Ultrasensitive optical detection of strontium ions by specific nanosensor with ultrahigh binding affinity

The release and escape of radioactive materials has posed tremendous threats to the global environment. Among various radioactive elements, 90Sr has attracted growing attention due to its long half-life and its tendency to accumulate in bone tissue. Nonetheless, the concentration of 90Sr in radioactive waste is exceedingly low, far below the detection limits of currently available strontium-targeting chemical sensors. Herein, we propose an optical nanosensor (Sr2+-nanosensor) that exhibits an ultra-low detection limit of 0.5 nM, surpassing the 90Sr in the treated radioactive water from the Fukushima. The sensor offers wide sensing range of eight orders of magnitude, rapid response of less than 10 s, and high selectivity against 31 common ions. These excellent performances are attributed to a specific ligand (Sr2+-ligand) for Sr2+ recognition. The Sr2+ is found to be bound by six oxygen atoms from the Sr2+-ligand with a stability constant at least two orders higher than that of other traditional ligands. This study offers invaluable insights for the design of Sr2+-sensing methodologies as well as a technique for detecting trace amounts of environmental radioactive pollution.

Unraveling the Possibilities: Recent Progress in DNA Biosensing

Due to the advantages of its numerous modification sites, predictable structure, high thermal stability, and excellent biocompatibility, DNA is the ideal choice as a key component of biosensors. DNA biosensors offer significant advantages over existing bioanalytical techniques, addressing limitations in sensitivity, selectivity, and limit of detection. Consequently, they have attracted significant attention from researchers worldwide. Here, we exemplify four foundational categories of functional nucleic acids: aptamers, DNAzymes, i-motifs, and G-quadruplexes, from the perspective of the structure-driven functionality in constructing DNA biosensors. Furthermore, we provide a concise overview of the design and detection mechanisms employed in these DNA biosensors. Noteworthy advantages of DNA as a sensor component, including its programmable structure, reaction predictility, exceptional specificity, excellent sensitivity, and thermal stability, are highlighted. These characteristics contribute to the efficacy and reliability of DNA biosensors. Despite their great potential, challenges remain for the successful application of DNA biosensors, spanning storage and detection conditions, as well as associated costs. To overcome these limitations, we propose potential strategies that can be implemented to solve these issues. By offering these insights, we aim to inspire subsequent researchers in related fields.

Unravelling the binding affinity and selectivity of molybdenum(II) phenanthroline complexes with DNA G-quadruplexes by using linear-scaling DFT studies. The important role of ancillary ligands

We have used near linear-scaling density functional theory (LS-DFT) methods including dispersion, for the first time, to study the interaction of two isomers, equatorial (Eq) and axial (Ax), of the [Mo(η³-C₃H₅)Br(CO)₂(phen)] metal complex with the DNA G-quadruplexes (GQ) to gain insight into its cytotoxicity. The LMKLL/DZDP level of calculation, which includes van der Waals contributions, with the SIESTA software was used to treat by means of first-principles computations the whole biological studied model system with ∼1000 atoms. Computed formation energies point to systems containing the Ax isomer as the most stable although the nearest system in energy containing the Eq isomer is only 7.5 kcal mol^-1 above. On the other hand, the energy decomposition analysis (EDA) favours interaction energies for the systems containing the Eq isomer. However, when solvent effects are taken into account the systems containing the Ax isomer are again the most stable. This Ax isomer was found interacting by means of end-stacking with the GQ and surprisingly totally inside the non-canonical secondary structure, where all the ligands of the metal complex produce several weak interactions with the DNA structure. On the other hand, the Eq isomer prefers to interact from outside by means of intercalation in which the ancillary ligands also have some role in the interaction. Such features and comparison with the results regarding the interaction of the [Mo(η³-C₃H₅)Br(CO)₂(phen)] metal complex with duplex DNA suggest that the [Mo(η³-C₃H₅)Br(CO)₂(phen)] would have a higher affinity and eventual selectivity for non-canonical DNA GQ structures.

A novel chemosensor for sensitive and facile detection of strontium ions based on ion-imprinted hydrogels modified with guanosine derivatives

A novel chemosensor is developed for the sensitive and facile detection of trace strontium ions (Sr²⁺) based on the ion-imprinted hydrogels. With Sr²⁺ as the templates, the ion-imprinted hydrogels are synthesized by copolymerizing the ion-responsive units 5'-O-acryloyl-2',3'-O-isopropylidene guanosine (APG) and the thermo-responsive units N-isopropylacrylamide (NIPAM). In the presence of Sr²⁺, APG units can self-assemble to form planar G-quartets via the complexation with Sr²⁺, which are introduced into the gel network during polymerization. Then Sr²⁺ templates can be removed by multiple repeated washing. When re-exposed to Sr²⁺, the relaxed G-quartets can recognize Sr²⁺, leading to the weakening of electrostatic repulsion between the four oxygen atoms in the G-quartets and inducing the shrinkage of the hydrogels. In this work, the Sr²⁺-imprinted chemosensors are designed as the grating systems for detecting trace Sr²⁺. Based on the array of hydrogel strings synthesized on a nano-scale, the smart grating systems thus constructed can convert and amplify the Sr²⁺ concentration signals to the easily-measurable optical signals. With the Sr²⁺-imprinted hydrogel gratings, trace Sr²⁺ (10^-11 M) in an aqueous solution can be detected sensitively. Moreover, the proposed Sr²⁺-imprinted chemosensors can be integrated with other smart systems for developing various detectors with high performance.

A label-free fluorescent peptide probe for sensitive and selective determination of copper and sulfide ions in aqueous systems

A label free fluorescent peptide probe (HDSGWEVHH) was used for Cu2+ and S2- determination in aqueous solution. Our results demonstrated that HDSGWEVHH is highly selective and sensitive for monitoring free Cu2+ concentration via quenching of the probe fluorescence upon Cu2+ binding. The mechanism of the complexation is investigated with Cyclic Voltammetry (CV), 1H nuclear magnetic resonance (NMR), electron paramagnetic resonance (EPR) spectroscopy and computational techniques. Theoretical calculation results indicated the binding ratio of the probe to Cu2+ is 2 : 1 and the binding constant was obtained as 1.72 × 10 8 M-1. Cu2+ concentration can be detected with the detection limit of 16 nM. Free Cu2+ concentration released from the metallothionein-Cu complex at different pH values was detected. Cu2+ concentration in real water and tea samples was also detected, and the results were consistent with the ones monitored by atomic absorption spectrometer. Because of the exceedingly small K sp value of CuS (1.27 × 10-36), S2- can sequester Cu2+ from HDSGWEVHH to restore the tryptophan (W) fluorescence. Thus the HDSGWEVHH-Cu2+ complex can also be used for S2- detection. The S2- concentrations can be monitored with a detection limit of 19 nM. The assay is also amenable to measurement of S2- concentration in pure water samples. Thus the probe designed herein is sensitive, label free, low cost, and environmentally friendly for Cu2+ and S2- determination in aqueous solutions.

Metalloenzyme-mimic innate G-quadruplex DNAzymes using directly coordinated metal ions as active centers

G-quadruplex DNAs (G4s) have been reported to exhibit the DNAzyme activities by binding with some metal complexes and functional organic ligands. However, there is a challenge to develop metalloenzyme-mimic G4-based innate DNAzymes using the complexed metal ions directly serving as the active centers. This will diversify DNAzymes for developing novel devices since G4 structures are more polymorphic than the other DNA foldings. In this work, we found that the lanthanide trivalent cerium ion of Ce3+ can bind to the human telomere G4 (htG4) according to a 1 : 2 binding mode favorable for creating metalloenzymes-mimic G4 DNAzymes. This Ce3+-G4 entity exhibits a peroxidase activity towards the oxidation of the substrate of 3,3,5,5-tetramethylbenzidine (TMB) by hydrogen peroxide. The 5' G4 tetrads with the orderly arranged carbonyl oxygen atoms are believed to be the coordination sites for Ce3+ and favor the conversion between Ce3+ and Ce4+. Our work provides an alternative feasibility in developing the G4-based innate DNAzymes for variant applications.

Ruthenium(II) and Iridium(III) Complexes as Tested Materials for New Anticancer Agents

The oncological use of cisplatin is hindered by its severe side effects and a very important resistance problem. To overcome these problems, scientists have attempted to design new generation transition-metal anticancer complexes. In this study, we present new complexes, ruthenium(II) [(η6-p-cymene)RuCl(py2CO)]PF6 (1), iridium(III) [(η5-Cp)IrCl(py2CO)]PF6 (2), and NH4[IrCl4(py2CO)]·H2O (3), based on di-2-pyridylketone (py2CO). The prepared complexes were characterized by FTIR, 1H, 13C, 15N NMR, UV-Vis, PL and elemental analysis techniques. The single-crystal X-ray structure analysis and comparative data revealed pseudo-octahedral half-sandwich 1 and 2 complexes and octahedral tetrachloroiridate(III) 3 with a rare chelating κ2N,O coordination mode of py2CO. The compounds were tested in vitro against three cancer cell lines-colorectal adenoma (LoVo), myelomonocytic leukaemia (MV-4-11), breast adenocarcinoma (MCF-7), and normal fibroblasts (BALB/3T3). The most promising results were obtained for iridium(III) complex 3 against MV-4-11 (IC50 = 35.8 ± 13.9 µg/mL) without a toxic effect against normal BALB/3T3, which pointed towards its selectivity as a potential anticancer agent. Extensive research into their mode of binding with DNA confirmed for 1 and 2 complexes non-classical binding modes, while the 3D circular dichroism (CD) experiment (ΔTm) suggested that 3 induced the probable formation of covalent bonds with DNA. In addition, the obtained iridium complexes induce ROS, which, in synergy with hydrolysis promoting DNA bonding, may lead to cancer cell death.

Recent developments of nanoenzyme-based colorimetric sensors for heavy metal detection and the interaction mechanism

This work highlights the application and interaction mechanism of metal nanoparticles, metal oxides, metal sulfides, graphene-based nanomaterials and G-quadruplex, etc. in nanoenzyme-based colorimetric sensors.

Polarity inversion sensitized G-quadruplex metal sensors with K+ tolerance

Due to the high abundance of K⁺ in environments and K⁺-induced high stability of G-quadruplex (G4), developing a selective G4-based fluorescent sensor for other metal ions with K⁺ tolerance is a great challenge. Herein, we found that even in the presence of 15000-fold excess of K⁺, Ba²⁺ exhibits a highly specific binding with a human telomeric G4 (htG4) in comparison with other G4-binding metal ions such as Pb²⁺ and Sr²⁺. This specific binding event can be recognized by a natural fluorophore of hypericin with a lighting-up fluorescence response. Interestingly, inverting the polarity of the most 3' G in htG4 can sensitize the Ba²⁺ response with the retaining Ba²⁺ specificity and K⁺ tolerance. This polarity inversion of htG4 causes a G4 conformation change in K⁺ and the polarity-inverted htG4 tends to favorably dimerize in response to the Ba²⁺ specific binding. To our knowledge, this is the first report that polarity inversion of G4 can be applied to construct a selective metal sensor with K⁺ tolerance. Our findings will open a new way to conveniently regulate the G4 conformation and stability by polarity inversion towards developing high-performance sensors.

Design and characterization of a 2-(2′-hydroxyphenyl)benzimidazole-based Sr2+-selective fluorescent probe in organic and micellar solution systems

Fluorescence detection of Sr(ii) by Sr(ii)-selective fluorescent probe BIC and its complex formed in solution.

Distinct differences in metal ion specificity of RNA and DNA G-quadruplexes

RNA G-quadruplexes, as their well-studied DNA analogs, require the presence of cations to fold and remain stable. This is the first comprehensive study on the interaction of RNA quadruplexes with metal ions. We investigated the formation and stability of two highly conserved and biologically relevant RNA quadruplex-forming sequences (24nt-TERRA and 18nt-NRAS) in the presence of several monovalent and divalent metal ions, namely Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺, NH₄⁺, Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺. Circular dichroism was used to probe the influence of these metal ions on the folded fraction of the parallel G-quadruplexes, and UV thermal melting experiments allowed to assess the relative stability of the structures in each cationic condition. Our results show that the RNA quadruplexes are more stable than their DNA counterparts under the same buffer conditions. We have observed that the addition of mainly Na⁺, K⁺, Rb⁺, NH₄⁺, as well as Sr²⁺ and Ba²⁺ in water, shifts the equilibrium to the folded quadruplex form, whereby the NRAS sequence responds stronger than TERRA. However, only K⁺ and Sr²⁺ lead to a significant increase in the stability of the folded structures, which is consistent with their coordination to the O6 atoms from the G-quartet guanosines. Compared to the respective DNA motives, dNRAS and htelo, the RNA sequences are not stabilized by Na⁺ ions. Finally, the difference in response between NRAS and TERRA, as well as to the corresponding DNA sequences with respect to different metal ions, could potentially be exploited for selective targeting purposes.

Quadruplex Turncoats: Cation-Dependent Folding and Stability of Quadruplex-DNA Double Switches

Quadruplex (G4) nucleic acids, a family of secondary structures formed by guanine-rich sequences, exhibit an important structural polymorphism. We demonstrate here that G-rich DNA sequences may function as a double switch based on different triggers, provided that their quadruplex structures and stability display a high dependence on cation nature and concentration. A first switch is based on a remarkable antiparallel-to-parallel conversion, taking place in a few seconds at room temperature by addition of low KCl amounts to a sodium-rich sample. The second switch involves the conversion of alternative antiparallel quadruplex structures binding only one cation, formed in the presence of sub-millimolar potassium or strontium concentrations, to parallel structures by increasing the cation concentration. Incidentally, extremely low K(+) or Sr(2+) concentrations (≤5 equiv) are sufficient to induce G4 formation in a buffer devoid of other G4-promoting cations, and we suggest that the alternative structures observed contain only two tetrads. Such DNA systems are biological relevant targets, can be used in nanotechnology applications, and are valuable methodological tools for understanding DNA quadruplex folding, notably at low cation concentrations. We demonstrate that this behavior is not restricted to a narrow set of sequences but can also be found for other G-quadruplex-forming motifs, arguing for widespread applications.

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity

A G-triplex luminescent switch-on probe for the detection of nuclease activity.

Group 9 organometallic compounds for therapeutic and bioanalytical applications

CONSPECTUS: Compared with organic small molecules, metal complexes offer several distinct advantages as therapeutic agents or biomolecular probes. Carbon atoms are typically limited to linear, trigonal planar, or tetrahedral geometries, with a maximum of two enantiomers being formed if four different substituents are attached to a single carbon. In contrast, an octahedral metal center with six different substituents can display up to 30 different stereoisomers. While platinum- and ruthenium-based anticancer agents have attracted significant attention in the realm of inorganic medicinal chemistry over the past few decades, group 9 complexes (i.e., iridium and rhodium) have garnered increased attention in therapeutic and bioanalytical applications due to their adjustable reactivity (from kinetically liable to substitutionally inert), high water solubility, stability to air and moisture, and relative ease of synthesis. In this Account, we describe our efforts in the development of group 9 organometallic compounds of general form [M(C(∧)N)2(N(∧)N)] (where M = Ir, Rh) as therapeutic agents against distinct biomolecular targets and as luminescent probes for the construction of oligonucleotide-based assays for a diverse range of analytes. Earlier studies by researchers had focused on organometallic iridium(III) and rhodium(III) half-sandwich complexes that show promising anticancer activity, although their precise mechanisms of action still remain unknown. More recently, kinetically-inert group 9 complexes have arisen as fascinating alternatives to organic small molecules for the specific targeting of enzyme activity. Research in our laboratory has shown that cyclometalated octahedral rhodium(III) complexes were active against Janus kinase 2 (JAK2) or NEDD8-activating enzyme (NAE) activity, or against NO production leading to antivasculogenic activity in cellulo. At the same time, recent interest in the development of small molecules as modulators of protein-protein interactions has stimulated our research group to investigate whether kinetically-inert metal complexes could also be used to target protein-protein interfaces relevant to the pathogenesis of certain diseases. We have recently discovered that cyclometalated octahedral iridium(III) and rhodium(III) complexes bearing C(∧)N ligands based on 2-phenylpyridine could function as modulators of protein-protein interactions, such as TNF-α, STAT3, and mTOR. One rhodium(III) complex antagonized STAT3 activity in vitro and in vivo and displayed potent antitumor activity in a mouse xenograft model of melanoma. Notably, these studies were among the first to demonstrate the direct inhibition of protein-protein interfaces by kinetically-inert group 9 metal complexes. Additionally, we have discovered that group 9 solvato complexes carrying 2-phenylpyridine coligands could function as inhibitors and probes of β-amyloid fibrillogenesis. Meanwhile, the rich photophysical properties of iridium complexes have made them popular tools for the design of luminescent labels and probes. Luminescent iridium(III) complexes benefit from a high quantum yield, responsive emissive properties, long-lived phosphorescence lifetimes, and large Stokes shift values. Over the past few years, our group has developed a number of kinetically-inert, organometallic iridium(III) complexes bearing various C(∧)N and N(∧)N ligands that are selective for G-quadruplex DNA, which is a DNA secondary structure formed from planar stacks of guanine tetrads stabilized by Hoogsteen hydrogen bonding. These complexes were then employed to develop G-quadruplex-based, label-free luminescence switch-on assays for nucleic acids, enzyme activity, small molecules, and metal ions.

A ruthenium(II) complex supported by trithiacyclononane and aromatic diimine ligand as luminescent switch-on probe for biomolecule detection and protein staining

A new ruthenium(II) complex has been developed for detection of biomolecules. This complex is highly selective for histidine over other amino acids and has been applied to protein staining in an SDS-PAGE gel.

A G-quadruplex-based platform for the detection of Hg2+ ions using a luminescent iridium(iii) complex

We report herein the synthesis of a series of cyclometalated iridium(iii) complexes as luminescent G-quadruplex-selective probes, which were used to construct an oligonucleotide-based platform for the dual detection and removal of Hg²⁺ ions.

G-quadruplexes as sensing probes

Guanine-rich sequences of DNA are able to create tetrastranded structures known as G-quadruplexes; they are formed by the stacking of planar G-quartets composed of four guanines paired by Hoogsteen hydrogen bonding. G-quadruplexes act as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplexes form a complex with anionic porphyrin hemin and exhibit peroxidase-like activity. This review focuses on overview of sensing techniques based on G-quadruplex complexes with anionic porphyrins for detection of various analytes, including metal ions such as K⁺, Ca²⁺, Ag⁺, Hg²⁺, Cu²⁺, Pb²⁺, Sr²⁺, organic molecules, nucleic acids, and proteins. Principles of G-quadruplex-based detection methods involve DNA conformational change caused by the presence of analyte which leads to a decrease or an increase in peroxidase activity, fluorescence, or electrochemical signal of the used probe. The advantages of various detection techniques are also discussed.

A label-free luminescent switch-on assay for ATP using a G-quadruplex-selective iridium(III) complex

We report herein the G-quadruplex-selective property of a luminescent cyclometallated iridium(III) complex for the detection of adenosine-5'-triphosphate (ATP) in aqueous solution. The ATP-binding aptamer was employed as the ATP recognition unit, while the iridium(III) complex was used to monitor the formation of the G-quadruplex structure induced by ATP. The sensitivity and fold enhancement of the assay were higher than those of the previously reported assay using the organic dye crystal violet as a fluorescent probe. This label-free luminescent switch-on assay exhibits high sensitivity and selectivity towards ATP with a limit of detection of 2.5 µM.

Label-free luminescent oligonucleotide-based probes

Breakthrough advances in chemistry and biology over the last two decades have vastly expanded the repertoire of nucleic acid structure and function with potential application in multiple areas of science and technology, including sensing and analytical applications. DNA oligonucleotides represent popular tools for the development of sensing platforms due to their low cost, rich structural polymorphism, and their ability to bind to cognate ligands with sensitivity and specificity rivaling those for protein enzymes and antibodies. In this review, we give an overview of the "label-free" approach that has been a particular focus of our group and others for the construction of luminescent DNA-based sensing platforms. The label-free strategy aims to overcome some of the drawbacks associated with the use of covalently-labeled oligonucleotides prevalent in electrochemical and optical platforms. Label-free DNA-based probes harness the selective interaction between luminescent dyes and functional oligonucleotides that exhibit a "structure-switching" response upon binding to analytes. Based on the numerous examples of label-free luminescent DNA-based probes reported recently, we envisage that this field would continue to thrive and mature in the years to come.

A highly sensitive G-quadruplex-based luminescent switch-on probe for the detection of polymerase 3'-5' proofreading activity

We report herein a luminescent switch-on label-free G-quadruplex-based assay for the rapid and sensitive detection of polymerase proofreading activity using a novel iridium(III) complex as a G-quadruplex-selective probe. The interaction of the iridium(III) complex with the G-quadruplex motif facilitates the highly sensitive switch-on detection of polymerase proofreading activity. Using T4 DNA polymerase (T4 pol) as a model enzyme, the assay achieved high sensitivity and selectivity for T4 pol over other tested enzymes.

A luminescent G-quadruplex switch-on probe for the highly selective and tunable detection of cysteine and glutathione

A G-quadruplex-selective luminescent iridium(III) switch-on probe has been developed for the detection of cysteine (Cys) in aqueous solution. The system is highly sensitive and selective towards Cys with a tunable range of detection. The detection of glutathione (GSH) is also examined.

Detection of base excision repair enzyme activity using a luminescent G-quadruplex selective switch-on probe

We report herein a simple and convenient luminescent assay for detection of base excision repair enzyme activity using an Ir(III) complex as a G-quadruplex selective probe. Using uracil-DNA glycosylase (UDG) as a model enzyme, the assay achieved high sensitivity and selectivity for UDG over other tested enzymes. The utility of the assay for screening potential UDG inhibitors was also demonstrated.

G-quadruplexes for luminescent sensing and logic gates

G-quadruplexes represent a versatile sensing platform for the construction of label-free molecular detection assays owing to their diverse structures that can be selectively recognized by G-quadruplex-specific luminescent probes. In this Survey and Summary, we highlight recent examples of the application of the label-free strategy for the development of G-quadruplex-based luminescent detection platforms with a view towards the potential application of tetraplex structures in the design of DNA logic gates.

A highly selective and non-reaction based chemosensor for the detection of Hg2+ ions using a luminescent iridium(III) complex

We report herein a novel luminescent iridium(III) complex with two hydrophobic carbon chains as a non-reaction based chemosensor for the detection of Hg(2+) ions in aqueous solution (<0.002% of organic solvent attributed to the probe solution). Upon the addition of Hg(2+) ions, the emission intensity of the complex was significantly enhanced and this change could be monitored by the naked eye under UV irradiation. The iridium(III) complex shows high specificity for Hg(2+) ions over eighteen other cations. The system is capable of detecting micromolar levels of Hg(2+) ions, which is within the range of many chemical systems.

Luminescent and colorimetric strategies for the label-free DNA-based detection of enzyme activity

Enzymes are critically involved in maintaining normal cellular physiology through the catalysis of highly specific and tightly regulated chemical reactions. The inhibition or undesired activation of particular enzymatic functions has been associated with the pathogenesis of a number of diseases. Consequently, the aberrant activity of certain enzymes can be regarded as biomarkers for the diagnosis or monitoring of particular diseases. With rapid technological advances in the field of DNA nanotechnology, oligonucleotides have recently emerged as attractive recognition units for monitoring the activity of enzymes compared with organic small molecules or protein antibodies. In this review article, we present an overview of advantages and versatility of the 'label-free' approach for the fabrication of DNA-based sensing platforms using colorimetric and luminescent molecules as signal transducing units and highlight recent examples of label-free strategies that have been employed for monitoring enzyme activity.