Interactions of Metal Ions with DNA and Some Applications

Structural diversity of nucleotide coordination polymers of cytidine mono-, di-, and tri-phosphates and their selective recognition of tryptophan and tyrosine

Understanding the coordination geometry of nucleotide mono-, di-, and triphosphates is pivotal for unraveling the intricate relationships between molecular structure and biological function, particularly in metal-ligand interactions and their role in biomolecular recognition. This study investigates the structure of nucleotide-metal polymers and their selective interactions with amino acids, specifically tryptophan (Trp) and tyrosine (Tyr). We synthesized and comprehensively analyzed five coordination polymers of cytidine nucleotides: cytidine monophosphate (CMP), deoxycytidine monophosphate (dCMP), cytidine diphosphate (CDP), and cytidine triphosphate (CTP), which are {[Cu(CMP)(bpa)(H2O)3](CMP)·3H2O}n (1), {[Cu2(dCMP)(4,4'-bipy)2(H2O)2]·4H2O}n (2), {[Cu2(CDP)2(azpy)(H2O)]·3H2O}n (3), {[Cd2(CDP)2(bpa)2(H2O)2]·8H2O}n (4), and {[Cu(CTP)(2,2'-bipy)]·2H2O}n (5), where (3), (4) and (5) mark the first report of CDP and CTP coordination complexes. Single-crystal X-ray diffraction unveiled the structure of the polymers to be one-dimensional (1, 5) or two-dimensional (2, 3, 4). Circular dichroism (CD) spectroscopy in both the solid and solution states elucidates the chirality-driven assembly in these nucleotide-metal polymers. The selective interactions of coordination polymers with tryptophan (Trp) and tyrosine (Tyr) were studied using spectroscopic titrations. Experimental and computational analyses reveal distinct interactions between all five coordination polymers and the amino acids, highlighting their biosensing potential. Binding affinity variations across the polymers offer insights into nucleotide-metal coordination chemistry and suggest applications in molecular recognition and functional materials.

Manganese-Driven Plasmid Nanofibers Formed In Situ for Cancer Gene Delivery and Metalloimmunotherapy

While nucleic-acid-based cancer vaccines hold therapeutic potential, their limited immunogenicity remains a challenge due in part to the low efficiency of cytoplasmic delivery caused by lysosomal entrapment. In this work, we found that plasmids encoding both an antigen and a STING agonist protein adjuvant can self-assemble into coordination nanofibers, triggered by manganese ions. We developed a strategy to construct a DNA vaccine, termed MnO2-OVA-CDA-mem, formed by the coencapsulation of manganese dioxide (MnO2), an antigen-expressing plasmid (encoding ovalbumin, OVA), and an adjuvant enzyme-expressing plasmid (encoding STING agonist, CDA) within dendritic cell (DC) membranes. Upon uptake into acidic lysosomes, Mn2+ released from MnO2 triggered the nucleic acids to undergo a morphological change from nanospheres (∼180 nm diameter) to nanofibers (∼1 μm length), resulting in an increase in mechanical strength by about 9-fold and consequently lysosomal membrane disruption. The antigen OVA and adjuvants Mn2+ and CDA in the cytoplasm triggered strong DC activation and antigen-specific CD8+ T cell metalloimmune responses, significantly inhibiting the growth of B16-OVA tumors and inducing long-term immune memory. Altogether, MnO2-OVA-CDA-mem holds potential as a platform for nucleic acid antigen and adjuvant delivery using an in situ self-assembly strategy in a metal-driven, stimulus-responsive, and programmable manner for cancer metalloimmunotherapy.

Metal-Coordinated Histidine-Functionalized Redox-Responsive Polyethyleneimine as a Smart Gene Delivery Vector

Despite significant advancements in gene delivery and CRISPR technology, several challenges remain. Chief among these are overcoming serum inhibition and achieving high transfection efficiency with minimal cytotoxicity. To address these issues, there is a need for novel vectors that exhibit lower toxicity, maintain stability in serum-rich environments, and effectively deliver plasmids of various sizes across diverse cell types. In this study, to convert common polyethylenimine (PEI1.8k) into high-performance DNA delivery vectors, an innovative multifunctional vector was constructed based on histidine linked to PEI1.8k by redox-responsive disulfide bonds. Apart from highly efficient transfection of both small and large plasmids into HEK 293T (Human Embryonic Kidney 293T cells) with negligible cytotoxicity, PEI1.8k-S-S-His showed great transfection potential even at low plasmid doses (0.5 µg), as well as at serum concentrations ranging from 5 to 30% into HEK 293T cells, and achieved excellent plasmid transfection into NIH/3T3 (Mouse Embryonic Fibroblast cells), and MCF7 (Human Breast Cancer cells). Additionally, several metals were tested (Co, Cu, Cd, Ni, Zn, and Mn) to promote the plasmid packaging functionality and improve transfection efficiency. We observed that, in comparison to PEI1.8k-S-S-His, the manganese-functionalized nanocarrier (PEI1.8k-S-S-His-Mn) could transfect a large plasmid with equal efficiency (~ 30%) into MSCs (Mesenchymal Stem Cells). Interestingly, PEI1.8k-S-S-His-Mn showed higher transfection efficiency with the small plasmid (~ 90%) and the large one (~ 80%) into HEK 293T cells, even better than its backbone. We propose that the presence of metal-coordinated His ligand, redox-responsive S-S bonds, and the cationic polymer can synergistically provide robust DNA binding, efficient endosomal disruption, tolerance of serum protein adsorption, and low cytotoxicity. These new vectors could be promising for gene delivery and may be therapeutically relevant.

Digoxin detection for therapeutic drug monitoring using target-triggered aptamer hairpin switch and nicking enzyme-assisted signal amplification

Digoxin, a cardiac glycoside drug, is commonly used to treat heart failure and arrhythmias. The therapeutic concentration range of digoxin, with a narrow therapeutic index, is between 0.5 and 2.0 ng mL-1. Hence, it is important for patients to monitor their blood levels after taking medication to achieve effective treatment and reduce the likelihood of experiencing drug side effects. Due to the complex steps and high cost of immunoassays, aptasensors that use aptamers to recognize the targets offer the advantages of low cost and good stability over other analysis methods. Nicking enzyme-assisted signal amplification is a novel isothermal signal amplification technology that relies on nicking enzymes to recognize and cleave restriction sites on one oligonucleotide strand. In this study, we develop a fluorescent aptasensor coupled with target-triggered aptamer hairpin switch and nicking enzyme-assisted signal amplification for digoxin detection in plasma for therapeutic drug monitoring. After optimizing the experimental parameters, we design hairpin probes with ten base pairs of the aptamer sequence and extended sequence complement to react with digoxin in a 10 mM Tris buffer containing 150 mM NaCl and 50 mM MgCl2 (pH 7.4). The signal amplification reactions were performed for 3 hours. The fluorescent aptasensor exhibited high sensitivity with a detection limit of 88 pg mL-1 for detecting digoxin in plasma and a linear range from 0.1 ng mL-1 to 5 ng mL-1. This technology was successfully used for digoxin detection to improve treatment effectiveness and minimize the risk of adverse side effects.

Determination of metal-biomolecule interactions by relative mobility shift partial filling affinity capillary electrophoresis

Metal ions and their interactions with biomolecules play an important role in human health. However, optical detectors commonly used for HPCE cannot directly detect metal ions without UV absorption. To make up for the shortcomings of existing HPCE detectors, a new universal HPCE detection system called an interface-induced current detector (IICRD) was constructed previously, with no need for derivatization procedures or complex instrumental modifications. Meanwhile, most of the reported studies on metal-biomolecule interactions only focused on the detection and analysis of biomolecules, commonly causing inaccurate or false-negative results, which is yet to be resolved. Here, the application of HPCE-IICRD realized the determination of metal-biomolecule interactions by directly measuring the electrophoretic parameters of metal ions for the first time, indicating that the interaction intensity can be measured more directly and accurately. Furthermore, an improved affinity capillary electrophoresis (ACE) method called relative mobility shift partial filling ACE-IICRD (rmsPF-ACE-IICRD) was originally developed to quantitatively analyze the binding strength. Binding behaviors between twelve free metal ions and three types of biomolecules (including two blood proteins, two enzyme proteins and two native DNAs) were investigated, and the values of the equilibrium dissociation constant (KD) of metal-biomolecule complexes were calculated and evaluated by the nonlinear chromatography (NLC) method. The experimental results were basically consistent with the literature values. In particular, heavy metal ions showed stronger interactions with proteins and enzymes, while metal ions tended to show stronger binding with native DNAs than proteins and enzymes, which were in agreement with literature results. The combined use of HPCE-IICRD and rmsPF-ACE showed great advantages such as no need for pretreatment, low operating cost, good repeatability, simple operation and no interference from coexisting substances, which is hopeful to become an efficient metal ion detection method and also to expand the application scope of IICRD in the future.

Exploring the influence of metal cations on individual hydrogen bonds in Watson-Crick guanine-cytosine DNA base pair: An interacting quantum atoms analysis

This study delves into the nature of individual hydrogen bonds and the relationship between metal cations and hydrogen bonding in the Watson-Crick guanine-cytosine (GC) base pair and its alkali and alkaline earth cation-containing complexes (Mn+-GC). The findings reveal how metal cations affect the nature and strength of individual hydrogen bonds. The study employs interacting quantum atoms (IQA) analysis to comprehensively understand three individual hydrogen bonds within the GC base pair and its cationic derivatives. These analyses unveil the nature and strength of hydrogen bonds and serve as a valuable reference for exploring the impact of cations (and other factors) on each hydrogen bond. All the H ⋯ D interactions (H is hydrogen and D is oxygen or nitrogen) in the GC base pair are primarily electrostatic in nature, with the charge transfer component playing a substantial role. Introducing a metal cation perturbs all H ⋯ D interatomic interactions in the system, weakening the nearest hydrogen bond to the cation (indicated by a) and reinforcing the other (b and c) interactions. Notably, the interaction a, the strongest H ⋯ D interaction in the GC base pair, becomes the weakest in the Mn+-GC complexes. A broader perspective on the stability of GC and Mn+-GC complexes is provided through interacting quantum fragments (IQF) analysis. This approach considers all pairwise interactions between fragments and intra-fragment components, offering a complete view of the factors that stabilize and destabilize GC and Mn+-GC complexes. The IQF analysis underscores the importance of electron sharing, with the dominant contribution arising from the inter-fragment exchange-correlation term, in shaping and sustaining GC and Mn+-GC complexes. From this point of view, alkaline and alkaline earth cations have distinct effects, with alkaline cations generally weakening inter-fragment interactions and alkaline earth cations strengthening them. In addition, IQA and IQF calculations demonstrate that the hydration of cations led to small changes in the hydrogen bonding network. Finally, the IQA interatomic energies associated with the hydrogen bonds and also inter-fragment interaction energies provide robust indicators for characterizing hydrogen bonds and complex stability, showing a strong correlation with total interaction energies.

DNA Framework-Templated Synthesis of Copper Cluster Nanozyme with Enhanced Activity and Specificity

Nanozymes have been developed to overcome the inherent limitations of natural enzymes, such as their low stability and high cost. However, their efficacy has been hindered by their relatively low specificity and activity. Here, we demonstrate the self-assembly of individual copper nanoclusters (CuNCs) via a simple yet fast (10 min) DNA nanosheet (DNS)-templated method, enhancing the peroxidase-like activity and specificity of CuNCs. Furthermore, we demonstrate the successful assembly of CuNCs on different DNA nanostructures by atomic force microscopy (AFM), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). The resulting micron-scale ultrathin DNA nanosheet-templated CuNCs (DNS@CuNCs) exhibit exceptional catalytic activity, with a specific activity reaching 1.79 × 103 U mg-1. Investigation into the catalytic process reveals that the enhanced activity and specificity arise from disparities in active intermediate content before and after CuNCs assembly. Significantly, the DNS@CuNCs-based biosensor demonstrates remarkable anti-interference capabilities, enabling the detection of H2O2 in undiluted human serum for the first time with a detection limit of 0.99 μM.

Micro-interfacial behavior of antibiotic-resistant bacteria and antibiotic resistance genes in the soil environment: A review

Overutilization and misuse of antibiotics in recent decades markedly intensified the rapid proliferation and diffusion of antibiotic resistance genes (ARGs) within the environment, thereby elevating ARGs to the status of a global public health crisis. Recognizing that soil acts as a critical reservoir for ARGs, environmental researchers have made great progress in exploring the sources, distribution, and spread of ARGs in soil. However, the microscopic state and micro-interfacial behavior of ARGs in soil remains inadequately understood. In this study, we reviewed the micro-interfacial behaviors of antibiotic-resistant bacteria (ARB) in soil and porous media, predominantly including migration-deposition, adsorption, and biofilm formation. Meanwhile, adsorption, proliferation, and degradation were identified as the primary micro-interfacial behaviors of ARGs in the soil, with component of soil serving as significant determinant. Our work contributes to the further comprehension of the microstates and processes of ARB and ARGs in the soil environments and offers a theoretical foundation for managing and mitigating the risks associated with ARG contamination.

Platinum-based chemotherapy: trends in organic nanodelivery systems

Despite the investment in platinum drugs research, cisplatin, carboplatin and oxaliplatin are still the only Pt-based compounds used as first line treatments for several cancers, with a few other compounds being approved for administration in some Asian countries. However, due to the severe and worldwide impact of oncological diseases, there is an urge for improved chemotherapeutic approaches. Furthermore, the pharmaceutical application of platinum complexes is hindered by their inherent toxicity and acquired resistance. Nanodelivery systems rose as a key strategy to overcome these challenges, with recognized versatility and ability towards improving the safety, bioavailability and efficacy of the available drugs. Among the known nanocarriers, organic systems have been widely applied, taking advantage of their potential as drug vehicles. Researchers have mainly focused on the development of lipidic and polymeric carriers, including supramolecular structures, with an overall improvement of encapsulated platinum complexes. Herein, an overview of recent trends and strategies is presented, with the main focus on the encapsulation of platinum compounds into organic nanocarriers, showcasing the evolution in the design and development of these promising systems. This comprehensive review highlights formulation methods as well as characterization procedures, providing insights that may be helpful for the development of novel platinum nanocarriers aiming at future pharmaceutical applications.

Role of Alkali Cations in DNA-Thioflavin T Interaction

This study investigates the role of alkali cations in modulating the interaction between deoxyribonucleic acid (DNA) and Thioflavin T (ThT) in dilute and condensed phases. The emission characteristics of ThT were analyzed in the presence of double-stranded DNA and G-quadruplex structures with a focus on the effects of four cations: sodium, potassium, calcium, and magnesium. The ThT emission in double-stranded DNA was influenced by direct DNA binding and steric hindrance within the hydration shell of DNA, which was modulated by the presence of alkali cations. Lasing spectroscopy experiments further highlighted ThT sensitivity to the spatial arrangement of water molecules in the DNA hydration shell. Lasing was exclusively observed in the presence of Mg2+ in the G-quadruplex structure, suggesting that the parallel propeller configuration of G4 provides an optimal environment for ThT light amplification. This study highlights the critical role of cations in DNA-dye interactions and reaffirms the significance of ThT in biophysical studies.

Supramolecular DNA-based catalysis in organic solvents

The distinct folding accompanied by its polymorphic character renders DNA G-quadruplexes promising biomolecular building blocks to construct novel DNA-based and supramolecular assemblies. However, the highly polar nature of DNA limits the use of G-quadruplexes to water as a solvent. In addition, the archetypical G-quadruplex fold needs to be stabilized by metal-cations, which is usually a potassium ion. Here, we show that a noncovalent PEGylation process enabled by electrostatic interactions allows the first metal-free G-quadruplexes in organic solvents. Strikingly, incorporation of an iron-containing porphyrin renders the self-assembled metal-free G-quadruplex catalytically active in organic solvents. Hence, these "supraG4zymes" enable DNA-based catalysis in organic media. The results will allow the broad utilization of DNA G-quadruplexes in nonaqueous environments.

Intermolecular hydrogen bonding in DNA base pairs interacting with different numbers of bare and hydrated Li+: NBO, QTAIM, and computational spectroscopic studies

In this study, the effect of different numbers of Li+ interacting with various sites of DNA base pairs (adenine-thymine (AT) and cytosine-guanine (GC)) on the base pair structures, the strength of hydrogen bonding between the bases, and spectroscopic properties (IR and absorption spectra) of the base pairs was investigated. Two quantum computational analyses, the natural bonding orbitals (NBO) and the quantum theory of atoms in molecules (QTAIM), were used to follow the change in the strength of hydrogen bonds between the bases in each pair. The type of base pair's site interacting with Li+ showed different effects on the change in the strength of the hydrogen bonds between the bases. The IR and absorption spectra of the lithiated base pairs were calculated and compared with those of bare base pairs. This comparison provided the changes in the spectra as a fingerprint for the structural identification of different lithiated base pairs. Also, the determination of the change in the strength of hydrogen bonds in the lithiated base pairs compared to their bare base pairs. In the other part of this study, the effect of the hydration of the attached Li+ in the structure of lithiated base pairs on the strength of their hydrogen bonds and spectra was investigated.

Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer

The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.

Spectrophotometric and nucleic acid-binding properties of halloysite clay nanotubes and kaolinite

Halloysite particles (HNTs) are naturally occurring aluminosilicate nanotubes of low toxicity that have shown great promise for drug and biomolecule delivery into human and animal cells. Kaolinite particles retain the same layered structure as HNT, but do not form nanotubes. In this study, the spectrophotometric and sedimentation properties of the two clays in aqueous solutions and their abilities to associate with both small and large nucleic acids have been investigated. Both clays scattered ultraviolet light strongly and this characteristic of HNT was not affected by either vacuum treatment to remove trapped gases or by sonication. Vacuum treatment increased the binding of small nucleic acids to HNT and this association was further enhanced by addition of divalent metal ions. By contrast, only small RNAs were bound efficiently by kaolinite in the presence of Mg²⁺ ions. Large linear double-stranded DNAs and circular plasmid DNAs bound poorly to kaolinite under all conditions, but these nucleic acids could form strong associations with HNT. Differences in binding data were largely consistent with measurements of the available surface areas of each clay. These results demonstrate that interactions with each clay are critically dependent on both the type and the conformation of each nucleic acid.

Metalated Nucleic Acid Nanostructures

Nucleic acid nanotechnology takes advantage of the self-assembling property of nucleic acids to form a variety of shapes and structures. The incorporation of metal ions into these structures introduces functionality for sensor and molecular electronic applications. Here, we describe a protocol for the incorporation of silver ions into polygonal nanoshapes that self-assemble from RNA and DNA modules.

Coordination Chemistry of Phosphate Groups in Systems Including Copper(II) Ions, Phosphoethanolamine and Pyrimidine Nucleotides

The activity of phosphate groups of phosphoethanolamine and pyrimidine nucleotides (thymidine 5-monophosphate, cytidine 5-monophosphate and uridine 5'monophosphate) in the process of complexation metal ions in aqueous solution was studied. Using the potentiometric method with computer calculation of the data and spectroscopic methods such as UV-Vis, EPR, ¹³C and ³¹P NMR as well as FT-IR, the overall stability constants of the complexes as well as coordination modes were obtained. At lower pH, copper(II) ions are complexed only by phosphate groups, whereas the endocyclic nitrogen atom of nucleotides has been identified as a negative center interacting with the -NH₃⁺ groups of phosphoethanolamine.

Spontaneous Transformation of Biomedical Polymeric Silver Salt into a Nanocomposite: Physical-Chemical and Antimicrobial Properties Dramatically Depend on the Initial Preparation State

An antimicrobial polyacrylic silver salt (freshly prepared, stored for one year and model-aged) was studied by physical–chemical techniques for nanoparticle detection. In all cases, this salt represents a composite of radical-enriched macromolecules and silver(0) nanoparticles. As time passed, the initial small spherical nanoparticles were converted into larger non-spherical silver nanoparticles. The initial highly water-soluble antimicrobial solid nanocomposite almost loses its solubility in water and cannot be used as an antimicrobial agent. Unlike insoluble solid silver polyacrylate, its freshly prepared aqueous solution retains a liquid-phase consistency after one year as well as pronounced antimicrobial properties. The mechanism of these spontaneous and model-simulated processes was proposed. These results have attracted attention for officinal biomedicinal silver salts as complex radical-enriched nanocomposite substances; they also indicate contrasting effects of silver polymeric salt storing in solid and solution forms that dramatically influence antimicrobial activity.

Highly selective detection of adenine and guanine by NH2-MIL-53(Fe)/CS/MXene nanocomposites with excellent electrochemical performance

Adenine (A) and guanine (G) are mainly found in deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) and play a crucial role in genetic information transfer and protein synthesis. In this study, NH₂-MIL-53(Fe)/CS/MXene nanocomposites were prepared for detecting guanine and adenine. With high specific surface area, excellent water dispersion, and numerous active sites, MXene (transition metal carbides, nitrides, and carbonitrides) provides a good platform for loading primitive metal-organic frameworks (MOFs). At the same time, the problem of poor conductivity and dispersion of MOFs is solved. The electrochemical catalytic oxidation of adenine and guanine of NH₂-MIL-53 (Fe)/CS/MXene nanocomposites was carried out by differential pulse voltammetry (DPV). Operating voltage of DPV: 0.7-0.9 V (vs. Ag/AgCl) for G, 1.0-1.2 V (vs. Ag/AgCl) for A, 0.8 V (vs. Ag/AgCl), and 1.1 V (vs. Ag/AgCl) for G and A. The concentration ranges for detecting A and G were 3-118 μM and 2-120 μM with detection limits of 0.57 μM and 0.17 μM (S/N = 3), respectively. The nanocomposite was used for detecting G and A in herring sperm DNA, and the content of G and A was found to be about 9 and 11 μM; the RSD values were 3.4 and 1.3%, respectively.

Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments

Force-spectroscopy techniques have led to significant progress in studying the physicochemical properties of biomolecules that are not accessible in bulk assays. The application of piconewton forces with laser optical tweezers to single nucleic acids has permitted the characterization of molecular thermodynamics and kinetics with unprecedented accuracy. Some examples are the hybridization reaction between complementary strands in DNA and the folding of secondary, tertiary, and other heterogeneous structures, such as intermediate and misfolded states in RNA. Here we review the results obtained in our lab on deriving the nearest-neighbor free energy parameters in DNA and RNA duplexes from mechanical unzipping experiments. Remarkable nonequilibrium effects are also observed, such as the large irreversibility of RNA unzipping and the formation of non-specific secondary structures in single-stranded DNA. These features originate from forming stem-loop structures along the single strands of the nucleic acid. The recently introduced barrier energy landscape model quantifies kinetic trapping effects due to stem-loops being applicable to both RNA and DNA. The barrier energy landscape model contains the essential features to explain the many behaviors observed in heterogeneous nucleic-acid folding.

Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly

Proper ionic concentrations are required for the functional dynamics of RNA and ribonucleoprotein (RNP) assemblies. While experimental and computational techniques have provided many insights into the properties of chelated ions, less is known about the energetic contributions of diffuse ions to large-scale conformational rearrangements. To address this, we present a model that is designed to quantify the influence of diffuse monovalent and divalent ions on the dynamics of biomolecular assemblies. This model employs all-atom (non-H) resolution and explicit ions, where effective potentials account for hydration effects. We first show that the model accurately predicts the number of excess Mg²⁺ ions for prototypical RNA systems, at a level comparable to modern coarse-grained models. We then apply the model to a complete ribosome and show how the balance between diffuse Mg²⁺ and K⁺ ions can control the dynamics of tRNA molecules during translation. The model predicts differential effects of diffuse ions on the free-energy barrier associated with tRNA entry and the energy of tRNA binding to the ribosome. Together, this analysis reveals the direct impact of diffuse ions on the dynamics of an RNP assembly.

Thy-AuNP-AgNP Hybrid Systems for Colorimetric Determination of Copper (II) Ions Using UV-Vis Spectroscopy and Smartphone-Based Detection

A colorimetric probe based on a hybrid sensing system of gold nanoparticles (AuNPs), silver nanoparticles (AgNPs), and thymine (Thy) was developed for easy and rapid detection of copper (II) ions (Cu2+) in solution. The underlying principle of this probe was the Cu2+-triggered aggregation of the nanoparticle components. Color change of the sensing solution (from red to purple) was clearly observed with naked eyes. The experimental parameters, including pH and concentration of tris buffer, thymine concentration and AgNP dilution ratios, were investigated and optimized. Once optimized, the limits of detection were found to be 1, 0.09 and 0.03 ppm for naked eyes, smartphone application and UV-vis spectrophotometer, respectively. Furthermore, determination of Cu2+ was accomplished within 15 min under ambient conditions. For quantitative analysis, the linearity of detection was observed through ranges of 0.09−0.5 and 0.03−0.5 ppm using smartphone application and UV-vis spectrophotometer, respectively, conforming to the World Health Organization guideline for detection of copper at concentrations < 2 ppm in water. This developed hybrid colorimetric probe exhibited preferential selectivity toward Cu2+, even when assessed in the presence of other metal ions (Al3+, Ca2+, Pb2+, Mn2+, Mg2+, Zn2+, Fe3+, Ni2+, Co2+, Hg2+ and Cd2+). The developed procedure was also successfully applied to quantification of Cu2+ in real water samples. The recovery and relative standard deviation (RSD) values from real water sample analysis were in the ranges of 70.14−103.59 and 3.21−17.63%, respectively. Our findings demonstrated a successful development and implementation of the Thy-AuNP-AgNP hybrid sensing system for rapid, simple and portable Cu2+ detection in water samples using a spectrophotometer or a smartphone-based device.

Magnesium ions reversibly bind to DNA double stranded helix in thin films

Effects of magnesium (Mg²⁺) ions on the stability and structural properties of double-stranded DNA are vitally important for DNA folding and functional behavior. Complementing our previous study on highly hydrated thin films of DNA with sodium counterions, with no buffer (pH ≈ 6) and surrounded with Mg²⁺ cations, here we use Fourier transform infrared spectroscopy and band shape analysis to explore in detail the vibrational signatures of DNA-magnesium interaction in the case when DNA charges are neutralized solely by Mg²⁺ cations, hereafter called MgDNA. Ion atmosphere has been controlled by the magnesium to phosphate molar concentration ratio r which varied between 0.0067 and 10. For r = 0 we find that spectral features in the base region remain similar as in DNA, whereas changes in the backbone region indicate that the B conformation becomes fully stabilized. With increasing r a pronounced structural reshaping occurs in the phosphate backbone region indicating a blue shift of the asymmetric band, while the symmetric band does not show any displacement in frequency. The band shape analysis of overlapping peaks in the respective phosphate regions demonstrates that the number of constituent modes as well as their positions in frequency do not change, whereas their intensities and bandwidths display disparate changes. The results reflect a variety of local environments at the DNA backbone due to a heterogeneous ion atmosphere with randomly distributed magnesium ions and local patterns of hydrogen bonds which change with increasing r. Remarkably, after crowded r = 10 ion atmosphere is depleted, Mg induced spectral changes vanish and structural features of MgDNA (r ≈ 0) are fully restored. Overall results strongly suggest that in MgDNA on highly hydrated thin films the hydrogen-base pairing remains preserved and that Mg²⁺ ions, similar to sodium ions, retain their mobility and interact with double helix via water-mediated electrostatic forces.

DNA-Assisted Creation of a Library of Ultrasmall Multimetal/Metal Oxide Nanoparticles Confined in Silica

Supported ultrasmall metal/metal oxide nanoparticles (UMNPs) with sizes in the range of 1-5 nm exhibit unique properties in sensing, catalysis, biomedicine, etc. However, the metal-support and metal-metal precursor interactions were not as well controlled to stabilize the metal nanoparticles on/in the supports. Herein, DNA is chosen as a template and a ligand for the silica-supported UMNPs, taking full use of its binding ability to metal ions via either electrostatic or coordination interactions. UMNPs thus are highly dispersed in silica via self-assembly of DNA and DNA-metal ion interactions with the assistance of a co-structural directing agent (CSDA). A large number of metal ions are easily retained in the mesostructured DNA-silica materials, and their growth is controlled by the channels after calcination. Based on this directing concept, a material library, consisting of 50 mono- and 54 bicomponent UMNPs confined within silica and with narrow size distribution, is created. Theoretical calculation proves the indispensability of DNA with combination of several organics in the synthesis of ultrasmall metal nanoparticles. The Pt-silica and Pt/Ni-silica chosen from the library exhibit good catalytic performance for toluene combustion. This generalizable and straightforward synthesis strategy is expected to widen the corresponding applications of supported UMNPs.

Single Molecular Chelation Dynamics Reveals That DNA Has a Stronger Affinity toward Lead(II) than Cadmium(II)

Lead ions can bind to DNA via nonelectrostatic interactions and hence alter its structure, which may be related to their adverse effects. The dynamics of Pb²⁺-DNA interaction has not been well understood. In this study, we report the monomolecular dynamics of the Pb²⁺-DNA interaction using a magnetic tweezers (MT) setup. We found that lead cations could induce DNA compaction at ionic strengths above 1 μM, which was also confirmed by morphology characterization. The chelation behavior of the Pb²⁺-DNA and the Cd²⁺-DNA complex solutions after adding EDTA were compared. The results showed that EDTA chelated with the bound metal ions on DNA and consequently led to restoring the DNA to its original length but with different restoration speeds for the two solutions. The fast binding dynamics and the slower chelation dynamics of the Pb²⁺ scenario compared to that of Cd²⁺ suggested that Pb²⁺ was more capable to induce DNA conformational change and that the Pb²⁺-DNA complex was more stable than the Cd²⁺-DNA complex. The stronger affinities for DNA bases and the inner binding of lead cations were two possible causes of the dynamics differences. Three agents, including EDTA, sodium gluconate, and SDBS, were used to remove the bound lead ions on DNA. It was shown that EDTA was the most efficient, and sodium gluconate could not fully restore DNA from its compact state. We concluded that both EDTA and SDBS were good candidates to restore the Pb²⁺-bound DNA to its original state.

Ion Pair Supramolecular Structure Identified by ATR-FTIR Spectroscopy and Simulations in Explicit Solvent*

The present work uses ATR-FTIR spectroscopy assisted by simulations in explicit solvent and frequency calculations to investigate the supramolecular structure of carboxylate alkali-metal ion pairs in aqueous solutions. ATR-FTIR spectra in the 0.25-4.0 M concentration range displayed cation-specific behaviors, which enabled the measurement of the appearance concentration thresholds of contact ion pairs between 1.9 and 2.6 M depending on the cation. Conformational explorations performed using a non-local optimization method associated to a polarizable force-field (AMOEBA), followed by high quantum chemistry level (RI-B97-D3/dhf-TZVPP) optimizations, mode-dependent scaled harmonic frequency calculations and electron density analyses, were used to identify the main supramolecular structures contributing to the experimental spectra. A thorough analysis enables us to reveal the mechanisms responsible for the spectroscopic sensitivity of the carboxylate group and the respective role played by the cation and the water molecules, highlighting the necessity of combining advanced experimental and theoretical techniques to provide a fair and accurate description of ion pairing.

DNA interfaces with dimensional materials for biomedical applications

DNA interfaces with nano, micro, and macro materials have gained widespread attention for various applications. Such interfaces exhibit distinct functions and properties not only due to the unique properties of interfacing materials but also sequence- and conformation-dependent characteristics of the DNA. Therefore, DNA interfaces with diverse dimensional materials have advanced our understanding of the interaction mechanisms and the properties of such interfaces. The unique interfacial properties of such novel materials have applications in nanotechnology, biophysics, cell biology, biosensing, and bioelectronics. The field is growing rapidly with the frequent emergence of new interfaces carrying remarkable interfacial character. In this review article, we have classified the DNA interfaces into 0D, 1D, 2D, and 3D categories based on the types of dimensional materials. We review the key efforts made in the last five years and focus on types of interfaces, interfacing mechanisms, and their state-of-the-art applications. This review will draw a general interest because of the diversity in the DNA materials science but also the unique applications that will play a cutting-edge role in biomedical and biosensing research.

A375 melanoma cells are sensitized to cisplatin-induced toxicity by a synthetic nitro-flavone derivative 2-(4-Nitrophenyl)-4H-chromen-4-one through inhibition of PARP1

BACKGROUND

Cisplatin has been extensively used in therapeutics for its broad-spectrum anticancer activity and frequently used for the treatment of solid tumors. However, it presents several side-effects and several cancers develop resistance. Combination therapy of cisplatin with poly (ADP-ribose) polymerase 1 (PARP1) inhibitors has been effective in increasing its efficacy at lower doses.

METHODS AND RESULTS

In this work, we have shown that the nitro-flavone derivative, 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO), can improve the sensitivity of cancer cells to cisplatin through inhibition of PARP1. The effect of 4NCO on cisplatin toxicity was studied through combination therapy in both exponential and density inhibited A375 melanoma cells. Combination index (CI) was determined from isobologram analysis. The mechanism of cell killing was assessed by lactate dehydrogenase (LDH) assay. Temporal nicotinamide adenine dinucleotide (NAD⁺) assay was done to show the inhibition of PARP1. We also performed in silico molecular modeling studies to know the binding mode of 4NCO to a modeled PARP1-DNA complex containing cisplatin-crosslinked adduct. The results from both in silico and in cellulo studies confirmed that PARP1 inhibition by 4NCO was most effective in sensitizing A375 melanoma cells to cisplatin. Isobologram analysis revealed that 4NCO reduced cell viability both in exponential and density inhibited A375 cells synergistically. The combination led to cell death through apoptosis.

CONCLUSION

The synthetic nitro-flavone derivative 4NCO effectively inhibited the important nuclear DNA repair enzyme PARP1 and therefore, could complement the DNA-damaging anticancer drug cisplatin in A375 cells and thus, could act as a potential adjuvant to cisplatin in melanoma therapy.

pH-dependent sedimentation of DNA in the presence of divalent, but not monovalent, metal ions

Precipitation of DNA is performed frequently in molecular biology laboratories for the purpose of purification and concentration of samples and also for transfer of DNA into cells. Metal ions are used to facilitate these processes, though their precise functions are not well characterized. In the current study we have investigated the precipitation of double-stranded DNA by group 1 and group 2 metal ions. Double-stranded DNAs were not sedimented efficiently by metals alone, even at high concentrations. Increasing the pH to 11 or higher caused strong DNA precipitation in the presence of the divalent group 2 metals magnesium, calcium, strontium and barium, but not group 1 metals. Group 2 sedimentation profiles were distinctly different from that of the transition metal zinc, which caused precipitation at pH 8. Analysis of DNAs recovered from precipitates formed with calcium revealed that structural integrity was retained and that sedimentation efficiency was largely size-independent above 400 bp. Several tests supported a model whereby single-stranded DNA regions formed by denaturation at high pH became bound by the divalent metal cations. Neutralization of negative surface charges reduced the repulsive forces between molecules, leading to formation of insoluble aggregates that could be further stabilized by cation bridging (ionic crosslinking).

A TD-DFT study of the excited dissociative electronic states of the DNA nucleobases bound to Li. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021;244:118862. [PMID: 32927359 DOI: 10.1016/j.saa.2020.118862]

In this work, the first and second dissociative potential curves of adenineLi⁺ (ADLi⁺), guanineLi⁺ (GUALi⁺), cytosineLi⁺(CYTLi⁺), and thymineLi⁺ (THYLi⁺) complexes, related to the dissociation of their LiO and LiN bonds, have been calculated in the gas phase and water, separately. For this purpose, the fifteen excited potential curves, in order of increasing energy, were calculated for each complex and the dissociative potential curves were distinguished from them considering the conical intersection points. The time-dependent density functional theory (TD-DFT) method employing the M06-2X functional was used for the calculations. It was observed that the electron transfer from the DNA base to the Li⁺ took place during the dissociation of complexes in the gas phase. The electrostatic field of water blocked this charge transfer and led to the excited DNA base and Li⁺ in its ground state. The vertical excitation energy for the desorption of the Li fragment as a neutral and cation species from the DNA bases was determined. The effect of the interaction site of Li⁺ on the dissociative potential curves was also investigated.

Mono and binuclear cobalt(II) mixed ligand complexes containing 1,10-phenanthroline and adenine using 1,3-diaminopropane as a spacer: synthesis, characterization, and antibacterial activity investigations

Background

Coordination compounds, in particular cobalt(II) mixed ligand complexes containing 1,10-phenantroline, have drawn the attention of many investigators as some of them are showing antimicrobial activities.

Result

Herein, we report three novel mixed ligand complexes of cobalt(II) having the formulae [Co(L1)2(H2O)2]Cl2, [Co(L1)2(L2)(H2O)]Cl2 and [Co2(L1)4(L2)2(L3)]Cl4 (L1 = 1,10-phenanthroline, L2 = adenine, L3 = 1,3-diaminepropane) were synthesized and characterized by elemental analysis, conductivity measurement, infrared, and UV-Vis spectroscopic techniques. Octahedral geometries are proposed to all the complexes. In vitro antibacterial activities of the ligands, salt, and metal complexes were tested on four pathogenic bacteria (Staphylococcus aureus, Salmonella typhus, Escherichia coli, and Staphylococcus epidermis) using disc diffusion method.

Conclusions

It is interesting to note that the newly synthesized cobalt(II) complexes are active against gram negative bacteria (Escherichia coli and Klebsiella pneumoniae) even though cobalt(II) complexes are well known for their activity against gram positive bacteria.

Are Titania Photocatalysts and Titanium Implants Safe? Review on the Toxicity of Titanium Compounds

Titanium and its compounds are broadly used in both industrial and domestic products, including jet engines, missiles, prostheses, implants, pigments, cosmetics, food, and photocatalysts for environmental purification and solar energy conversion. Although titanium/titania-containing materials are usually safe for human, animals and environment, increasing concerns on their negative impacts have been postulated. Accordingly, this review covers current knowledge on the toxicity of titania and titanium, in which the behaviour, bioavailability, mechanisms of action, and environmental impacts have been discussed in detail, considering both light and dark conditions. Consequently, the following conclusions have been drawn: (i) titania photocatalysts rarely cause health and environmental problems; (ii) despite the lack of proof, the possible carcinogenicity of titania powders to humans is considered by some authorities; (iii) titanium alloys, commonly applied as implant materials, possess a relatively low health risk; (iv) titania microparticles are less toxic than nanoparticles, independent of the means of exposure; (v) excessive accumulation of titanium in the environment cannot be ignored; (vi) titanium/titania-containing products should be clearly marked with health warning labels, especially for pregnant women and young children; (vi) a key knowledge gap is the lack of comprehensive data about the environmental content and the influence of titania/titanium on biodiversity and the ecological functioning of terrestrial and aquatic ecosystems.

Cisplatin adducts of DNA as precursors for nanostructured catalyst materials

The synthesis and characterisation of novel metal-modified DNA precursors for fuel cell catalyst development are described. Material precursors in the form of metal-DNA complexes were prepared through the reaction of DNA with cisplatin at various loadings and spectroscopically tested to confirm the platinum binding mode and the degree of complexation. The surface morphology of the DNA-metal material was analysed by Scanning Transmission Electron Microscopy (STEM), which revealed the extent of platinum nanocluster formation, with low metal loadings leading to observation of individual platinum atoms. Electrochemical measurements showed a greater electrocatalytic activity for the hydrogen evolution reaction (HER) with increased platinum loadings, shifting the half wave potential, E _1/2, away from the glassy carbon limit towards that of a bulk Pt electrode. This is explained further by Tafel plots, from which a change in the mechanism of the apparent rate limiting step for proton reduction from a Volmer to a Heyrovsky mechanism is postulated as the platinum loading increases.

Divalent metal ions and intermolecular interactions facilitate DNA network formation

The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn²⁺, Zn²⁺, Co²⁺, Ni²⁺, and Cd²⁺), except Mg²⁺ and Ca²⁺, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion-DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.

A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs

The structures and properties of metal cationized complexes of 9-ethylguanine (9eG) and 1-methylcytosine (1mC), (9eG:1mC)M⁺, where M⁺ = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ as well as the protonated complex, (9eG:1mC)H⁺, have been studied using a combination of IRMPD spectroscopy and computational methods. For (9eG:1mC)H⁺, the dominant structure is a Hoogsteen type complex with the proton covalently bound to N3 of 1mC despite this being the third best protonation site of the two bases; based on proton affinities N7 of 9eG should be protonated. However, this structural oddity can be explained considering both the number of hydrogen bonds that can be formed when N3 of 1mC is protonated as well as the strong ion-induced dipole interaction that exists between an N3 protonated 1mC and 9eG due to the higher polarizability of 9eG. The anomalous dissociation of (9eG:1mC)H⁺, forming much more (1mC)H⁺ than would be predicted based on the computed thermochemistry, can be explained as being due to the structural oddity of the protonation site and that the barrier to proton transfer from N3 of 1mC to N7 of 9eG grows dramatically as the base pair begins to dissociate. For the (9eG:1mC)M⁺; M = Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ complexes, single unique structures could not be assigned. However, the experimental spectra were consistent with the computed spectra. For (9eG:1mC)Li⁺, the lowest energy structure is one in which Li⁺ is bound to O6 of 9eG and both O2 and N3 of 1mC; there is also an interbase hydrogen bond from the amine of 1mC to N7 of 9eG. For Na⁺, K⁺, and Rb⁺, similar binding of the metal cation to 1mC is calculated but, unlike Li⁺, the lowest energy structure is one in which the metal cation is bound to N7 of 9eG; there is also an interbase hydrogen bond between the amine of 1mC and the carbonyl of 9eG. The lowest energy structure for the Cs complex is the Watson-Crick type base pairing with Cs⁺ binding only to 9eG through O6 and N7 and with three hydrogen bonds between 9eG and 1mC. It also interesting to note that the Watson-Crick base pairing structure gets lower in Gibbs energy relative to the lowest energy complexes as the metal gets larger. This indicates that the smaller, more densely charged cations have a greater propensity to interfere with Watson-Crick base pairing than do the larger, less densely charged metal cations.

Syntheses and crystal structures of new aurate salts of adenine or guanine nucleobases

Two new gold(III) complexes with adenine or guanine nitrogenous bases as counter-cations were synthesized. These are 6-amino-7H-purine-1,9-diium tetrachloridogold(III) chloride monohydrate, (C₅H₇N₅)[AuCl₄]Cl·H₂O, 1, and 2-amino-6-oxo-6,7-dihydro-1H-purin-9-ium tetrachloridogold(III) hemihydrate, (C₅H₆N₅O)[AuCl₄]·0.5H₂O, 2. Their crystal structures were studied using single-crystal X-ray diffraction and FT-IR spectroscopic techniques. The arrangement of species in the studied crystal structures implies π-stacking interactions, as well as concomitant C-H...π interactions, hydrogen bonds and other types of noncovalent interactions, which were studied qualitatively and quantitatively using the method of molecular Voronoi-Dirichlet polyhedra. The variation of the nitrogenous base from adenine to guanine results in evident differences in the packing of the species in the crystals of 1 and 2. The splitting and shifting of bands in the FT-IR spectra of the title compounds reveals several features representative of noncovalent interactions in their crystal structures.

Characterization and application of fluidic properties of trinucleotide repeat sequences by wax-on-plastic microfluidics

Trinucleotide repeat (TNR) sequences introduce sequence-directed flexibility in the genomic makeup of all living species leading to unique non-canonical structure formation. In humans, the expansions of TNR sequences are responsible for almost 24 neurodegenerative and neuromuscular diseases because their unique structures disrupt cell functions. The biophysical studies of these sequences affect their electrophoretic mobility and spectroscopic signatures. Here, we demonstrate a novel strategy to characterize and discriminate the TNR sequences by monitoring their capillary flow in the absence of an external driving force using wax-on-plastic microchannels. The wax-on-plastic microfluidic system translates the sequence-directed flexibility of TNR into differential flow dynamics. Several variables were used to characterize sequences including concentration, single- vs. double-stranded samples, type of repeat sequence, length of the repeat sequence, presence of mismatches in duplex, and presence of metal ion. All these variables were found to influence the flow velocities of TNR sequences as these factors directly affect the structural flexibility of TNR at the molecular level. An overall trend was observed as the higher flexibility in the TNR structure leads to lower capillary flow. After testing samples derived from relevant cells harboring expanded TNR sequences, it is concluded that this approach may transform into a reagent-free and pump-free biosensing platform to detect microsatellite expansion diseases.

Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects

Classical molecular dynamics simulations reveal size-dependent trends of alkaline earth metal ions binding to DNA are due to ion size and hydration behavior.

Silver-Mediated Homochiral and Heterochiral α-dC/β-dC Base Pairs: Synthesis of α-dC through Glycosylation and Impact of Consecutive, Isolated, and Multiple Metal Ion Pairs on DNA Stability

Isolated and consecutive heterochiral α-dC- base pairs have been incorporated into 12-mer oligonucleotide duplexes at various positions, thereby replacing Watson-Crick pairs. To this end, a new synthesis of the α-d anomer of dC has been developed, and oligonucleotides containing α-dC residues have been synthesized. Silver-mediated base pairs were formed upon the addition of silver ions. Furthermore, we have established that heterochiral α-dC-dC base pairs can approach the stability of a Watson-Crick pair, whereas homochiral dC-dC pairs are significantly less stable. A positional change of the silver-mediated base pairs affects the duplex stability and reveals the nearest-neighbor influence. When the number of silver ions was equivalent to the number of duplex base pairs (12), non-melting silver-rich complexes were formed. Structural changes have been supported by circular dichroism (CD) spectra, which showed that the B-DNA structure was maintained whilst the silver ion concentration was low. At high silver ion concentration, silver-rich complexes displaying different CD spectra were formed.

Multivalent Cation-Induced Actuation of DNA-Mediated Colloidal Superlattices

Nanoparticles functionalized with DNA can assemble into ordered superlattices with defined crystal habits through programmable DNA "bonds". Here, we examine the interactions of multivalent cations with these DNA bonds as a chemical approach for actuating colloidal superlattices. Multivalent cations alter DNA structure on the molecular scale, enabling the DNA "bond length" to be reversibly altered between 17 and 3 nm, ultimately leading to changes in the overall dimensions of the micrometer-sized superlattice. The identity, charge, and concentration of the cations each control the extent of actuation, with Ni²⁺ capable of inducing a remarkable >65% reversible change in crystal volume. In addition, these cations can increase "bond strength", as evidenced by superlattice thermal stability enhancements of >60 °C relative to systems without multivalent cations. Molecular dynamics simulations provide insight into the conformational changes in DNA structure as the bond length approaches 3 nm and show that cations that screen the negative charge on the DNA backbone more effectively cause greater crystal contraction. Taken together, the use of multivalent cations represents a powerful strategy to alter superlattice structure and stability, which can impact diverse applications through dynamic control of material properties, including the optical, magnetic, and mechanical properties.