DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays

Cutting-edge nanotechnology: unveiling the role of zinc oxide nanoparticles in combating deadly gastrointestinal tumors

Zinc oxide nanoparticles (ZnO-NPs) have gained significant attention in cancer therapy due to their unique physical and chemical properties, particularly in treating gastrointestinal (GI) cancers such as gastric, colorectal, and hepatocellular carcinoma. These nanoparticles generate reactive oxygen species (ROS) upon entering cancer cells, causing oxidative stress that leads to cellular damage, DNA fragmentation, and apoptosis. ZnO-NPs affect the expression of key proteins involved in apoptosis, including p53, Bax, and Bcl-2, which regulate cell cycle arrest and programmed cell death. Additionally, ZnO-NPs can reduce mitochondrial membrane potential, further enhancing apoptosis in cancer cells. Furthermore, ZnO-NPs inhibit cancer cell proliferation by interfering with cell cycle progression. They reduce levels of cyclins and cyclin-dependent kinases (CDKs), leading to cell cycle arrest. ZnO-NPs also exhibit anti-metastatic properties by inhibiting the migration and invasion of cancer cells through modulation of signaling pathways that affect cell adhesion and cytoskeletal dynamics. The efficacy of ZnO-NPs in overcoming chemotherapy resistance has been demonstrated by their ability to reduce the IC50 values of chemotherapeutic agents, making cancer cells more susceptible to drug-induced cell death. In this review, we summarize the mechanisms by which ZnO-NPs exert anticancer effects in GI cancers, focusing on apoptosis, cell cycle regulation, and metastasis inhibition, while also highlighting the current limitations in translating these findings into effective clinical treatments.

Toxicity, Antibacterial, Antioxidant, Antidiabetic, and DNA Cleavage Effects of Dextran-Graft-Polyacrylamide/Zinc Oxide Nanosystems

Synthesis of metal oxide nanoparticles-polymer nanocomposites is an emerging strategy in nanotechnology to improve targeted delivery and reduce the toxicity of nanoparticles. In this study, we report biological effects of previously described hybrid nanocomposites containing dextran-graft-polyacrylamide/zinc oxide nanoparticles (D-PAA/ZnO NPs) prepared from zinc sulfate (D-PAA/ZnONPs(SO42-)) and zinc acetate (D-PAA/ZnONPs(-OAc)) focusing primarily on their antimicrobial activity. D-PAA/ZnONPs(SO42-) and D-PAA/ZnONPs(-OAc) nanosystems were tested in a complex way to assess their antioxidant activity (DPPH assay), antidiabetic potential (α-amylase inhibition), DNA cleavage activity, antimicrobial, and antibiofilm activity. In addition, the toxicity of D-PAA/ZnONPs(SO42-) and D-PAA/ZnONPs(-OAc) nanosystems against primary murine splenocytes was tested using MTT assay. The studied nanosystems inhibited E.coli growth. For all the investigated strains, minimum inhibitory concentrations (MICs) of D-PAA/ZnONPs(SO42-) and D-PAA/ZnONPs(-OAc) were in the range of 8 mg/L-128 mg/L and 16 mg/L-128 mg/L, respectively. The nanocomposites demonstrated effective antibiofilm properties as 94.27% and 86.43%. The compounds showed good antioxidant, anti-α-amylase, and DNA cleavage activities. D-PAA/ZnONPs(SO42-) and D-PAA/ZnONPs(-OAc) nanosystems reduced cell viability and promoted cell death of primary murine spleen cells at concentrations higher than those that proved to be antibacterial indicating the presence of therapeutic window. D-PAA/ZnONPs(SO42-) and D-PAA/ZnONPs(-OAc) nanosystems show antioxidant, antidiabetic, DNA cleavage, antimicrobial, and antibiofilm activity against the background of good biocompatibility suggesting the presence of therapeutic potential, which should be further investigated in vivo.

A comprehensive adsorption and desorption study on the interaction of DNA oligonucleotides with TiO2 nanolayers

The utilization of TiO2 nanolayers that possess excellent biocompatibility and physical properties in DNA sensing and sequencing remains largely to be explored. To examine their applicability in gene sequencing, a comprehensive study on the interaction of DNA oligonucleotides with TiO2 nanolayers was performed through adsorption and desorption experiments. TiO2 nanolayers with 10 nm thickness were fabricated via magnetron sputtering onto a 6-inch silicon wafer. A simple chip block method, validated via quartz crystal microbalance experiments with dissipation monitoring (QCM-D), was proposed to study the adsorption behaviors and interaction mechanisms under a variety of critical influencing factors, including DNA concentration, length, and type, adsorption time, pH, and metal ions. It is determined that the adsorption takes 2 h to reach saturation in the MES solution and the adsorption capacity is significantly enhanced by lowering the pH due to the isoelectric point being pH = 6 for TiO2. The adsorption percentages of nucleobases are largely similar in the MES solution while following 5T = 5G > 5C > 5A in HEPES buffer for an adsorption duration of 2.5 h. Through pre-adsorption experiments, it is deduced that DNA oligonucleotides are horizontally adsorbed on the nanolayer. This further demonstrates that mono-, di-, and tri-valent metal ions promote the adsorption, whereas Zn2+ has strong adsorption by inducing DNA condensation. Based on the desorption experiments, it is revealed that electrostatic force dominates the adsorption over van der Waals force and hydrogen bonds. The phosphate group is the main functional group for adsorption, and the adsorption strength increases with the length of the oligonucleotide. This study provides comprehensive data on the adsorption of DNA oligonucleotides onto TiO2 nanolayers and clarifies the interaction mechanisms therein, which will be valuable for applications of TiO2 in DNA-related applications.

ZnO nanostructures: A promising frontier in immunosensor development

This review addresses the design of immunosensors, which employ ZnO nanostructures. Various methods of modifying ZnO nanostructures with antibodies or antigens are discussed, including covalent and non-covalent approaches and cross-linking techniques. Immunosensors based on different properties of ZnO nanomaterials are described and compared. This article provides a comprehensive review of electrochemical immunosensors based on ZnO nanostructures and various detection techniques, including cyclic voltammetry (CV), differential pulse voltammetry (DPV), photoelectrochemical (PEC) detection, electrochemical impedance spectroscopy (EIS), and other electrochemical methods. In addition, this review article examines the application of optical detection techniques, including photoluminescence (PL) and electrochemiluminescence (ECL), in the development of immunosensors based on ZnO nanostructures.

Encapsulation of ZnO and Ho:ZnO Nanoparticles in the Core of Wrinkled Mesoporous Silica

Wrinkled mesoporous silica (WMS) has a flower- or dendritic-like morphology, tunable pore size, and highly ordered and accessible three-dimensional (3D) pore structures. In this research, a method to encapsulate semiconductor nanoparticles in the core of the wrinkled mesoporous silica during synthesis is described. Highly uniform zinc oxide and holmium-doped zinc oxide nanoparticles have been synthesized by a sonochemical method. Zinc oxide and holmium-doped zinc oxide nanoparticles have been encapsulated in wrinkled mesoporous silica during synthesis. The ZnO@WMS and Ho:ZnO@WMS particles have been characterized by transmission electron microscopy (TEM), scanning electron microscopy (SEM), UV-vis spectroscopy, fluorescence, dynamic light scattering (DLS), confocal microscopy, and X-ray diffraction (XRD).

Nano zinc Oxide-Ruthenium (III) complex of novel coumarin derivative: Synthesis, Characterization, DNA Cleavage, anticancer and bioimaging activities

The uniqueness of nanofunctionalized metal complexes would play a prominent role in medicinal chemistry, especially in cancer chemotherapy. Among the metal based chemotherapeutic drugs, ruthenium complexes exhibit different oxidation states, lower toxicity and remarkable antitumor activities than other anticancer drugs. In this investigation bioactive ruthenium(III) complex has been synthesized from novel coumarin derivative and it is functionalized with nanostructured zinc oxide (ZnO) under well defined condition. An octahedral geometry is proposed for the ruthenium complex based on analytical and spectrochemical characterization techniques (UV, FT-IR and NMR). The g|| and g⊥ values obtained from the ESR spectrum indicated high symmetry and octahedral field around ruthenium ion. The XRD patterns of all synthesized compounds explicit average particle sizes are nanometer range. The morphology and particle size of Nano ZnO-Ru(III) complex is also confirmed by using SEM and TEM analysis. The nanofunctionalized material exhibited enhanced fluorescence emissions at 674 nm and 681 nm. The evaluation of DNA cleavage study indicated compounds were effectively cleaved supercoiled pUC18 DNA by gel electrophoresis method. The examinations of in-vitro anticancer activities of compounds were studied against human breast (MCF-7) and leukemia (K-562) cancer cell lines. The ruthenium complex showed greater effect against MCF-7 with < 10 IC50 value. Nowadays, the cell imaging property of nanofunctionalized materials receive more attention. The fluorescence microscopic images of Nano ZnO-Ru(III) complex displayed higher luminescence at 100 μg/ mL against L6 rat skeletal muscle cell line.

Enhancement of Salmonella Enteritidis Detection Using Nanoparticle-Assisted Real-Time Polymerase Chain Reaction

Improved; fast; and specific detection of pathogens has always been of great importance; more so with the increase of human population and human interaction. In this work we investigate the application of metal oxide nanoparticles (ZnO; Fe2O3; and TiO2) in the detection of the pathogen Salmonella enteritidis using real-time quantitative PCR (qPCR). The nanoparticles were synthesized and characterized; and then they were added at different concentrations to qPCR for Salmonella enteritidis detection. qPCR provides numerical data such as threshold cycle (Ct); efficiency; and DNA yield which make comparing the different tested conditions easier and more accurate. It has been observed that adding all three types of NPs at an optimum concentration 4×10−11 M for ZnO NPs, and 4×10−9 for Fe2O3 and TiO2 nanoparticles has led to increasing the efficiency of the reaction to 100% and to lowering the threshold cycle value by up to 6.6 for ZnO nanoparticles; hence increasing the DNA yield of the reaction; and lowering the detection time of the pathogen by up to 50%.

Zn2+ -Coordination-Driven RNA Assembly with Retained Integrity and Biological Functions

Metal-coordination-directed biomolecule crosslinking in nature has been used for synthesizing various biopolymers, including DNA, peptides, proteins, and polysaccharides. However, the RNA biopolymer has been avoided so far, as due to the poor stability of the RNA molecules, the formation of a biopolymer may alter the biological function of the molecules. Herein, for the first time, we report Zn²⁺ -driven RNA self-assembly forming spherical nanoparticles while retaining the integrity and biological function of RNA. Various functional RNAs of different compositions, shapes, and lengths from 20 to nearly 1000 nucleotides were used, highlighting the versatility of this approach. The assembled nanospheres possess a superior RNA-loading efficiency, pharmacokinetics, and bioavailability. In-vitro and in-vivo evaluation demonstrated mRNA delivery for expressing GFP proteins, and microRNA delivery to triple-negative breast cancer. This coordination-directed self-assembly behavior amplifies the horizons of RNA coordination chemistry and the application scope of RNA-based therapeutics.

Oxygen vacancy assisted condensation of DNA molecule observed on ZnO thin film

An exotic condensation of DNA molecules is observed on the nanostructured ZnO surface. The ZnO nanostructures (NS) fabricated by thermal vapor deposition technique were associated with a large number of oxygen vacancies on the surface. These oxygen vacancies induced changes in the DNA conformation which further reflected through changes in the persistence length of the DNA molecules. This indicates a reinforcement of the bonds and binding in both the phosphate and the base regions of the DNA molecules with the positively charged core vacancy sites on the ZnO nanostructured surface through strong interaction mediated via long-range electrostatic forces which effectively reduced the end-to-end distance of the λ-DNA molecule. This strongly suggests a transition of the λ-DNA molecule through structural modification into a more compact higher-order fractal dimension from its native state.

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.

Metal-Doped Polydopamine Nanoparticles for Highly Robust and Efficient DNA Adsorption and Sensing

Controlling DNA adsorption on nanomaterials is crucial for a wide range of applications in analytical and biomedical sciences. Polydopamine (PDA) is a versatile material that can be coated on nearly any surface, and thus adsorbing DNA onto PDA can be a general method for indirect DNA functionalization of surfaces. Polyvalent metal ions were reported to promote DNA adsorption on PDA nanoparticles (NPs), but previous works added the metal ions after the formation of PDA. Herein, we compared the effect of polyvalent metal ions added during the synthesis of PDA NPs (called metal-doped) with the effect of polyvalent metal ions added after the synthesis (metal-adsorbed). A series of metal ions including Ca²⁺, Zn²⁺, Ni²⁺, Fe³⁺, and Gd³⁺ were tested, and Zn²⁺ was studied in detail due to its excellent ability for promoting DNA adsorption. With 100 μM Zn²⁺, metal-doped NPs were ∼30% more efficient than metal-adsorbed NPs for DNA adsorption in buffer attributable to a higher metal loading on the surface of the metal-doped NPs. Metal leaching was negligible from the metal-doped NPs, and they showed a remarkably higher robustness than the metal-adsorbed NPs, resulting in a 20-fold higher DNA extraction efficiency from serum. Based on the desorption studies, a higher adsorption affinity for the metal-doped NPs was confirmed. Finally, the Zn²⁺-doped PDA NPs were used for sensitive DNA detection with a limit of detection of 0.45 nM, and the sensor was highly resistant to nonspecific protein and phosphate displacement.

Guanosine-rich aptamers@Cu2O nanoparticles: enhanced peroxidase activity and specific recognition capability at neutral pH

The decoration of Cu2O nanoparticles with guanosine-rich aptamers can significantly enhance their peroxidase activity at neutral pH and endow them with specific recognition capabilities. Both the phosphate backbone and guanine of the aptamers contribute to the enhancement. The excellent enzyme-like properties of this Cu2O-aptamer system make it a versatile platform for the development of neutral pH biosensors.

Sensing ATP: Zeolitic Imidazolate Framework-67 Is Superior to Aptamers for Target Recognition

In a typical biosensor, a biomolecule such as an aptamer is used for target recognition, and a nanomaterial is used for signal generation. Herein, we communicate a reverse system using a nanomaterial for target recognition and a DNA for signaling. We discovered that a classic metal-organic framework material, zeolitic imidazolate framework (ZIF)-67, has ultrahigh selectivity for recognizing adenosine triphosphate (ATP), allowing a fluorescently labeled DNA oligonucleotide to be used for signal generation. This sensor showed up to a 24-fold increase in fluorescence upon adding 1 mM ATP, while the fluorescence increase after adding adenosine or guanosine triphosphate was less than twofold. Its selectivity is much better than that of the ATP aptamer, which binds adenosine even better. Using isothermal titration calorimetry, the selective binding of ATP was independently verified. This sensor has a detection limit of 29 nM ATP and it can even detect ATP in serum. By replacing Co²⁺ with Zn²⁺ to form ZIF-8 or by using CoO, the selectivity for ATP was lost. Therefore, by sophisticated material design, ultrahigh selectivity for molecular recognition can be achieved.

Polyvalent Metal Ion Promoted Adsorption of DNA Oligonucleotides by Montmorillonite

Montmorillonite (MMT) is a two-dimensional (2D) clay material. Its abundance on the early earth has attracted studies for its role in prebiotic reactions, and adsorption of DNA to MMT is potentially important for understanding the origin of life. Although several possible models of DNA adsorption on MMT have been established, a consensus on the adsorption mechanism has yet to be formed, thereby a fundamental adsorption study is performed here. Adding up to 300 mM NaCl failed to promote DNA adsorption on MMT, Al₂O₃, or SiO₂ nanoparticles. For polyvalent metals, DNA adsorption was achieved following the order Ce³⁺ > Cu²⁺ > Ni²⁺ > Zn²⁺. Among them, Ce³⁺ and Cu²⁺ inverted the surface charge of MMT to positive. In addition, using washing experiments, Cu²⁺- and Ce³⁺-mediated adsorption mainly depended on the DNA phosphate backbone, while Ni²⁺ and Zn²⁺ interacted with the backbone phosphate groups and adenine bases of DNA. Overall, these polyvalent metal ions promoted DNA adsorption via a cation bridge model. This research provides new insights into the surface interactions of MMT and DNA, which is conducive to future work on the interaction between clays and biopolymers.

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications

Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn²⁺ is a very important one among them. Zn²⁺ has good biocompatibility and can be used for intracellular applications. Chemically, Zn²⁺ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn²⁺ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn²⁺ a unique cofactor for DNAzyme reactions. This review summarizes Zn²⁺ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn²⁺ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn²⁺ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn²⁺ , which can facilitate practical applications of Zn²⁺ -dependent DNAzymes.

Promoting DNA Adsorption by Acids and Polyvalent Cations: Beyond Charge Screening

Adsorbing DNA oligonucleotides onto nanoparticles is the first step in developing DNA-based biosensors, drug delivery systems, and smart materials. Since DNA is a polyanion, it is repelled by negatively charged nanoparticles, which constitute the majority of commonly used nanomaterials. Adding salt such as NaCl to screen charge repulsion is a standard method of promoting DNA adsorption. However, Na⁺ does not supply additional attractive forces. In addition, adding a high concentration of NaCl can cause the aggregation of nanomaterials. In this feature article, we mainly summarize the methods developed in our laboratory to promote DNA adsorption by lowering the pH and by adding polyvalent metal ions, especially transition-metal ions. Various materials including noble metals (gold, silver, and platinum), 2D materials (graphene oxide, MoS₂, WS₂, and MXene), polydopamine, and several metal oxides are discussed. In general, low pH can protonate DNA bases and nanoparticle surfaces, reducing charge repulsion and even leading to attraction, although DNA folding at low pH can sometimes be detrimental to adsorption. Polyvalent metal ions can bridge additional interactions to achieve otherwise impossible adsorption. On the basis of the current understanding, a few future research directions are proposed to further improve DNA adsorption.

Selected DNA aptamers as hydroxyapatite affinity reagents

DNA aptamers were selected for their ability to bind specifically and quickly to crystalline hydroxyapatite (Ca₁₀(PO₄)₆(OH)₂; HAP), the primary mineral component of enamel and bone. Aptamers were found to have an enhanced percent of G-nucleotides and a propensity for forming a G-quadruplex secondary structure. One aptamer was studied in comparison to control sequences and was found to bind with high affinity and at high loading capacity, with enhanced binding kinetics, and with specificity for crystalline HAP material over amorphous calcium phosphate (ACP) and β-tricalcium phosphate (TCP). The fluorescently-functionalized aptamer was demonstrated to specifically label HAP in a surface binding experiment and suggests the usefulness of this selected aptamer in biomedical or biotechnology fields where the labeling of specific calcium phosphate materials is required.

Leakage and Rupture of Lipid Membranes by Charged Polymers and Nanoparticles

Understanding and controlling the interactions between lipid membranes and nanomaterials are important for drug delivery, toxicity studies, and sensing. In the literature, the perception is that cationic nanomaterials can damage lipid membranes, although some reports suggest the opposite. In this work, instead of using different materials for testing the effect of charge, we used the same material and adjusted the pH. A total of three types of liposomes including zwitterionic phosphocholine (PC) and negatively charged phosphoserine (PS) with saturated and unsaturated tails were tested with three types of metal oxide nanoparticles and two types of cationic polymers. A calcein leakage assay was used to probe membrane leakage. We found that cationic polymers had very little advantage for leaking PC liposomes. On the other hand, the PS liposomes were leaked by TiO₂ nanoparticles regardless of their charge tuned by pH. ZnO with a high pK_a value was studied in detail, and it only leaked the 1,2-dioleoyl-sn-glycero-3-phosphocholine liposomes at low pH when ZnO was positively charged, but leakage was inhibited by adding NaCl to weaken electrostatic attraction and by capping ZnO. In addition, dissolution of adsorbed ZnO also caused leakage, suggesting that adsorption and desorption induced reversible lipid phase transitions. Overall, the interaction strength was a key factor for leakage. Leakage does not necessarily mean membrane damage, and cryogenic transmission electron microscopy was used to study membrane integrity. Previously observed cationic polymer/nanoparticle-induced damages in supported membranes could be due to electrostatic attraction between the polymers and the underlying negatively charged supporting surface.

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.

Zinc oxide nanoparticles for therapeutic purposes in cancer medicine

Zinc oxide nanoparticles are characterized by a good biocompatibility while providing a versatile potential as innovative therapeutic agents in cancer medicine.

The Two Classic Pb2+ -Selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity

In 1994, the first DNAzyme named GR5 was reported, which specifically requires Pb²⁺ for its RNA cleavage activity. Three years later, the 8-17 DNAzyme was isolated. The 8-17 DNAzyme and the related 17E DNAzyme are also most active with Pb²⁺ , although other divalent metals can work as well. GR5 and 17E have the same substrate sequence, and their catalytic loops in the enzyme strands also have a few similar and conserved nucleotides. Considering these, we hypothesized that 17E might be a special form of GR5. To test this hypothesis, we performed systematic rational evolution experiments to gradually mutate GR5 toward 17E. By using the activity ratio in the presence of Pb²⁺ and Mg²⁺ for defining these two DNAzymes, the critical nucleotide was identified to be T₁₂ in 17E for metal specificity. In addition, G₉ in GR5 is a position not found in most 17E or 8-17 DNAzymes, and G₉ needs to be added to rescue GR5 activity if T₁₂ becomes a cytosine. This study highlights the links between these two classic and widely used DNAzymes, and offers new insight into the sequence-activity relationship related to metal selectivity.

Nanoceria as a DNase I mimicking nanozyme

We herein communicate the DNase I like activity of nanoceria (CeO2 nanoparticles). Both CeO2 and DNase I cleave polyadenine (poly-A) DNA down to ∼5-mer fragments as the major products, although further cleavage to even shorter fragments was observed with CeO2. Mass spectrometry indicates a hydrolytic cleavage mechanism instead of oxidative cleavage.

Growing a Nucleotide/Lanthanide Coordination Polymer Shell on Liposomes

Coating liposomes with a shell is a useful strategy to increase membrane stability and prevent leakage or fusion. Nucleotide/lanthanide coordination nanoparticles (NPs) are formed by a simple mixing at ambient conditions. Because some lipid headgroups contain lanthanide binding ligands, they may direct the growth of such coordination NPs. Herein, a gadolinium/adenosine monophosphate (Gd³⁺/AMP) shell was formed on liposomes (liposome@Gd³⁺/AMP) using lipids containing phosphoserine (PS) or cholinephosphate (CP) headgroups, while phosphocholine liposomes did not support the shell. Liposome binding Gd³⁺ is confirmed by transmission electron microscopy (TEM). The negatively charged CP and PS liposomes reversed to positive upon Gd³⁺ binding, while other metals such as Ca²⁺ and Zn²⁺ did not reverse the charge. Binding of Gd³⁺ did not leak the PS liposomes. Then, AMP was further added to cross-link Gd³⁺ on the liposome surface. A shell was formed as indicated by TEM, and the content inside the liposome remained for the PS liposomes. While adding Triton X-100 still induced leakage of the encapsulated liposomes, the shell protected the liposomes from leakage induced by ZnO NPs, suggesting a porous structure of the Gd³⁺/AMP shell which allowed penetration of Triton X-100 but not the larger ZnO NPs. This work provides a simple method to coat liposomes, and also offers a fundamental understanding of liposome adsorption of lanthanide ions.

Nonviolent Self-Catabolic DNAzyme Nanosponges for Smart Anticancer Drug Delivery

The development of self-assembled DNA nanomedicine requires a facile and accurate DNA degradation strategy for precisely programmable drug release. Conventional DNA catabolic strategies are restrained with the fragile and unclear enzymatic reactions that might lead to inefficient and uncontrollable digestion of DNA scaffolds and thus might bring undesirable side effects to the sophisticated biosystems. Herein we reported a versatile self-sufficient DNAzyme-driven drug delivery system consisting of the rolling circle polymerized DNAzyme-substrate scaffolds and the encapsulated pH-responsive ZnO nanoparticles (NPs). The full DNAzyme nanosponges (NSs) were also encoded with multivalent tandem aptamer sequences to facilitate their efficient delivery into cancer cells, where the acidic endo/lysosomal microenvironment stimulates the dissolution of ZnO into Zn²⁺ ions as DNAzyme cofactors and therapeutic reactive oxygen species generators. The supplement Zn²⁺ cofactors mediated the nonviolent DNAzyme-catalyzed cleavage of DNA scaffolds for precise and efficient drug administrations with synergistically enhanced therapeutic performance. The facile design of DNAzyme, together with their cost-effective and intrinsic robust features, is anticipated to provide extensive insights for the development of DNA-based therapeutic platforms by activating the specific intracellular biocatalytic reactions. As an intelligent and nonviolent self-driven drug delivery platform, the present DNAzyme NS system could be engineered with more therapeutic sequences and agents and was anticipated to show exceptional promise and versatility for applications in biomedicine and bioengineering.

DNA-Functionalized Nanoceria for Probing Oxidation of Phosphorus Compounds

Chemical reactions without an obvious optical signal change, such as fluorescence or color, are difficult to monitor. Often, more advanced analytical techniques such as high-performance liquid chromatography and mass spectroscopy are needed. It would be useful to convert such reactions to those with changes in optical signals. In this work, we demonstrate that fluorescently labeled DNA oligonucleotides adsorbed on nanomaterials can probe such reactions, and oxidation of phosphorus-containing species was used as an example. Various metal oxides were tested, and CeO2 nanoparticles were found to be the most efficient for this purpose. Among phosphate, phosphite, and hypophosphite, only phosphate produced a large signal, indicating its strongest adsorption on CeO2 to displace the DNA. This was further used to screen oxidation agents to convert lower oxidation-state compounds to phosphate, and bleach was found to be able to oxidize phosphite. Canonical discriminant analysis was performed to discriminate various phosphorus species using a sensor array containing different metal oxides. On the basis of this, glyphosate was studied for its adsorption and oxidation. Although this method is not specific enough for selective biosensors, it is useful as a tool to produce sensitive optical signals to follow important chemical transformations.

Graphene quantum dots in alveolar macrophage: uptake-exocytosis, accumulation in nuclei, nuclear responses and DNA cleavage

BACKGROUND

Given the tremendous potential for graphene quantum dots (QDs) in biomedical applications, a thorough understanding of the interaction of these materials with macrophages is essential because macrophages are one of the most important barriers against exogenous particles. Although the cytotoxicity and cellular uptake of graphene QDs were reported in previous studies, the interaction between nuclei and the internalized graphene QDs is not well understood. We thus systematically studied the nuclear uptake and related nuclear response associated with aminated graphene QDs (AG-QDs) exposure.

RESULTS

AG-QDs showed modest 24-h inhibition to rat alveolar macrophages (NR8383), with a minimum inhibitory concentration (MIC) of 200 μg/mL. Early apoptosis was significantly increased by AG-QDs (100 and 200 μg/mL) exposure and played a major role in cell death. The internalization of AG-QDs was mainly via energy-dependent endocytosis, phagocytosis and caveolae-mediated endocytosis. After a 48-h clearance period, more than half of the internalized AG-QDs remained in the cellular cytoplasm and nucleus. Moreover, AG-QDs were effectively accumulated in nucleus and were likely regulated by two nuclear pore complexes genes (Kapβ2 and Nup98). AG-QDs were shown to alter the morphology, area, viability and nuclear components of exposed cells. Significant cleavage and cross-linking of DNA chains after AG-QDs exposure were confirmed by atomic force microscopy investigation. Molecular docking simulations showed that H-bonding and π-π stacking were the dominant forces mediating the interactions between AG-QDs and DNA, and were the important mechanisms resulting in DNA chain cleavage. In addition, the generation of reactive oxygen species (ROS) (e.g., •OH), and the up-regulation of caspase genes also contributed to DNA cleavage.

CONCLUSIONS

AG-QDs were internalized by macrophages and accumulated in nuclei, which further resulted in nuclear damage and DNA cleavage. It is demonstrated that oxidative damage, direct contact via H-bonding and π-π stacking, and the up-regulation of caspase genes are the primary mechanisms for the observed DNA cleavage by AG-QDs.

One-dimensional vs. two-dimensional proton transport processes at solid-liquid zinc-oxide-water interfaces

Neural network molecular dynamics simulations unravel the long-range proton transport properties of ZnO–water interfaces.

Long-range charge transport is important for many applications like batteries, fuel cells, sensors, and catalysis. Obtaining microscopic insights into the atomistic mechanism is challenging, in particular if the underlying processes involve protons as the charge carriers. Here, large-scale reactive molecular dynamics simulations employing an efficient density-functional-theory-based neural network potential are used to unravel long-range proton transport mechanisms at solid–liquid interfaces, using the zinc oxide–water interface as a prototypical case. We find that the two most frequently occurring ZnO surface facets, (101[combining macron]0) and (112[combining macron]0), that typically dominate the morphologies of zinc oxide nanowires and nanoparticles, show markedly different proton conduction behaviors along the surface with respect to the number of possible proton transfer mechanisms, the role of the solvent for long-range proton migration, as well as the proton transport dimensionality. Understanding such surface-facet-specific mechanisms is crucial for an informed bottom-up approach for the functionalization and application of advanced oxide materials.

Sequence-Specific Control of Inorganic Nanomaterials Morphologies by Biomolecules

Controlling morphologies of nanomaterials such as their shapes and surface features has been a major endeavor in the field of nanoscale science and engineering, because the morphology is a major determining factor for functional properties of nanomaterials. Compared with conventional capping ligands based on organic molecules or polymers, the programmability of biomolecules makes them attractive alternatives for morphology-controlled nanomaterials synthesis. Towards the goal of predictable control of the synthesis, many studies have been performed on using different sequences of biomolecules to generate specific nanomaterial morphology. In this review, we summarize recent studies in the past few years on using DNA and peptide sequences to control inorganic nanomaterial morphologies, focusing on both case studies and mechanistic investigations. The functional properties resulting from such a sequence-specific control are also discussed, along with strengths and limitations of different approaches to achieving the goal.

NiO Nanoparticles for Exceptionally Stable DNA Adsorption and Its Extraction from Biological Fluids

Selective extraction of a small amount of nucleic acids from complex biological samples containing a high concentration of proteins is critical for bioanalytical chemistry. A number of previously published studies have focused on long, double-stranded DNA such as plasmid DNA. On the other hand, we are interested in short oligonucleotides. Nucleic acids have a negatively charged phosphate backbone that interacts with metal oxides strongly, and this may be used to distinguish them from proteins. In this work, a few metal oxide nanoparticles were screened, including NiO, CoO, ZnO, TiO₂, CeO₂, and Fe₃O₄ for DNA recovery. NiO had the highest DNA adsorption efficiency from mixtures containing bovine serum albumin or human blood serum. The adsorption of DNA by NiO was further characterized as a function of the pH, salt concentration, DNA length, and DNA sequence. The adsorption mechanism was studied by adding competing chemicals or denaturing agents. A striking observation was the extremely high adsorption affinity of NiO, much higher than that of the other tested oxides. Polyphosphate was the most effective agent for displacing adsorbed DNA, whereas simple inorganic phosphate was less effective. NiO was able to concentrate DNA from a serum mixture by 33- to 55-fold, depending on the serum concentration. NiO is thus a promising candidate for extracting DNA from biological samples.

Fluorescent ZnO-Au Nanocomposite as a Probe for Elucidating Specificity in DNA Interaction

In this work, we report the interaction of a fluorescent ZnO-Au nanocomposite with deoxyribonucleic acid (DNA), leading to AT-specific DNA interaction, which is hitherto not known. For this study, three natural double-stranded (ds) DNAs having different AT:GC compositions were chosen and a ZnO-Au nanocomposite has been synthesized by anchoring a glutathione-protected gold nanocluster on the surface of egg-shell-membrane (ESM)-based ZnO nanoparticles. The ESM-based bare ZnO nanoparticles did not show any selective interaction toward DNA, whereas intrinsic fluorescence of the ZnO-Au nanocomposite shows an appreciable blue shift (Δλ_max = 18 nm) in the luminescence wavelength of 520 nm in the presence of ds calf thymus (CT) DNA over other studied DNAs. In addition, the interaction of the nanocomposite through fluorescence studies with single-stranded (ss) CT DNA, synthetic polynucleotides, and nucleobases/nucleotides (adenine, thymine, deoxythymidine monophosphate, deoxyadenosine monophosphate) was also undertaken to delineate the specificity in interaction. A minor blue shift (Δλ_max = 5 nm) in the emission wavelength at 520 nm was observed for single-stranded CT DNA, suggesting the proficiency of the nanocomposite for discriminating ss and ds CT DNA. More importantly, fluorescence signals from the nano-bio-interaction could be measured directly without any modification of the target, which is the foremost advantage emanated from this study compared with other previous reports. The AT base-pair-induced enhancement was also found to be highest for the melting temperature of CT DNA (ΔT_mCT = 6.7 °C). Furthermore, spectropolarimetric experiments followed by calorimetric analysis provided evidence for specificity in AT-rich DNA interaction. This study would lead to establish the fluorescent ZnO-Au nanocomposite as a probe for nanomaterial-based DNA-binding study, featuring its specific interaction toward AT-rich DNA.

Adsorption of Phosphate and Polyphosphate on Nanoceria Probed by DNA Oligonucleotides

Phosphate-containing molecules exist in many forms in biology and the environment, and their interaction with metal oxides is an important aspect of their chemistry and biochemistry. In this work, phosphates with different degrees of polymerization (e.g., orthophosphate, pyrophosphate (PPi), sodium triphosphate (STPP), sodium trimetaphosphate (STMP), and polyphosphate with 25 phosphate units) and phosphates with one or two capping groups were studied. CeO₂ nanoparticles (nanoceria) were used as a model metal oxide. DNA is also a polyphosphate, and a fluorescently labeled DNA oligonucleotide was mixed with nanoceria. These phosphate species were individually added to displace the adsorbed DNA. Longer phosphate chains were more efficient when each molecule was used at the same molar concentration, whereas PPi and STPP were most efficient at the same total phosphorus atom concentration. By capping the phosphate with organic groups, the affinity was significantly decreased. Isothermal titration calorimetry (ITC) was also performed to quantitatively measure thermodynamic parameters. Although STMP was very slow at displacing DNA, it was still adsorbed very strongly by nanoceria from ITC, indicating kinetic effects likely due to its ring structure. This observation allowed us to use the DNA as a probe to study the hydrolysis of STMP to form STPP. In summary, this study provides a systematic understanding of phosphate species interacting with metal oxides, and interestingly, it demonstrates an analytical application as well.

Fluorescent DNA Probing Nanoscale MnO2: Adsorption, Dissolution by Thiol, and Nanozyme Activity

Manganese dioxide (MnO₂) is an interesting material due to its excellent biocompatibility and magnetic properties. Adsorption of DNA to MnO₂ is potentially of interest for drug delivery and sensing applications. However, little fundamental understanding is known about their interactions. In this work, carboxyfluorescein (FAM)-labeled DNA oligonucleotides were used to explore the effect of salt concentration, pH, and DNA sequence and length for adsorption by MnO₂, and comparisons were made with graphene oxide (GO). The DNA desorbs from MnO₂ by free inorganic phosphate, while it desorbs from GO by adenosine and urea. Therefore, DNA is mainly adsorbed on MnO₂ through its phosphate backbone, and DNA has a stronger affinity on MnO₂ than on GO based on a salt-shock assay. At the same time, DNA was used to study the effect of thiol containing compounds on the dissolution of MnO₂. Adsorbed DNA was released from MnO₂ after its dissolution by thiol, but not from other metal oxides with lower solubility such as CeO₂, TiO₂, and Fe₃O₄. DNA-functionalized MnO₂ was then used for detecting glutathione (GSH) with a detection limit of 383 nM. Finally, DNA was found to inhibit the peroxidase-like activity of MnO₂. This study has offered many fundamental insights into the interaction between MnO₂ and two important biomolecules: DNA and thiol-containing compounds.

Highly active fluorogenic oxidase-mimicking NiO nanozymes

NiO nanoparticles can quickly catalyze oxidation of Amplex red to produce fluorescent products for intracellular imaging, much more efficiently than other types of tested nanozymes.

Multi-metal-dependent nucleic acid enzymes

Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈10¹⁴ random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.

Interfacing DNA Oligonucleotides with Calcium Phosphate and Other Metal Phosphates

Calcium phosphate (CaP) has long been used for DNA delivery, although its fundamental interaction with DNA, especially with single-stranded DNA oligonucleotides, remains to be fully understood. Using fluorescently labeled oligonucleotides, we herein studied DNA adsorption isotherm and the effect of DNA length and sequence. Longer DNAs are adsorbed more strongly, and at neutral pH, poly-C DNAs are adsorbed more than the other three DNA homopolymers. However, at near pH 11, the pH of CaP synthesis, T₃₀ DNA is adsorbed more strongly than C₃₀ or A₃₀. This can explain why T₃₀ and G₃₀ can fully inhibit the growth of CaP, while A₃₀ and C₃₀ only retarded its growth kinetics. DNA adsorption also reduces aggregation of CaP. DNA desorption experiments were carried out using concentrated urea, thymidine, or inorganic phosphate as competitors, and desorption was observed only in the presence of phosphate, suggesting that DNA uses its phosphate backbone to interact with the CaP surface. Desorption was also promoted by raising the NaCl concentration suggesting the electrostatic nature of interaction. Finally, ten different metal phosphate materials were synthesized by co-precipitating each metal ion (Ce³⁺, Fe³⁺, Ca²⁺, Ni²⁺, Zn²⁺, Mn²⁺, Ba²⁺, Cu²⁺, Sr²⁺, Co²⁺), and DNA adsorption by these phosphate precipitants was found to be related to their surface charge and metal chemistry. This work has revealed fundamental surface science of DNA adsorption by CaP and other metal phosphate salts, and this knowledge might be useful for gene delivery, biomineralization, and DNA-directed assembly of metal phosphate materials.

Zn2+ Induced Irreversible Aggregation, Stacking, and Leakage of Choline Phosphate Liposomes

The interaction between lipids and metal ions is important for metal sensing, cellular signal transduction, and oxidative lipid damage. While most previous work overlooked the phosphate group of lipids for metal binding, we herein highlight its importance. Phosphocholine (PC) and its headgroup inversed choline phosphate (CP) lipids were used to prepare liposomes. From dynamic light scattering (DLS), Zn²⁺ causes significant aggregation or fusion of the CP liposomes, but not PC liposomes. The size change induced by Zn²⁺ is not fully reversed by adding EDTA, implying liposome fusion induced by Zn²⁺. Isothermal titration calorimetry (ITC) shows that binding between Zn²⁺ and CP liposomes is endothermic with a K_d of 110 μM Zn²⁺, suggesting an entropy driven reaction likely due to the release of bound water. In comparison, no heat was detected by titrating Zn²⁺ into PC liposomes or Ca²⁺ into CP liposomes. Furthermore, Zn²⁺ causes a transient leakage of the CP liposomes, and further leakage is observed upon removing Zn²⁺ by EDTA. Transmission electron microscopy (TEM) with negative stained samples showed multilamellar CP lipid structures attributable to Zn²⁺ sandwiched between lipid bilayers, leading to a proposed reaction mechanism. This work provides an interesting system for studying metal interacting with terminal phosphate groups in liposomes, affecting the size, charge, and membrane integrity of the liposomes.