interlocked systems are also discussed. Full article

The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems. Full article

At each round of cell division, the DNA must be correctly duplicated and distributed between the two daughter cells to maintain genome identity. In order to achieve proper chromosome replication and segregation, sister chromatids must be recognized as such and kept together until their separation. This process of cohesion is mainly achieved through proteinaceous linkages of cohesin complexes, which are loaded on the sister chromatids as they are generated during S phase. Cohesion between sister chromatids must be fully removed at anaphase to allow chromosome segregation. Other (non-proteinaceous) sources of cohesion between sister chromatids consist of DNA linkages or sister chromatid intertwines. DNA linkages are a natural consequence of DNA replication, but must be timely resolved before chromosome segregation to avoid the arising of DNA lesions and genome instability, a hallmark of cancer development. As complete resolution of sister chromatid intertwines only occurs during chromosome segregation, it is not clear whether DNA linkages that persist in mitosis are simply an unwanted leftover or whether they have a functional role. In this review, we provide an overview of DNA linkages between sister chromatids, from their origin to their resolution, and we discuss the consequences of a failure in their detection and processing and speculate on their potential role. Full article

The Stoddart’s blue box (BB) (cyclobis(paraquat-p-phenylene))/iodide binary system was recently demonstrated to give rise to porous three-dimensional networks which can hardly be classified as common XOF-type materials (X = M, C, S, i.e., metal, covalent, or supramolecular organic frameworks), leading to the definition of permutable organized frameworks (POFs). The ternary BB/iodide/iodine system was reported to generate pentaiodide-based structures constituted by the most complex interlocked polyiodides so far isolated (up to an infinite supramolecular pseudopolyrotaxane with a poly[3]catenane axle). The missing link, i.e., the XRD structure of the BB/triiodide complex, is herein reported: structural similarities and novel Raman evidence, opening perspectives in the genesis of solid-state BB-based complex polyiodide networks from solution. Full article

Cyclodextrins (CDs) are cone-shaped molecular rings that have been widely employed in supramolecular/host–guest chemistry because of their low cost, high biocompatibility, stability, wide availability in multiple sizes, and their promiscuity for binding a range of molecular guests in water. Consequently, CD-based host–guest complexes are often employed as templates for the synthesis of mechanically bonded molecules (mechanomolecules) such as catenanes, rotaxanes, and polyrotaxanes in particular. The conical shape and cyclodirectionality of the CD “bead” gives rise to a symmetry-breaking effect when it is threaded onto a molecular “string”; even symmetrical guests are rendered asymmetric by the presence of an encircling CD host. This review focuses on the stereochemical implications of this symmetry-breaking effect in mechanomolecules, including orientational isomerism, mechanically planar chirality, and topological chirality, as well as how they support applications in regioselective and stereoselective chemical synthesis, the design of molecular machine prototypes, and the development of advanced materials. Full article

Thiolate-protected metal nanoclusters have highly size- and structure-dependent physicochemical properties and are a promising class of nanomaterials. As a consequence, for the rationalization of their synthesis and for the design of new clusters with tailored properties, a precise characterization of their composition and structure at the atomic level is required. We report a combined ion mobility-mass spectrometry approach with density functional theory (DFT) calculations for determination of the structural and optical properties of ultra-small gold nanoclusters protected by thioglycolic acid (TGA) as ligand molecules, Au₁₀(TGA)₁₀. Collision cross-section (CCS) measurements are reported for two charge states. DFT optimized geometrical structures are used to compute CCSs. The comparison of the experimentally- and theoretically-determined CCSs allows concluding that such nanoclusters have catenane structures. Full article

DNA catenanes are characterized by their flexible and dynamic motions and have been regarded as one of the key players in sophisticated DNA-based molecular machines. There, the linking number (Lk) between adjacent interlocked rings is one of the most critical factors, since it governs the feasibility of dynamic motions. However, there has been no established way to synthesize catenanes in which Lk is controlled to a predetermined value. This paper reports a new methodology to selectively synthesize Lk 1 catenanes composed of single-stranded DNA rings, in which these rings can most freely rotate each other due to minimal inter-ring interactions. To the mixture for the synthesis, two holder strands (oligonucleotides of 18–46 nt) were added, and the structure of the quasi-catenane intermediate was interlocked through Watson–Crick base pairings into a favorable conformation for Lk 1 catenation. The length of the complementary part between the two quasi-rings was kept at 10 bp or shorter. Under these steric constraints, two quasi-rings were cyclized with the use of T4 DNA ligase. By this simple procedure, the formation of undesired topoisomers (Lk ≥ 2) was almost completely inhibited, and Lk 1 catenane was selectively prepared in high yield up to 70 mole%. These Lk 1 catenanes have high potentials as dynamic parts for versatile DNA architectures. Full article