Lanthanide-mediated DNA hydrolysis

Two decades of ceria nanoparticle research: structure, properties and emerging applications

Cerium oxide nanoparticles (CeNPs) are versatile materials with unique and unusual properties that vary depending on their surface chemistry, size, shape, coating, oxidation states, crystallinity, dopant, and structural and surface defects. This review encompasses advances made over the past twenty years in the development of CeNPs and ceria-based nanostructures, the structural determinants affecting their activity, and translation of these distinct features into applications. The two oxidation states of nanosized CeNPs (Ce3+/Ce4+) coexisting at the nanoscale level facilitate the formation of oxygen vacancies and defect states, which confer extremely high reactivity and oxygen buffering capacity and the ability to act as catalysts for oxidation and reduction reactions. However, the method of synthesis, surface functionalization, surface coating and defects are important factors in determining their properties. This review highlights key properties of CeNPs, their synthesis, interactions, and reaction pathways and provides examples of emerging applications. Due to their unique properties, CeNPs have become quintessential candidates for catalysis, chemical mechanical planarization (CMP), sensing, biomedical applications, and environmental remediation, with tremendous potential to create novel products and translational innovations in a wide range of industries. This review highlights the timely relevance and the transformative potential of these materials in addressing societal challenges and driving technological advancements across these fields.

Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase

Lanthanide ions have ideal chemical properties for catalysis, such as hard Lewis acidity, fast ligand-exchange kinetics, high coordination-number preferences and low geometric requirements for coordination. As a result, many small-molecule lanthanide catalysts have been described in the literature. Yet, despite the ability of enzymes to catalyse highly stereoselective reactions under gentle conditions, very few lanthanoenzymes have been investigated. In this work, the mononuclear binding of europium(III) and gadolinium(III) to the active site of a mutant of the model enzyme phosphotriesterase are described using X-ray crystallography at 1.78 and 1.61 Å resolution, respectively. It is also shown that despite coordinating a single non-natural metal cation, the PTE-R18 mutant is still able to maintain esterase activity.

Advanced Biological Applications of Cerium Oxide Nanozymes in Disease Related to Oxidative Damage

Due to their excellent catalytic activities, cerium oxide nanoparticles have promise as biological nanoenzymes. A redox reaction occurs between Ce3+ ions and Ce4+ ions during which they undergo conversion by acquiring or losing electrons as well as forming oxygen vacancies (or defects) in the lattice structure, which can act as antioxidant enzymes and simulate various enzyme activities. A number of cerium oxide nanoparticles have been engineered with multienzyme activities, including catalase, superoxide oxidase, peroxidase, and oxidase mimetic properties. Cerium oxide nanoparticles have nitric oxide radical clearing and radical scavenging properties and have been widely used in a number of fields of biology, including biomedicine, disease diagnosis, and treatment. This review provides a comprehensive introduction to the catalytic mechanisms and multiple enzyme activities of cerium oxide nanoparticles, along with their potential applications in the treatment of diseases of the brain, bones, nerves, and blood vessels.

Magnetic Bead Spherical Nucleic Acid Microstructure for Reliable DNA Preservation and Repeated DNA Reading

DNA is an attractive medium for long-term data storage because of its density, ease of copying, sustainability, and longevity. Recent advances have focused on the development of new encoding algorithms, automation, and sequencing technologies. Despite progress in these subareas, the most challenging hurdle in the deployment of DNA storage remains the reliability of preservation and the repeatability of reading. Herein, we report the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure and its use as a cost-effective platform for reliable DNA preservation and repeated reading. MB-SNA has an inner core of silica@γ-Fe2O3@silica microbeads and an outer spherical shell of double-stranded DNA (dsDNA) with a density as high as 34 pmol/cm2. For MB-SNA, each strand of dsDNA stored a piece of data, and the high-density packing of dsDNA achieved high-capacity storage. MB-SNA was advantageous in terms of reliable preservation over free DNA. By accelerated aging tests, the data of MB-SNA is demonstrated to be readable after 0.23 million years of preservation at -18 °C and 50% relative humidity. Moreover, MB-SNA facilitated repeated reading by facile PCR-magnetic separation. After 10 cycles of PCR access, the retention rate of dsDNA for MB-SNA is demonstrated to be as high as 93%, and the accuracy of sequencing is more than 98%. In addition, MB-SNA makes cost-effective DNA storage feasible. By serial dilution, the physical limit for MB-SNA to achieve accurate reading is probed to be as low as two microstructures.

Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes

The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.

Chemoselective Labeling and Immobilization of Phosphopeptides with Phosphorimidazolide Reagents

Protein phosphorylation is one of the most ubiquitous post-translational modifications, regulating numerous essential processes in cells. Accordingly, the large-scale annotation of phosphorylation sites continues to provide central insight into the regulation of signaling networks. The global analysis of the phosphoproteome typically relies on mass spectrometry analysis of phosphopeptides, with an enrichment step necessary due to the sub-stoichiometric nature of phosphorylation. Several affinity-based methods and chemical modification strategies have been developed to date, but the choice of enrichment method can have a considerable impact on the results. Here, we show that a biotinylated, photo-cleavable phosphorimidazolide reagent permits the immobilization and subsequent cleavage of phosphopeptides. The method is capable of the capture and release of phosphopeptides of varying characteristics, and this mild and selective strategy expands the current repertoire for phosphopeptide chemical modification with the potential to enrich and identify new phosphorylation sites in the future.

A Study on Repositioning Nalidixic Acid via Lanthanide Complexation: Synthesis, Characterization, Cytotoxicity and DNA/Protein Binding Studies

“Drug repositioning” is a modern strategy used to uncover new applications for out-of-date drugs. In this context, nalidixic acid, the first member of the quinolone class with limited use today, has been selected to obtain nine new metal complexes with lanthanide cations (La³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺); the experimental data suggest that the quinolone acts as a bidentate ligand, binding to the metal ion via the keto and carboxylate oxygen atoms, findings that are supported by DFT calculations. The cytotoxic activity of the complexes has been studied using the tumoral cell lines, MDA-MB-231 and LoVo, and a normal cell line, HUVEC. The most active compounds of the series display selective activity against LoVo. Their affinity for DNA and the manner of binding have been tested using UV–Vis spectroscopy and competitive binding studies; our results indicate that major and minor groove binding play a significant role in these interactions. The affinity towards serum proteins has also been evaluated, the complexes displaying higher affinity towards albumin than apotransferrin.

Design and applications of metallo-vesicular structures using inorganic-organic hybrids

In advanced biomedical diagnosis, various supramolecular assemblies based on inorganic-organic hybrids have found great interest as functional materials. These assemblies describe a new field of metallovesicles where the introduction of metal ions enables the chemical manipulation of assemblies in terms of their structural stability, redox activity, and pH stability. Additionally, they mimic the elaborative architecture of natural liposomal assemblies and exhibit hierarchical morphologies, and promise novel functions. With the constant developments in this field, various supramolecular assemblies such as MCsomes, Polymersomes, and Metallosomes, etc. came into existence. These hybrid assemblies have been utilized for several applications such as drug delivery, MRI contrasting, DNA delivery, and catalytic activity. The key advantage of these assemblies is their ability to deliver therapeutics to specific locations due to their biomimetic properties and release their contents at the desired time. Hence, they provide a valuable platform for the treatment of a variety of diseases. Through the present article, we intend to provide insights into the latest developments made in this field. This modularity underscores the tremendous promise of supramolecular assemblies as an emerging interdisciplinary research branch at the interface of chemistry and biological sciences.

Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch

Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5'-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson-Crick base-pairing. We show that 5'-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5'-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.

Nanoscale Cerium Oxide: Synthesis, Biocatalytic Mechanism, and Applications

Nanoscale cerium oxide has excellent catalytic performance due to its unique surface properties and has very important applications in various fields. In this paper, the synthesis methods, catalytic mechanism and activity regulation of nanoscale cerium oxide in recent years are reviewed. Secondly, the application of cerium oxide in the detection of organic and inorganic molecules is summarized, and its latest progress and applications in antibacterial, antioxidant and anticancer are discussed. Finally, the future development prospect of nanoscale cerium oxide is summarized and prospected.

Evaluation of general stress, detoxification pathways, and genotoxicity in rainbow trout exposed to rare earth elements dysprosium and lutetium

Rare earth elements (REEs) have been recently identified as emergent contaminants because of their numerous and increasing applications in technology. The impact of REEs on downstream ecosystems, notably aquatic organisms, is of particular concern, but has to date been largely overlooked. The purpose of this study was thus to evaluate the toxicity of lanthanide metals, lutetium (Lu) and dysprosium (Dy) in rainbow trout after 96 h of exposure. The lethal concentration (LC50) was determined and the expression of 14 genes involved in different pathways such as oxidative stress, xenobiotic detoxification, mitochondrial respiration, DNA repair, protein folding and turnover, inflammation, calcium binding and ammonia metabolism were quantified in surviving fish. In parallel, lipid peroxidation (LPO), DNA damage (DSB), metallothionein level (MT) and cyclooxygenase activity (COX) were examined. The acute 96 h-LC₅₀ data revealed that Lu was more toxic than Dy (1.9 and 11.0 mg/L, respectively) and was able to affect all investigated pathways by changing the expression of the studied genes, to the exception of superoxide dismutase (SOD), catalase (CAT) and glutathione-S-transferase (GST). It also induced a decrease in DNA repair at concentrations 29 times below the LC₅₀. This suggests that Lu could trigger a general stress to disrupt the cell homeostasis leading to genotoxicity without promoting oxidative stress. However, Dy induced modulation in the expression of genes involved in the protection against oxidative stress, detoxification, mitochondrial respiration, immunomodulation, protein turnover and an increase in the DNA strand breaks at concentrations 170 times lower than LC₅₀. Changes in mRNA level transcripts could represent an early signal to prevent against toxicity of Dy, which exhibited inflammatory and genotoxic effects. This study thus provides useful knowledge enhancing our understanding of survival strategies developed by rainbow trout to cope with the presence of lanthanides in the environment.

A systematic study of halide-template effects in the assembly of lanthanide hydroxide cluster complexes with histidine

Controlled hydrolysis of lanthanide ions in the presence of histidine and halide templates of different sizes produced dodeca- and pentadecanuclear lanthanide hydroxide clusters.

Rare-Earth Metal Complexes of the Antibacterial Drug Oxolinic Acid: Synthesis, Characterization, DNA/Protein Binding and Cytotoxicity Studies

"Drug repositioning" is a current trend which proved useful in the search for new applications for existing, failed, no longer in use or abandoned drugs, particularly when addressing issues such as bacterial or cancer cells resistance to current therapeutic approaches. In this context, six new complexes of the first-generation quinolone oxolinic acid with rare-earth metal cations (Y³⁺, La³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺) have been synthesized and characterized. The experimental data suggest that the quinolone acts as a bidentate ligand, binding to the metal ion via the keto and carboxylate oxygen atoms; these findings are supported by DFT (density functional theory) calculations for the Sm³⁺ complex. The cytotoxic activity of the complexes, as well as the ligand, has been studied on MDA-MB 231 (human breast adenocarcinoma), LoVo (human colon adenocarcinoma) and HUVEC (normal human umbilical vein endothelial cells) cell lines. UV-Vis spectroscopy and competitive binding studies show that the complexes display binding affinities (K_b) towards double stranded DNA in the range of 9.33 × 10⁴ - 10.72 × 10⁵. Major and minor groove-binding most likely play a significant role in the interactions of the complexes with DNA. Moreover, the complexes bind human serum albumin more avidly than apo-transferrin.

DNA Intercalating Near-Infrared Luminescent Lanthanide Complexes Containing Dipyrido[3,2-a:2',3'-c]phenazine (dppz) Ligands: Synthesis, Crystal Structures, Stability, Luminescence Properties and CT-DNA Interaction

In order to create near-infrared (NIR) luminescent lanthanide complexes suitable for DNA-interaction, novel lanthanide dppz complexes with general formula [Ln(NO₃)₃(dppz)₂] (Ln = Nd³⁺, Er³⁺ and Yb³⁺; dppz = dipyrido[3,2-a:2′,3′-c]phenazine) were synthesized, characterized and their luminescence properties were investigated. In addition, analogous compounds with other lanthanide ions (Ln = Ce³⁺, Pr³⁺, Sm³⁺, Eu³⁺, Tb³⁺, Dy³⁺, Ho³⁺, Tm³⁺, Lu³⁺) were prepared. All complexes were characterized by IR spectroscopy and elemental analysis. Single-crystal X-ray diffraction analysis of the complexes (Ln = La³⁺, Ce³⁺, Pr³⁺, Nd³⁺, Eu³⁺, Er³⁺, Yb³⁺, Lu³⁺) showed that the lanthanide’s first coordination sphere can be described as a bicapped dodecahedron, made up of two bidentate dppz ligands and three bidentate-coordinating nitrate anions. Efficient energy transfer was observed from the dppz ligand to the lanthanide ion (Nd³⁺, Er³⁺ and Yb³⁺), while relatively high luminescence lifetimes were detected for these complexes. In their excitation spectra, the maximum of the strong broad band is located at around 385 nm and this wavelength was further used for excitation of the chosen complexes. In their emission spectra, the following characteristic NIR emission peaks were observed: for a) Nd³⁺: ⁴F_3/2 → ⁴I_9/2 (870.8 nm), ⁴F_3/2 → ⁴I_11/2 (1052.7 nm) and ⁴F_3/2 → ⁴I_13/2 (1334.5 nm); b) Er³⁺: ⁴I_13/2 → ⁴I_15/2 (1529.0 nm) c) Yb³⁺: ²F_5/2 → ²F_7/2 (977.6 nm). While its low triplet energy level is ideally suited for efficient sensitization of Nd³⁺ and Er³⁺, the dppz ligand is considered not favorable as a sensitizer for most of the visible emitting lanthanide ions, due to its low-lying triplet level, which is too low for the accepting levels of most visible emitting lanthanides. Furthermore, the DNA intercalation ability of the [Nd(NO₃)₃(dppz)₂] complex with calf thymus DNA (CT-DNA) was confirmed using fluorescence spectroscopy.

Aromatic and heteroaromatic azacrown compounds: advantages and disadvantages of rigid macrocyclic ligands

Current approaches to the synthesis of aromatic and heteroaromatic azamacrocycles and their derivatives are summarized and systematized. The relationship between the structure of azacrown compounds and their complexation behaviour towards metal cations is analyzed. The diversity of practical applications of azamacrocyclic derivatives in medicine, biology and analytical and organic chemistry, as well as for the design of molecular devices is demonstrated.

The bibliography includes 307 references.

Cerium oxide nanoparticles: properties, biosynthesis and biomedical application

Cerium oxide nanoparticles have revolutionized the biomedical field and is still in very fast pace of development. Hence, this work elaborates the physicochemical properties, biosynthesis, and biomedical applications of cerium oxide nanoparticles.

Fabrication of highly active phosphatase-like fluorescent cerium-doped carbon dots for in situ monitoring the hydrolysis of phosphate diesters

The hydrolytic cleavage of BNPP was catalyzed and monitored by the fluorescent CeCDs.

Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes

In this study, mechanisms of phosphodiester hydrolysis catalyzed by six di- and tetravalent metal-cyclen (M-C) complexes (Zn-C, Cu-C, Co-C, Ce-C, Zr-C and Ti-C) have been investigated using DFT calculations. The activities of these complexes were studied using three distinct mechanisms: (1) direct attack ( DA ), (2) catalyst-assisted ( CA ), and (3) water-assisted ( WA ). All divalent metal complexes (Zn-C, Cu-C and Co-C) coordinated to the BNPP substrate in a monodentate fashion and activated its scissile phosphoester bond. However, all tetravalent metal complexes (Ce-C, Zr-C, and Ti-C) interacted with BNPP in a bidentate manner and strengthened this bond. The DA mechanism was energetically the most feasible for all divalent M-C complexes, while the WA mechanism was favored by the tetravalent complexes, except Ce-C. The divalent complexes were found to be more reactive than their tetravalent counterparts. Zn-C catalyzed the hydrolysis with the lowest barrier among all M-C complexes, while Ti-C was the most reactive tetravalent complex. The activities of Ce-C and Zr-C, except Ti-C, were improved with an increase in the coordination number of the metal ion. The structural and mechanistic information provided in this study will be very helpful in the development of more efficient metal complexes for this critical reaction.

Metal-Assisted Hydrolysis Reactions Involving Lipids: A Review

This report covers major advances in the use of metal ions and complexes to hydrolyze ester and phosphate ester lipid bonds. These metal-based Lewis acids have been investigated as catalysts to isolate fatty acids from biological sources, as probes to study phospholipid bilayer properties, as tools to examine signal transduction pathways, and as lead compounds toward the discovery of therapeutic agents. Metal ions that accelerate phosphate ester hydrolysis under mild conditions of temperature and pH may have the potential to mimic phospholipase activity in biochemical applications.

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?

Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.

Response of the freshwater mussel, Dreissena polymorpha to sub-lethal concentrations of samarium and yttrium after chronic exposure

Samarium (Sm) and yttrium (Y) are commonly used rare earth elements (REEs) but there is a scarcity of information concerning their biological effects in non-target aquatic organisms. The purpose of this study was to determine the bioavailability of those REEs and their toxicity on Dreissena polymorpha after exposure to increasing concentration of Sm and Y for 28 days at 15 °C. At the end of the exposure period, the gene expression of superoxide dismutase (SOD), catalase (CAT), metallothionein (MT), glutathione-S-transferase (GST), cytochrome c oxidase 1 (CO1) and cyclin D (Cyc D) were analysed. In addition, we examined lipid peroxidation (LPO), DNA strand breaks (DSB), GST and prostaglandin cyclooxygenase (COX) activities. Results showed a concentration dependent increase in the level of the REEs accumulated in the soft tissue of mussels. Both REEs decreased CAT but did not significantly modulated SOD and MT expressions. Furthermore, Sm³⁺ up-regulated GST, CO1 and Cyc D, while Y³⁺ increased and decreased GST and CO1 transcripts levels, respectively. Biomarker activities showed no oxidative damage as evidenced by LPO, while COX activity was decreased and DNA strand breaks levels were changed suggesting that Sm and Y exhibit anti-inflammatory and genotoxic effects. Factorial analysis revealed that the major impacted biomarkers by Sm were LPO, CAT, CO1 and COX, while GST gene expression, COX, Cyc D and CAT as the major biomarkers affected by Y. We conclude that these REEs display different mode of action but further investigations are required in order to define the exact mechanism involved in their toxicity.

Expression, purification, and characterization of N-terminal His-tagged proteins with mutations in zinc finger 3 of zinc finger protein ZNF191(243-368)

Zinc finger protein ZNF191(243-368), the zinc finger region of ZNF191, is potentially associated with cell proliferation in hepatocellular carninoma. A His-tag expression system was used to express and purify proteins with mutations in the zinc finger 3 of ZNF191(243-368) for analysis of protein properties, structure, and functions. The purification of the His-tag fusion proteins was simpler and faster than that of the ZNF191(243-368) inclusion bodies. The properties and structures of the His-tag fusion mutant proteins were investigated using spectrographic techniques and DNA hydrolysis experiment. The His₆-tag system could be used to express ZNF191(243-368). The presence of the His₆-tag at the N-terminus of ZNF191(243-368) did not evidently affect its properties and structure. However, the site-directed mutations in zinc finger 3 affected the structure of the protein. The DNA hydrolase activity of His₆-ZF-F3/H4 suggested that four histidines in zinc finger 3 might form a structure similar to that of the active center in a hydrolase. This work reports that continuous histidines need to form a certain structure for specific functions, and provides new insights into the design of an artificial nuclease.

Inorganic lanthanides induce PCR bias towards shorter amplicons

Rare earth elements have many uses, and are frequently included in products such as fluorescent materials, hydride batteries, catalytic materials and lasers. In this study, it was observed that trivalent lanthanide ions (Ln[III] ions) appeared to inhibit the synthesis of large fragments in PCR assays, thus resulting in the preferential amplification of shorter sequences. It is therefore speculated that this Ln(III) ion-mediated bias could be utilized to improve the success rates for amplification of shorter products.

Nuclease Activity of Diaza-Crown Ether Complexes of Cerium(III) with Different Functional Groups as Side Arms

Cerium(III) complexes of two ligands of a diaza-crown ether with different functional groups as side arms were synthesised and characterised. The catalytic ability of the cerium(III) complexes for pUC19 DNA cleavage was investigated and compared using agarose gel electrophoresis. The results indicate that the catalytic activity of the complex CeL2 [L2 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diacetamide] with two carbamoylmethyl groups is significantly higher than the complex CeL1 [L1 = 2,2′- (1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl) diethanol] with two hydroxyethyl groups under the same conditions. The optimum catalytic concentrations of CeL1 and CeL2 were 7.69 × 10−5 and 3.08 × 10−5 mol L−1 respectively and excessively high concentrations of the complexes can reduce their catalytic efficiency due to the formation of inactive μ-hydroxo dimers. The optimum catalytic acidities of CeL1 and CeL2 were pH 7.0 and 7.5 respectively and excessively high pH of the reaction system can reduce the catalytic efficiency of the complexes due to the formation of cerium(III) hydroxide. DNA cleavage promoted by the two complexes takes place via the same hydrolytic pathway and so the activity difference of the two complexes is attributed to the stability of the complexes, rather than the catalytic mechanism.

Uranyl acetate induced DNA single strand breaks and AP sites in Chinese hamster ovary cells

The aim of this study is to characterize the genotoxicity of depleted uranium (DU) in Chinese Hamster Ovary cells (CHO) with mutations in various DNA repair pathways. CHO cells were exposed to 0-300 μM of soluble DU as uranyl acetate (UA) for 0-48 h. Intracellular UA concentrations were measured via inductively coupled mass spectrometry (ICP-MS) and visualized by transmission electron microscopy (TEM). Cytotoxicity was assessed in vitro by clonogenic survival assay. DNA damage response was assessed via Fast Micromethod® to determine UA-induced DNA single strand breaks. Results indicate that UA is entering the CHO cells, with the highest concentration localizing in the nucleus. Clonogenic assays show that UA is cytotoxic in each cell line with the greatest cytotoxicity in the base excision repair deficient EM9 cells and the nuclear excision repair deficient UV5 cells compared to the non-homologous end joining deficient V3.3 cells and the parental AA8 cells after 48 h. This indicates that UA is producing single strand breaks and forming UA-DNA adducts rather than double strand breaks in CHO cells. Fast Micromethod® results indicate an increased amount of single strand breaks in the EM9 cells after 48 h UA exposure compared to the V3.3 and AA8 cells. These results indicate that DU induces DNA damage via strand breaks and uranium-DNA adducts in treated cells. These results suggest that: (1) DU is genotoxic in CHO cells, and (2) DU is inducing single strand breaks rather than double strand breaks in vitro.

Effects of Pressure and pH on the Hydrolysis of Cytosine: Implications for Nucleotide Stability around Deep-Sea Black Smokers

The relatively low chemical stability of cytosine compared with other nucleobases is a key concern in origin-of-life scenarios, but the effect of pressure on the rate of hydrolysis of cytosine to uracil remains unknown. Through in situ NMR spectroscopy measurements, it has been determined that the half-life of cytosine at 373.15 K decreases from (18.0±0.7) days at ambient pressure (0.1 MPa) to (8.64±0.18) days at high pressure (200 MPa). This yields an activation volume for hydrolysis of (-11.8±0.5) cm³  mol^-1 ; a decrease that is similar to the molar volume of water (18.0 cm³  mol^-1 ) and consistent with a tetrahedral 3,3-hydroxyamine transition-state/intermediate species. Similar behaviour was also observed for cytidine. At both ambient and high pressures, the half-life of cytosine decreases significantly as the pH decreases from 7.0 to 6.0. These results provide scant support for the notion that RNA-based life forms originated in high-temperature, high-pressure, acidic environments.

Synthesis, characterisation, crystal structures and biological studies of palladium(ii) complexes containing 5-(2-hydroxy-3-methoxy-phenyl)-2,4-dihydro[1,2,4]triazole-3-thione derivatives

New structurally different palladium(ii) complexes have been synthesized and characterized and evaluated for their cytotoxic nature against human breast cancer cell line (MCF 7) which showed significant activity.

New Lanthanide Tag for the Generation of Pseudocontact Shifts in DNA by Site-Specific Ligation to a Phosphorothioate Group

Pseudocontact shifts (PCS) generated by paramagnetic lanthanides provide a rich source of long-range structural restraints that can readily be measured by nuclear magnetic resonance (NMR) spectroscopy. Many different lanthanide-binding tags have been designed for site-specific tagging of proteins, but established routes for tagging DNA with a single metal ion rely on difficult chemical synthesis. Here we present a simple and practical strategy for site-specific tagging of inexpensive phosphorothioate (PT) oligonucleotides. Commercially available PT oligonucleotides are diastereomers with S and R stereoconfiguration at the backbone PT site. The respective S_P and R_P diastereomers can readily be separated by HPLC. A new alkylating lanthanide-binding tag, C10, was synthesized that delivered quantitative tagging yields with both diastereomers. PCSs were observed following ligation with the complementary DNA strand to form double-stranded DNA duplexes. The PCSs were larger for the S_P than the R_P oligonucleotide and good correlation between back-calculated and experimental PCSs was observed. The C10 tag can also be attached to cysteine residues in proteins, where it generates a stable thioether bond. Ligated to the A28C mutant of ubiquitin, the tag produced excellent fits of magnetic susceptibility anisotropy (Δχ) tensors, with larger tensors than for the tagged PT oligonucleotides, indicating that the tag is not completely immobilized after ligation with a PT group.

De novo design of a hydrolytic DNA cleavage agent, mono nitratobis(phen)cobalt(ii) aqua nitrate complex

Demonstration of DNA intercalation and hydrolytic cleavage by complex1.

Phosphate Ester Bond Hydrolysis Promoted by Lanthanide-Substituted Keggin-type Polyoxometalates Studied by a Combined Experimental and Density Functional Theory Approach

Hydrolytic cleavage of 4-nitrophenyl phosphate (NPP), a commonly used DNA model substrate, was examined in the presence of series of lanthanide-substituted Keggin-type polyoxometalates (POMs) [Me₂NH₂]₁₁[Ce^III(PW₁₁O₃₉)₂], [Me₂NH₂]₁₀[Ce^IV(PW₁₁O₃₉)₂] (abbreviated as (Ce^IV(PW₁₁)₂), and K₄[EuPW₁₁O₃₉] by means of NMR and luminescence spectroscopies and density functional theory (DFT) calculations. Among the examined complexes, the Ce(IV)-substituted Keggin POM (Ce^IV(PW₁₁)₂) showed the highest reactivity, and its aqueous speciation was fully determined under different conditions of pD, temperature, concentration, and ionic strength by means of ³¹P and ³¹P diffusion-ordered NMR spectroscopy. The cleavage of the phosphoester bond of NPP in the presence of (Ce^IV(PW₁₁)₂) proceeded with an observed rate constant k_obs = (5.31 ± 0.06) × 10^-6 s^-1 at pD 6.4 and 50 °C. The pD dependence of NPP hydrolysis exhibits a bell-shaped profile, with the fastest rate observed at pD 6.4. The formation constant (K_f = 127 M^-1) and catalytic rate constant (k_c = 19.41 × 10^-5 s^-1) for the NPP-Ce(IV)-Keggin POM complex were calculated, and binding between Ce^IV(PW₁₁)₂ and the phosphate group of NPP was also evidenced by the change of the chemical shift of the ³¹P nucleus in NPP upon addition of the POM complex. DFT calculations revealed that binding of NPP to the parent catalyst Ce^IV(PW₁₁)₂ is thermodynamically unlikely. On the contrary, formation of complexes with the monomeric 1:1 species, Ce^IVPW₁₁, is considered to be more favorable, and the most stable complex, [Ce^IVPW₁₁(H₂O)₂(NPP-κO)₂]^7-, was found to involve two NPP ligands coordinated to the Ce^IVcenter of Ce^IVPW₁₁ in the monodentate fashion. The formation of such species is considered to be responsible for the hydrolytic activity of Ce^IV(PW₁₁)₂ toward phosphomonoesters. On the basis of these findings a principle mechanism for the hydrolysis of NPP by the POM is proposed.

Comparison of catalytic activities of new La (III) and Ce (III) complexes with different diaza-crown ether ligands for DNA hydrolytic cleavage

A new diaza-crown ether with double hydroxypropyl branches (L = 1,1'-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyl)dipropan-2-ol) and its two lanthanide complexes (LaL and CeL) were synthesised and characterised. Their nuclease activities on pUC19 DNA cleavage were investigated using agarose gel electrophoresis, and pseudo-first-order rate constants kobs of 0.067 h–1 for LaL, 0.041 h–1 for CeL, 0.013 h–1 for LaL0, and 0.027 h–1 CeL0 were obtained (L0 = 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane). The results indicated that the CeL complex was more efficient than the LaL complex for DNA cleavage at low concentrations, but the LaL complex was more efficient than the CeL complex at high concentrations. Moreover, kinetic studies demonstrated that introducing hydroxypropyl side arms in the ring of the diaza-crown ether can improve the catalytic ability of the complexes in DNA cleavage, which may be due to the hydroxypropyl side arms enhancing the bonding interaction between the complex and the DNA molecule by hydrogen bonding. A hydrolytic mechanism for DNA cleavage was demonstrated by applying several oxygen scavengers to the DNA catalytic cleavage. A proposed mechanism for the DNA cleavage shows that the hydroxypropyl side groups can recognise and bind the phosphodiester bond of DNA by hydrogen bonding and electrostatic interaction.

Efficient non-enzymatic cleavage of Staphylococcus aureus plasmid DNAs mediated by neodymium ions

Staphylococcus aureus plasmids are the main factor in the spreading of antibacterial resistance among bacterial strains that has emerged on a worldwide scale. Plasmids recovered from 12 clinical and food isolates of S. aureus were treated with 10 mM free lanthanide Nd(3+) ions (non-enzymatic cleavage agent) in Hepes buffer (pH 7.5) at 70 °C. Topological forms of plasmids-closed circular (ccc), open circular (oc), and linear (lin)-produced by cleavage at different times were separated using pulsed-field agarose gel electrophoresis. The method is proposed to detect and differentiate several plasmids in the same bacterial strain according to their size.

Near-infrared luminescence and RNA cleavage ability of lanthanide Schiff base complexes derived from N,N'-bis(3-methoxysalicylidene)ethylene-1,2-diamine ligands

A complete series of lanthanide Schiff base salen-type complexes were prepared with trivalent lanthanide ions (Ln³⁺) and the N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine ligand (Ln³⁺=La³⁺, Ce³⁺, Pr³⁺, Nd³⁺, Sm³⁺, Eu³⁺, Gd³⁺, Tb³⁺, Dy³⁺, Ho³⁺, Er³⁺, Tm³⁺, Yb³⁺, Lu³⁺). Three unique crystal structures of La³⁺ and Pr³⁺N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine complexes, with the La³⁺ complex prepared in two different synthetic approaches, are reported, namely a dimeric [La(H₂L)(NO₃)₃]₂ (H₂L=N,N'-bis-(3-methoxysalicylidene)ethylene-1,2-diamine) complex, an asymmetric two-centered [La₂(H₂L)₂(NO₃)₆] complex and a discrete mononuclear [Pr(H₂L)(NO₃)₂(H₂O)₂] complex. For Nd³⁺ and Sm³⁺, an isotypic mononuclear [Nd(H₂L)(NO₃)₃] and 1D polymeric [Sm(H₂L)(NO₃)₃(MeOH)]_n structure was obtained, respectively. The whole series of complexes was tested for their ability to cleave the 20-mer RNA oligonucleotide 5'-AGC-GAU-AAG-AUU-CAU-AUA-UC-3'. Additionally three complexes (Ln³⁺=Nd³⁺, Sm³⁺, Ho³⁺) were tested for the cleavage of the 12-mer RNA oligonucleotide 5'-GCA-CCC-UGU-CAG-3'. A detailed luminescence study was additionally carried out and revealed that the Eu³⁺ complex emitted bright red light upon excitation at both 285.8nm and 394.4nm. The Nd³⁺, Er³⁺, and Yb³⁺ complexes showed strong emission in the near-infrared region after excitation at 380nm.