Study of the Function of G‐Rich Aptamers Selected for Lung Adenocarcinoma

Guanine (G)‐rich oligonucleotides have attracted considerable interest as therapeutic agents. Two G‐rich aptamers were selected against epidermal growth factor receptor (EGFR)‐transfected A549 cells, and their G‐rich domains (S13 and S50) were identified to account for the binding of parental aptamers. Circular dichroism (CD) spectra showed that S13 and S50 bound to their targets by forming parallel quadruplexes. Their binding, internalization, and antiproliferation activity in cancer and noncancer cells were investigated by flow cytometry and 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium (MTS) assay, and compared with those of nucleolin‐binding AS1411 and thrombin‐binding aptamer. The two truncated aptamers (S13 and S50) have good binding and internalization in cancer cells and noncancer cells; however, only S50, similar to AS1411, shows potent antiproliferation against cancer cells. Our data suggest that tumor‐selective antiproliferation of G‐rich oligonucleotides does not directly depend on the binding of the G‐rich aptamer to cells.     

Towards the Development of Structure‐Selective G‐Quadruplex‐Binding Indolo[3,2‐b]quinolines

The interaction of phenyl‐substituted indolo[3,2‐b]quinolines with DNA G‐quadruplexes of different topology were studied by using a combination of spectroscopic and calorimetric methodologies. N5‐Methylated indoloquinoline derivatives (^MePIQ) with an aminoalkyl side chain exhibit high affinities for the parallel‐stranded MYC quadruplex and a (3+1)‐hybrid structure combined with an excellent discrimination against the antiparallel thrombin‐binding aptamer (TBA) and the human telomeric (HT) quadruplexes. Dissociation constants for the binding of the ligand to the MYC quadruplex are in the submicromolar range, being below the corresponding dissociation constants for the antiparallel‐stranded quadruplexes by about one order of magnitude. Competition experiments with double‐helical DNA reveal the impact of indoloquinoline structural features on the selectivity for the parallel quadruplex relative to duplex DNA. Based on a calorimetric analysis binding to MYC is shown to be equally driven by favorable enthalpic and entropic contributions with no significant impact on the type of cation present.     

G‐Quadruplex‐Based DNAzymes Aptasensor for the Amplified Electrochemical Detection of Thrombin

A novel G‐quadruplex‐based DNAzymes aptasensor for the amplified electrochemical detection of thrombin has been described. The aptasensor utilized a combination of hemin and guanine‐rich thrombin‐binding aptamer (TBA) to form horseradish peroxidase (HRP)‐mimicking DNAzymes with peroxidase catalytic activity. In the presence of thrombin, the enzyme activity could be extensively promoted, thereby providing the amplified electrochemical readout signals for detecting thrombin. This aptasensor exhibited high sensitivity and selectivity for thrombin determination, which enabled the analysis of thrombin with a detection limit of 6×10^–11 M. On the basis of results, this method could have broad applications in the detection of proteins and other biomolecules.     

Specific Binding of a d‐RNA G‐Quadruplex Structure with an l‐RNA Aptamer

G‐quadruplex (G4) structures are of general importance in chemistry and biology, such as in biosensing, gene regulation, and cancers. Although a large repertoire of G4‐binding tools has been developed, no aptamer has been developed to interact with G4. Moreover, the G4 selectivity of current toolkits is very limited. Herein, we report the first l ‐RNA aptamer that targets a d ‐RNA G‐quadruplex (rG4). Using TERRA rG4 as an example, our results reveal that this l ‐RNA aptamer, Ap3‐7, folds into a unique secondary structure, exhibits high G4 selectivity and effectively interferes with TERRA‐rG4–RHAU53 binding. Our approach and findings open a new door in further developing G4‐specific tools for diverse applications.     

G‐Quadruplex‐Linked Supersandwich DNA Structure for Electrochemical Amplified Detection of Thrombin

In this paper, a novel strategy of electrochemical amplified detection of thrombin based on G‐quadruplex‐linked supersandwich structure was described. In the presence of K⁺ and hemin, the original hairpin DNA sequence activated an autonomous cross‐opening process to build up hemin/G‐quadruplex structure and can hybridize to form supersandwich structure containing multiple signal labels. With the addition of thrombin, it conjugated with its aptamer, leading to a remarkably descended signal. The supersandwich‐amplified electrochemical sensor system was highly sensitive in the concentration range from 10^?6 to 10^?10 M with a detection limit of 10 pM and also demonstrated excellent selectivity. The amplifying supersandwich structure with multiple labels can be implemented as a versatile sensing platform for analyzing other DNA in the presence of the appropriate probe.     

Pattern‐Based Detection of Toxic Metals in Surface Water with DNA Polyfluorophores

Heavy metal contamination of water can be toxic to humans and wildlife; thus the development of methods to detect this contamination is of high importance. Here we describe the design and application of DNA‐based fluorescent chemosensors on microbeads to differentiate eight toxic metal ions in water. We developed and synthesized four fluorescent 2′‐deoxyribosides of metal‐binding ligands. A tetramer‐length oligodeoxy‐fluoroside (ODF) library of 6561 members was constructed and screened for sequences responsive to metal ions, of which seven sequences were selected. Statistical analysis of the response patterns showed successful differentiation of the analytes at concentrations as low as 100 nM . Sensors were able to classify water samples from 13 varied sites and quantify metal contamination in unknown specimens. The results demonstrate the practical potential of bead‐based ODF chemosensors to analyze heavy metal contamination in water samples by a simple and inexpensive optical method.     

Luminescent Strategies for Label‐Free G‐Quadruplex‐Based Enzyme Activity Sensing

By catalyzing highly specific and tightly controlled chemical reactions, enzymes are essential to maintaining normal cellular physiology. However, aberrant enzymatic activity can be linked to the pathogenesis of various diseases. Therefore, the unusual activity of particular enzymes can represent testable biomarkers for the diagnosis or screening of certain diseases. In recent years, G‐quadruplex‐based platforms have attracted wide attention for the monitoring of enzymatic activities. In this Personal Account, we discuss our group's works on the development of G‐quadruplex‐based sensing system for enzyme activities by using mainly iridium(III) complexes as luminescent label‐free probes. These studies showcase the versatility of the G‐quadruplex for developing assays for a variety of different enzymes.     

Multifunctional G‐Quadruplex Aptamers and Their Application to Protein Detection

Two significant G‐quadruplex aptamers named AGRO100 and T30695 are identified as multifunctional aptamers that can bind the protein ligands nucleolin or HIV‐1 integrase and hemin. Besides their strong binding to target proteins, both AGRO100 and T30695 exhibit high hemin‐binding affinities comparable to that of the known aptamer (termed PS2M) selected by the in vitro evolution process. Most importantly, their corresponding hemin–DNA complexes reveal excellent peroxidase‐like activities, higher than that of the reported hemin–PS2M DNAzyme. This enables these multifunctional aptamers to be applied to the sensitive detection of proteins, which is demonstrated by applying AGRO100 to the chemiluminescence detection of nucleolin expressed at the surface of HeLa cells. Based on the specific AGRO100–nucleolin interaction, the surface‐expressed nucleolin of HeLa cells is labeled in situ with the hemin–AGRO100 DNAzyme, and then determined in the luminol–H₂O₂ system. Through this approach, the sensitive detection of total nucleolin expressed at the surface of about 6000 HeLa cells is accomplished. Our results suggest that exploiting new functions of existing aptamers will help to extend their potential applications in the biochemical field.     

Base‐Pairing Directed Folding of a Bimolecular G‐Quadruplex: New Insights into G‐Quadruplex‐Based DNAzymes

Base pairs, magic hands : An additional base‐pairing duplex is utilized to control the folding topologies of a bimolecular G‐quadruplex formed by two G‐rich single‐stranded DNAs (see picture), which is dependent on the position of base pairs. This study clearly reveals an important intrinsic role of additional base pairs in the G‐quadruplex structure, and also provides a clue to the formation mechanism of the G‐quadruplex‐based DNAzyme.

     

Quantitative Detection of G‐Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination

G‐quadruplex DNA show structural polymorphism, leading to challenges in the use of selective recognition probes for the accurate detection of G‐quadruplexes in vivo. Herein, we present a tripodal cationic fluorescent probe, NBTE , which showed distinguishable fluorescence lifetime responses between G‐quadruplexes and other DNA topologies, and fluorescence quantum yield (Φ_f) enhancement upon G‐quadruplex binding. We determined two NBTE ‐G‐quadruplex complex structures with high Φ_f values by NMR spectroscopy. The structures indicated NBTE interacted with G‐quadruplexes using three arms through π–π stacking, differing from that with duplex DNA using two arms, which rationalized the higher Φ_f values and lifetime response of NBTE upon G‐quadruplex binding. Based on photon counts of FLIM, we detected the percentage of G‐quadruplex DNA in live cells with NBTE and found G‐quadruplex DNA content in cancer cells is 4‐fold that in normal cells, suggesting the potential applications of this probe in cancer cell detection.     

Complex Formation of d‐Metal Ions at the Interface of TbIII‐Doped Silica Nanoparticles as a Basis of Substrate‐Responsive TbIII‐Centered Luminescence

The complex formation of d‐metal ions at the interface of Tb^III‐doped silica nanoparticles modified by amino groups is introduced as a route to sensing d‐metal ions and some organic molecules. Diverse modes of surface modification (covalent and noncovalent) are used to fix amino groups onto the silica surface. The interfacial binding of d‐metal ions and complexes is the reason for the Tb^III‐centered luminescence quenching. The regularities and mechanisms of quenching are estimated for the series of d‐metal ions and their complexes with chelating ligands. The obtained results reveal the interfacial binding of Cu^II ions as the basis of their quantitative determination in the concentration range 0.1–2.5 μM by means of steady‐state and time‐resolved fluorescence measurements. The variation of chelating ligands results in a significant effect on the quenching regularities due to diverse binding modes (inner or outer sphere) between amino groups at the interface of nanoparticles and Fe^III ions. The applicability of the steady‐state and time‐resolved fluorescence measurements to sense both Fe^III ions and catechols in aqueous solution by means of Tb^III‐doped silica nanoparticles is also introduced.     

Synthesis,Structure, and Physico‐optical Properties of Manganate(II)‐Based Ionic Liquids

Several ionic liquids (ILs) based on complex manganate(II) anions with chloro, bromo, and bis(trifluoromethanesulfonyl)amido (Tf₂N) ligands have been synthesized. As counterions, n‐alkyl‐methylimidazolium (C_nmim) cations of different chain length (alkyl=ethyl (C₂), propyl (C₃), butyl (C₄), hexyl (C₆)) were chosen. Except for the 1‐hexyl‐3‐methylimidazolium ILs, all of the prepared compounds could be obtained in a crystalline state at room temperature. However, each of the compounds displayed a strong tendency to form a supercooled liquid. Generally, solidification via a glass transition took place below ?40 °C. Consequently, all of these compounds can be regarded as ionic liquids. Depending on the local coordination environment of Mn²⁺, green (tetrahedrally coordinated Mn²⁺) or red (octahedrally coordinated Mn²⁺) luminescence emission from the ⁴T(G) level is observed. 1 The local coordination of the luminescent Mn²⁺ centre has been unequivocally established by UV/Vis as well as Raman and IR vibrational spectroscopies. Emission decay times measured at room temperature in the solid state (crystalline or powder) were generally a few ms, although, depending on the ligand, values of up to 25 ms were obtained. For the bromo compounds, the luminescence decay times proved to be almost independent of the physical state and the temperature. However, for the chloro‐ and bis(trifluoromethanesulfonyl)amido ILs, the emission decay times were found to be dependent on the temperature even in the solid state, indicating that the measured values are strongly influenced by nuclear motion and the vibration of the atoms. In the liquid state, the luminescence of tetrahedrally coordinated Mn²⁺ could only be observed when the tetrachloromanganate ILs were diluted with the respective halide ILs. However, for [C₃mim][Mn(Tf₂N)₃], in which Mn²⁺ is in an octahedral coordination environment, a weak red emission from the pure compound was found even in the liquid state at elevated temperatures.     

[Ru(bpy)2(dcbpy)NHS] Labeling/Aptamer‐Based Biosensor for the Detection of Lysozyme by Increasing Sensitivity with Gold Nanoparticle Amplification

A novel [Ru(bpy)₂(dcbpy)NHS] labeling/aptamer‐based biosensor combined with gold nanoparticle amplification for the determination of lysozyme with an electrochemiluminescence (ECL) method is presented. In this work, an aptamer, an ECL probe, gold nanoparticle amplification, and competition assay are the main protocols employed in ECL detection. With all the protocols used, an original biosensor coupled with an aptamer and [Ru(bpy)₂(dcbpy)NHS] has been prepared. Its high selectivity and sensitivity are the main advantages over other traditional [Ru(bpy)₃]²⁺ biosensors. The electrochemical impedance spectroscopy (EIS) and atomic force microscopy (AFM) characterization illustrate that this biosensor is fabricated successfully. Finally, the biosensor was applied to a displacement assay in different concentrations of lysozyme solution, and an ultrasensitive ECL signal was obtained. The ECL intensity decreased proportionally to the lysozyme concentration over the range 1.0×10^?13–1.0×10^?8 mol L^?1 with a detection limit of 1.0×10^?13 mol L^?1. This strategy for the aptasensor opens a rapid, selective, and sensitive route for the detection of lysozyme and potentially other proteins.     

NMR Structure of a Triangulenium‐Based Long‐Lived Fluorescence Probe Bound to a G‐Quadruplex

An NMR structural study of the interaction between a small‐molecule optical probe (DAOTA‐M2) and a G‐quadruplex from the promoter region of the c‐myc oncogene revealed that they interact at 1:2 binding stoichiometry. NMR‐restrained structural calculations show that binding of DAOTA‐M2 occurs mainly through π–π stacking between the polyaromatic core of the ligand and guanine residues of the outer G‐quartets. Interestingly, the binding affinities of DAOTA‐M2 differ by a factor of two for the outer G‐quartets of the unimolecular parallel G‐quadruplex under study. Unrestrained MD calculations indicate that DAOTA‐M2 displays significant dynamic behavior when stacked on a G‐quartet plane. These studies provide molecular guidelines for the design of triangulenium derivatives that can be used as optical probes for G‐quadruplexes.     

DNA Triplexes‐Guided Assembly of G‐Quadruplexes for Constructing Label‐free Fluorescent Logic Gates

Assembly of G‐quadruplexes guided by DNA triplexes in a controlled manner is achieved for the first time. The folding of triplex sequences in acidic conditions brings two separated guanine‐rich sequences together and subsequently a G‐quadruplex structure is formed in the presence of K⁺. Based on this novel platform, label‐free fluorescent logic gates, such as AND, INHIBIT, and NOR, are constructed with ions as input and the fluorescence of a G‐quadruplex‐specific fluorescent probe NMM as output.     

Carbon‐Monoxide‐Releasing Molecules for the Delivery of Therapeutic CO In Vivo

The development of carbon‐monoxide‐releasing molecules (CORMs) as pharmaceutical agents represents an attractive and safer alternative to administration of gaseous CO. Most CORMs developed to date are transition‐metal carbonyl complexes. Although such CORMs have showed promising results in the treatment of a number of animal models of disease, they still lack the necessary attributes for clinical development. Described in this Minireview are the methods used for CORM selection, to date, and how new insights into the reactivity of metal‐carbonyl complexes in vivo, together with advances in methods for live‐cell CO detection, are driving the design and synthesis of new CORMs, CORMs that will enable controlled CO release in vivo in a spatial and temporal manner without affecting oxygen transport by hemoglobin.     

Molecular Recognition of the Hybrid‐2 Human Telomeric G‐Quadruplex by Epiberberine: Insights into Conversion of Telomeric G‐Quadruplex Structures

Human telomeres can form DNA G‐quadruplex (G4), an attractive target for anticancer drugs. Human telomeric G4s bear inherent structure polymorphism, challenging for understanding specific recognition by ligands or proteins. Protoberberines are medicinal natural‐products known to stabilize telomeric G4s and inhibit telomerase. Here we report epiberberine (EPI) specifically recognizes the hybrid‐2 telomeric G4 predominant in physiologically relevant K⁺ solution and converts other telomeric G4 forms to hybrid‐2, the first such example reported. Our NMR structure in K⁺ solution shows EPI binding induces extensive rearrangement of the previously disordered 5′‐flanking and loop segments to form an unprecedented four‐layer binding pocket specific to the hybrid‐2 telomeric G4; EPI recruits the (?1) adenine to form a “quasi‐triad” intercalated between the external tetrad and a T:T:A triad, capped by a T:T base pair. Our study provides structural basis for small‐molecule drug design targeting the human telomeric G4.     

A Promising MgII‐Ion‐Selective Luminescent Probe: Structures and Properties of Dy–Mn Polymers with High Symmetry

Two Dy–Mn polymers, {[Dy(L¹)₃Mn_1.5(H₂O)₃]?3.125 H₂O}_n ( 1 , L¹=pyridine‐2,6‐dicarboxylic acid) and {[Dy(L²)₃Mn_1.5(H₂O)₆]?8.25 H₂O}_n ( 2 , L² = 4‐hydroxylpyridine‐2,6‐dicarboxylic acid), with high symmetry (S₆) have been prepared. Polymer 1 has a nanoporous 3D framework with channel of about 17.6 Å diameter, while 2 has a honeycomb‐type 2D structure with the cavity of approximately 14.4 Å diameter. In the construction of multidimensional porous polymers with 3d–4f mixed metals, it is the first observation that a ligand substituent effect leads to dramatic differences in the structures formed. Luminescent studies reveal that the emission intensities of 1 and 2 increase significantly upon the addition of Mg²⁺, whereas the introduction of other metal ions leaves the intensity unchanged or even weakens it; hence, both of them may serve as good candidates of Mg²⁺ luminescent probes. To our knowledge, complex 1 is also the first example of a 3d–4f metal‐based nanoporous polymer to exhibit luminescent selectivity for Mg²⁺. Magnetic susceptibility measurements reveal a rather rare ferromagnetic interaction in 2 . Thermal gravimetric analyses and powder X‐ray diffraction investigations have also been performed, suggestive of high thermal stability of 1 .     

Bioactive Luminescent Transition‐Metal Complexes for Biomedical Applications

The serendipitous discovery of the anticancer drug cisplatin cemented medicinal inorganic chemistry as an independent discipline in the 1960s. Luminescent metal complexes have subsequently been widely applied for sensing, bio‐imaging, and in organic light‐emitting diode applications. Transition‐metal complexes possess a variety of advantages that make them suitable as therapeutics and as luminescent probes for biomolecules. It is thus highly desirable to develop new luminescent metal complexes that either interact with DNA through different binding modes or target alternative cellular machinery such as proteins as well as to provide a more effective means of monitoring disease progression. In this Review, we highlight recent examples of biologically active luminescent metal complexes that can target and probe a specific biomolecule, and offer insights into the future potential of these compounds for the investigation and treatment of human diseases.