Metal-ion-dependent folding of a uranyl-specific DNAzyme: insight into function from fluorescence resonance energy transfer studies

Fluorescence resonance energy transfer (FRET) has been used to study the global folding of an uranyl (UO₂²⁺)‐specific 39E DNAzyme in the presence of Mg²⁺, Zn²⁺, Pb²⁺, or UO₂²⁺. At pH 5.5 and physiological ionic strength (100 mM Na⁺), two of the three stems in this DNAzyme folded into a compact structure in the presence of Mg²⁺ or Zn²⁺. However, no folding occurred in the presence of Pb²⁺ or UO₂²⁺; this is analogous to the “lock‐and‐key” catalysis mode first observed in the Pb²⁺‐specific 8–17 DNAzyme. However, Mg²⁺ and Zn²⁺ exert different effects on the 8–17 and 39E DNAzymes. Whereas Mg²⁺ or Zn²⁺‐dependent folding promoted 8–17 DNAzyme activity, the 39E DNAzyme folding induced by Mg²⁺ or Zn²⁺ inhibited UO₂²⁺‐specific activity. Group IIA series of metal ions (Mg²⁺, Ca²⁺, Sr²⁺) also caused global folding of the 39E DNAzyme, for which the apparent binding affinity between these metal ions and the DNAzyme decreases as the ionic radius of the metal ions increases. Because the ionic radius of Sr²⁺ (1.12 Å) is comparable to that of Pb²⁺ (1.20 Å), but contrary to Pb²⁺, Sr²⁺ induces the DNAzyme to fold under identical conditions, ionic size alone cannot account for the unique folding behaviors induced by Pb²⁺ and UO₂²⁺. Under low ionic strength (30 mM Na⁺), all four metal ions (Mg²⁺, Zn²⁺, Pb²⁺, and UO₂²⁺), caused 39E DNAzyme folding, suggesting that metal ions can neutralize the negative charge of DNA‐backbone phosphates in addition to playing specific catalytic roles. Mg²⁺ at low (<2 mM ) concentration promoted UO₂²⁺‐specific activity, whereas Mg²⁺ at high (>2 mM ) concentration inhibited the UO₂²⁺‐specific activity. Therefore, the lock‐and‐key mode of DNAzymes depends on ionic strength, and the 39E DNAzyme is in the lock‐and‐key mode only at ionic strengths of 100 mM or greater.     

ESI‐MS studies of the non‐covalent interactions between biologically important metal ions and N‐sulfonylcytosine derivatives

The aim of this report is to present the electrospray ionization mass spectrometry results of the non‐covalent interaction of two biologically active ligands, N‐1 ‐ (p‐toluenesulfonyl)cytosine, 1‐TsC, 1 and N‐1 ‐ methanesulfonylcytosine, 1‐MsC, 2 and their Cu(II) complexes Cu(1‐TsC‐N3)₂Cl₂, 3 and Cu(1‐MsC‐N3)₂Cl₂ and 4 with biologically important cations: Na⁺, K⁺, Ca²⁺, Mg²⁺ and Zn²⁺. The formation of various complex metal ions was observed. The alkali metals Na⁺ and K⁺ formed clusters because of electrostatic interactions. Ca²⁺ and Mg²⁺ salts produced the tris ligand and mixed ligand complexes. The interaction of Zn²⁺ with 1–4 produced monometal and dimetal Zn²⁺ complexes as a result of the affinity of Zn²⁺ ions toward both O and N atoms. Copyright © 2016 John Wiley & Sons, Ltd.     

Syntheses,structures of N‐(substituted)‐2‐aza‐[3]‐ferrocenophanes and their application as redox sensor for Cu2+ ion

Rigid N‐(substituted)‐2‐aza‐[3]‐ferrocenophanes L1 and L2 were easily synthesized from 1,1 ‐dicarboxyaldehydeferrocene and the corresponding amines. Ligands L1 and L2 were characterized by ¹H NMR, ¹³C NMR and single‐crystal X‐ray crystallography. The coordination abilities of L1 and L2 with metal ions such as Cu²⁺, Mg²⁺, Ni²⁺, Zn²⁺, Pb²⁺ and Cd²⁺ were evaluated by cyclic voltammetry. The electrochemical shift (ΔE_1/2) of 125 mV was observed in the presence of Cu²⁺ ion, while no significant shift of the Fc/Fc + couple was observed when Mg²⁺, Ni²⁺, Zn²⁺, Pb²⁺, Cd²⁺ metal ions were added to the solution of L1 in the mixture of MeOH and H₂O. Moreover, the extent of the anodic shift of redox potentials was approximately equal to that induced by Cu²⁺ alone when a mixture of Cu²⁺, Mg²⁺, Ni²⁺, Zn²⁺, Pb²⁺ and Cd²⁺ was added to a solution of L1. Ligand L1 was proved to selectively sense Cu²⁺ in the presence of large, excessive first‐row transition and late‐transition metal cations. The coordination model was proposed from the results of controlled experiments and quantum calculations. Copyright © 2012 John Wiley & Sons, Ltd.     

DNAzyme‐Loaded Metal–Organic Frameworks (MOFs) for Self‐Sufficient Gene Therapy

DNAzymes have been recognized as potent therapeutic agents for gene therapy, while their inefficient intracellular delivery and insufficient cofactor supply precludes their practical biological applications. Metal–organic frameworks (MOFs) have emerged as promising drug carriers without in‐depth consideration of their disassembled ingredients. Herein, we report a self‐sufficient MOF‐based chlorin e6‐modified DNAzyme (Ce6‐DNAzyme) therapeutic nanosystem for combined gene therapy and photodynamic therapy (PDT). The ZIF‐8 nanoparticles (NPs) could efficiently deliver the therapeutic DNAzyme without degradation into cancer cells. The pH‐responsive ZIF‐8 NPs disassemble with the concomitant release of the guest DNAzyme payloads and the host Zn²⁺ ions that serve, respectively, as messenger RNA‐targeting agent and required DNAzyme cofactors for activating gene therapy. The auxiliary photosensitizer Ce6 could produce reactive oxygen species (ROS) and provide a fluorescence signal for the imaging‐guided gene therapy/PDT.     

Detection of Metal Ions (Cu2+, Hg2+) and Cocaine by Using Ligation DNAzyme Machinery

The Cu²⁺‐dependent ligation DNAzyme is implemented as a biocatalyst for the colorimetric or chemiluminescence detection of Cu²⁺ ions, Hg²⁺ ions, or cocaine. These sensing platforms are based on the structural tailoring of the sequence of the Cu²⁺‐dependent ligation DNAzyme for specific analytes. The tethering of a subunit of the hemin/G‐quadruplex DNAzyme to the ligation DNAzyme sequence, and the incorporation of an imidazole‐functionalized nucleic‐acid sequence, which acts as a co‐substrate for the ligation DNAzyme that is tethered to the complementary hemin/G‐quadruplex subunit. In the presence of different analytes, Cu²⁺ ions, Hg²⁺ ions, or cocaine, the pretailored Cu²⁺‐dependent ligation DNAzyme sequence stimulates the respective ligation process by combining the imidazole‐functionalized co‐substrate with the ligation DNAzyme sequence. These reactions lead to the self‐assembly of stable hemin/G‐quadruplex DNAzyme nanostructures that enable the colorimetric analysis of the substrate through the DNAzyme‐catalyzed oxidation of 2,2′‐azinobis(3‐ethylbenzothiazoline‐6‐sulfonic acid), ABTS^2?, by H₂O₂ into the colored product ABTS^.?, or the chemiluminescence detection of the substrate through the DNAzyme‐catalyzed oxidation of luminol by H₂O₂. The detection limits for the sensing of Cu²⁺ ions, Hg²⁺ ions, and cocaine correspond to 1 nM , 10 nM and 2.5 μM , respectively. These different sensing platforms also reveal impressive selectivities.     

One‐Step Synthesis of Small‐Sized and Water‐Soluble NaREF4 Upconversion Nanoparticles for In Vitro Cell Imaging and Drug Delivery

Small (2–28 nm) NaREF₄ (rare earth (RE)=Nd–Lu, Y) nanoparticles (NPs) were prepared by an oil/water two‐phase approach. Meanwhile, hydrophilic NPs can be obtained through a successful phase‐transition process by introducing the amphiphilic surfactant sodium dodecylsulfate (SDS) into the same reaction system. Hollow‐structured NaREF₄ (RE=Y, Yb, Lu) NPs can be fabricated in situ by electron‐beam lithography on solid NPs. The MTT assay indicates that these hydrophilic NPs with hollow structures exhibit good biocompatibility. The as‐prepared hollow‐structured NPs can be used as anti‐cancer drug carriers for drug storage/release investigations. Doxorubicin hydrochloride (DOX) was taken as model drug. The release of DOX from hollow α‐NaLuF₄:20 % Yb³⁺, 2 % Er³⁺ exhibits a pH‐sensitive release patterns. Confocal microscopy observations indicate that the NPs can be taken up by HeLa cells and show obvious anti‐cancer efficacy. Furthermore, α‐NaLuF₄:20 % Yb³⁺, 2 % Er³⁺ NPs show bright‐red emission under IR excitation, making both the excitation and emission light fall within the “optical window” of biological tissues. The application of α‐NaLuF₄:20 % Yb³⁺, 2 % Er³⁺ in the luminescence imaging of cells was also investigated, which shows a bright‐red emission without background noise.     

Ion‐Responsive Hemin–G‐Quadruplexes for Switchable DNAzyme and Enzyme Functions

Programmed nucleic acid sequences undergo K⁺ ion‐induced self‐assembly into G‐quadruplexes and separation of the supramolecular structures by the elimination of K⁺ ions by crown ether or cryptand ion‐receptors. This process allows the switchable formation and dissociation of the respective G‐quadruplexes. The different G‐quadruplex structures bind hemin, and the resulting hemin–G‐quadruplex structures reveal horseradish peroxidase DNAzyme catalytic activities. The following K⁺ ion/receptor switchable systems are described: 1) The K⁺‐induced self‐assembly of the Mg²⁺‐dependent DNAzyme subunits into a catalytic nanostructure using the assembly of G‐quadruplexes as bridging unit. 2) The K⁺‐induced stabilization of the anti‐thrombin G‐quadruplex nanostructure that inhibits the hydrolytic functions of thrombin. 3) The K⁺‐induced opening of DNA tweezers through the stabilization of G‐quadruplexes on the “tweezers’ arms" and the release of a strand bridging the tweezers into a closed structure. In all of the systems reversible, switchable, functions are demonstrated. For all systems two different signals are used to follow the switchable functions (fluorescence and the catalytic functions of the derived hemin–G‐quadruplex DNAzyme).     

Metal Analyses in Environmental and Pharmaceutical Samples by Capillary Electrophoresis with Methyl 3‐Amino‐3‐(pyridin‐3‐yl)propanoate Dihydrochloride as a New Ion‐Pairing Reagent

Separation and determination of some common metal ions was achieved with methyl 3‐amino‐3‐(pyridin‐3‐yl)propanoate dihydrochloride (MAPP) as an ion‐pairing reagent and pyridine as a detectable counter‐ion for indirect UV detection at 254 nm. The effects of the complexing reagent and chromophore concentrations, applied voltage, and organic solvent content on the separation were investigated. The optimized separation was carried out in a running electrolyte containing 16 mM MAPP and 20 mM pyridine at pH 4.0 and was successfully applied to the qualitative and quantitative analysis of Li⁺, Na⁺, Mg²⁺, Ca²⁺, Ba²⁺, Ni²⁺, and Zn²⁺ in pharmaceutical vitamin preparations and various water samples.     

Synthesis and Structures of the Novel Biferrocenamine‐Based Receptor and its Voltammetric Responses to Transition Metal Ions

Reactions of formylferrocene and 1,2‐di‐(o‐aminophenoxy)ethane yield the novel bis(ferrocenyl) receptor (FcL). This compound has been characterized by IR, ¹H NMR and elemental analysis. In addition, the electrochemical behavior of FcL was investigated in detail in 0.1 M tetra‐n‐butylammonium perchlorate (TBAP) + CH₃CN by cyclic voltammetry (CV) and chronoamperometry. Its co‐ordination properties with metal ions in acetonitrile were also studied. The FcL shows a two‐wave behavior for H⁺, Cu²⁺, Zn²⁺ and Ni²⁺, but was unresponsive to Mg²⁺ and Ca²⁺. The maximum oxidation peak shift of about 250 mV was found for FcL in the presence of Cu²⁺, Zn²⁺ or Ni²⁺.     

Membrane Transport of Pb(II) with a Cooperative Carrier Composed of Dibenzyldiaza‐18‐Crown‐6 and Palmitic Acid

A chloroform membrane system containing a given mixture of dibenzyldiaza‐18‐crown‐6 and palmetic acid was applied for transport of Pb²⁺ ions. The transport was capable of moving metal ions “uphill”. Thus, it was possible to follow the transfer of Pb(II) from the aqueous source phase to the organic layer and from the organic layer to the receiving phase. The effects of thiosulfate concentration in the receiving phase, palmetic acid and dibenzyldiaza‐18‐crown‐6 concentration in the organic phase on the efficiency of the transport system were examined. By using S₂O₃^2? ion as metal ion acceptor in the receiving phase, the amount of lead ion transport across the liquid membrane after 150 minutes is 96 ± 1.5%. The selectivity and efficiency of lead transport from aqueous solution containing Cu²⁺, Tl⁺, Ag⁺, Co²⁺, Ni²⁺, Mg²⁺, Zn²⁺, Hg²⁺, Cd²⁺, Ca²⁺ were investigated. In the presence of thiosulfate as a suitable masking agent in the source phase, the interfering effects of Ag⁺ and Cu²⁺ were diminished drastically.     

Enzyme‐Mediated Endogenous and Bioorthogonal Control of a DNAzyme Fluorescent Sensor for Imaging Metal Ions in Living Cells

Bioorthogonal control of metal‐ion sensors for imaging metal ions in living cells is important for understanding the distribution and fluctuation of metal ions. Reported here is the endogenous and bioorthogonal activation of a DNAzyme fluorescent sensor containing an 18‐base pair recognition site of a homing endonuclease (I‐SceI), which is found by chance only once in 7×10¹⁰ bp of genomic sequences, and can thus form a near bioorthogonal pair with I‐SceI for DNAzyme activation with minimal effect on living cells. Once I‐SceI is expressed inside cells, it cleaves at the recognition site, allowing the DNAzyme to adopt its active conformation. The activated DNAzyme sensor is then able to specifically catalyze cleavage of a substrate strand in the presence of Mg²⁺ to release the fluorophore‐labeled DNA fragment and produce a fluorescent turn‐on signal for Mg²⁺. Thus I‐SceI bioorthogonally activates the 10–23 DNAzyme for imaging of Mg²⁺ in HeLa cells.     

Amphiphilic Schiff Base Organogels: Metal‐Ion‐Mediated Chiral Twists and Chiral Recognition

New amphiphilic gelators that contained both Schiff base and L ‐glutamide moieties, abbreviated as o‐SLG and p‐SLG, were synthesized and their self‐assembly in various organic solvents in the absence and presence of metal ions was investigated. Gelation test revealed that o‐SLG formed a thermotropic gel in many organic solvents, whilst p‐SLG did not. When metal ions, such as Cu²⁺, Zn²⁺, Mg²⁺, Ni²⁺, were added, different behaviors were observed. The addition of Cu²⁺ induced p‐SLG to from an organogel. In the case of o‐SLG, the addition of Cu²⁺ and Mg²⁺ ions maintained the gelating ability of the compound, whilst Zn²⁺ and Ni²⁺ ions destroyed the gel. In addition, the introduction of Cu²⁺ ions caused the nanofiber gel to perform a chiral twist, whilst the Mg²⁺ ions enhanced the fluorescence of the gel. More interestingly, the Mg²⁺‐ion‐mediated organogel showed differences in the fluorescence quenching by D ‐ and L ‐tartaric acid, thus showing a chiral recognition ability.     

Programmed catalysis within stimuli-responsive mechanically unlocked nanocavities in DNA origami tiles

The assembly of reversible stimuli-responsive locked DNA origami tiles being unlocked, in the presence of appropriate triggers, to form nanocavities in the origami rafts, is introduced. In the presence of ATP, K⁺-ion-stabilized G-quadruplexes or pH-responsive T-A·T triggers and appropriately engineered “helper units”, the origami rafts are unlocked to form nanocavities. By the application of appropriate counter-triggers, the nanocavities are relocked, thus establishing the switchable and reversible “mechanical” opening and closure mechanism of the nanocavities. The interconnection of the stimuli-responsive origami tiles into dimer structures enables the programmed triggered unlocking of each of the origami tiles, or both of the origami tiles, to yield dictated nanocavity-containing tiles. In addition, the functionalization of the opposite faces of the origami tiles with Mg²⁺-ion-dependent DNAzyme subunits leads, upon the triggered unlocking of the nanocavities, to the self-assembly of the active DNAzymes in the confined cavities. By the cyclic opening and closure of the cavities the reversible “ON”/“OFF” activation of the Mg²⁺-ion-dependent DNAzyme is demonstrated. Furthermore, upon the tethering of different Mg²⁺-ion-dependent subunits to the opposite faces of stimuli-responsive dimer origami tiles, the triggered programmed catalytic operation of different Mg²⁺-ion-dependent DNAzymes in the confined nanocavities, associated with the origami tiles, is demonstrated.

Programmed unlocking of nanocavities in origami dimer structures using different auxiliary triggers.     

Rare‐Earth‐Based Nanoparticles with Simultaneously Enhanced Near‐Infrared (NIR)‐Visible (Vis) and NIR‐NIR Dual‐Conversion Luminescence for Multimodal Imaging

Multifunctional NaGdF₄:Yb³⁺,Er³⁺,Nd³⁺@NaGdF₄:Nd³⁺ core–shell nanoparticles (called Gd:Yb³⁺,Er³⁺,Nd³⁺@Gd:Nd³⁺ NPs) with simultaneously enhanced near‐infrared (NIR)‐visible (Vis) and NIR‐NIR dual‐conversion (up and down) luminescence (UCL/DCL) properties were successfully synthesized. The resulting core–shell NPs simultaneously emitted enhanced UCL at 522, 540, and 660 nm and DCL at 980 and 1060 nm under the excitation of a 793 nm laser. The enhanced UCL and DCL can be explained by complex energy‐transfer processes, Nd³⁺→Yb³⁺→Er³⁺ and Nd³⁺→Yb³⁺, respectively. The effects of Nd³⁺ concentration and shell thickness on the UCL/DCL properties were systematically investigated. The UCL and DCL properties of NPs were observed under the optimal conditions: a shell Nd³⁺ content of 20 % and a shell thickness of approximately 5 nm. Moreover, the Gd:Yb³⁺,Er³⁺,Nd³⁺@Gd:20 % Nd³⁺ NPs exhibited remarkable magnetic resonance imaging (MRI) properties similar to that of a clinical agent, Omniscan. Thus, the core–shell NPs with excellent UCL/DCL/magnetic resonance imaging (MRI) properties have great potential for both in vitro and in vivo multimodal bioimaging.     

Micelles as Containers for Self‐Assembled Nanodevices: A Fluorescent Sensor for Lipophilicity

Potentiometric titrations, fluorescence versus pH titrations, dynamic light scattering and fluorescence polarization anisotropy studies demonstrate that inside the nanodimensioned Triton X‐100 micelles, 1‐pyrenecarboxylic acid, PCOO^?, forms an apical complex with the Zn²⁺ cation encircled by a lipophilic cyclen ligand and hugely increasing its fluorescence. The ability of the Zn²⁺‐cyclen‐PCOO^? complex plus its micellar container to act as a fluorescent sensor to evaluate the lipophilicity of molecular species is demonstrated on the fatty acid series CH₃(CH₂)_xCOOH (x=0–16). At pH 7.4 a decrease in fluorescence is observed on the addition of fatty acids that is directly related to their chain length, that is, to their tendency to enter the micellar containers, where they dislocate PCOO^? from the Zn²⁺ centre. The independent determination of fatty acid pK_a values in the presence of Triton X‐100 micelles confirms that our fluorescent micellar device is capable of sensing their lipophilicity.     

A Highly Copper‐Selective Ratiometric Fluorescent Sensor Based on BODIPY

A new ratiometric fluorescent sensor ( 1 ) for Cu²⁺ based on 4,4‐difluoro‐4‐bora‐3a,4a‐diaza‐s‐indacene (BODIPY) with di(2‐picolyl)amine (DPA) as ion recognition subunit has been synthesized and investigated in this work. The binding abilities of 1 towards different metal ions such as alkali and alkaline earth metal ions (Na⁺, K⁺, Mg²⁺, Ca²⁺) and other metal ions ( Ba²⁺, Zn²⁺, Cd²⁺, Fe²⁺, Fe³⁺, Pb²⁺, Ni²⁺, Co²⁺, Hg²⁺, Ag⁺) have been examined by UV‐vis and fluorescence spectroscopies. 1 displays high selectivity for Cu²⁺ among all test metal ions and a ～10‐fold fluorescence enhancement in I₅₈₂/I₅₅₈ upon excitation at visible excitation wavelength. The binding mode of 1 and Cu²⁺ is a 1:1 stoichiometry determined via studies of Job plot, the nonlinear fitting of the fluorometric titration and ESI mass.     

Carbonic Anhydrase‐Mimetic Bolaamphiphile Self‐Assembly for CO2 Hydration and Sequestration

A biomimetic catalyst was prepared through the self‐assembly of a bolaamphiphilic molecule with histidine moieties for the sequestration of carbon dioxide. The histidyl bolaamphiphilic molecule bis(N‐α‐amidohistidine)‐1,7‐heptane dicarboxylate has been synthesized and self‐assembled to produce analogues of the active sites of carbonic anhydrase (CA) after association with Zn²⁺ ions. Spectroscopic analysis demonstrated the coordination of the Zn²⁺ ions with histidine imidazole moieties, which is the core conformation of CA active sites. The Zn‐associated self‐assembly worked as a CA‐mimetic catalyst that shows catalytic activity for CO₂ hydration. Evaluation of the kinetics of using para‐nitrophenylacetate revealed that the kinetic parameters of the CA‐mimetic catalyst were maximized at the optimal Zn concentration and that excess Zn ions resulted in deteriorated catalytic activity. The performance of the CA‐mimetic catalyst was enhanced by changing the pH value and temperature of the reaction, which implies that the hydrolysis of the substrate is the rate‐determining step. The catalyst‐assisted sequestration of CO₂ was demonstrated by CaCO₃ precipitation upon the addition of Ca²⁺ ions. This study offers an easy way to prepare enzyme analogues for CO₂ sequestration through the self‐assembly of bolaamphiphile molecules with designer biochemical moieties.     

Synthesis of Novel 4‐((Substituted bis‐indolyl)methyl)‐benzo‐15‐crown‐5 for the Colorimetric Detection of Hg2+ Ions in an Aqueous Medium

A practical, two‐step synthesis of novel 4‐(substituted bis‐indolyl)methyl)benzo‐15‐crown‐5 has been reported. The strategy employed for the synthesis of the desired molecules involved Duff formylation of benzo‐15‐crown‐5 to get 4‐formyl benzo‐15‐crown‐5 followed by subsequent reactions with substituted indoles in trifluoroacetic acid to yield novel 4‐(substituted bis‐indolyl)methyl)benzo‐15‐crown‐5 in moderate to good yield. One of the reported novel molecule tested for the complexation behavior with various metal cations, such as Li⁺, Na⁺, K⁺, Mg²⁺ Ca²⁺, Al³⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Sn²⁺, Ba²⁺, Hg²⁺, and Pb²⁺, showed a visual colorimetric probe for the detection of mercury cations (Hg²⁺) in an aqueous medium.     

A New Fluorescent Chemosensor for Cu2+ Based on 1,2,3,4,5,6,7,8,9,10‐Decahydroacridine‐1,8‐dione Fluorophore

A new chemosensor for Cu²⁺ was synthesized based on 1,2,3,4,5,6,7,8,9,10‐decahydroacridine‐1,8‐dione dyes, which exhibited an obvious fluorescent selectivity to the sensing of Cu²⁺ ions over other cations, such as Na⁺, K⁺, Ca²⁺, Cd²⁺, Co²⁺, Hg²⁺, Mg²⁺, Mn²⁺, Ni²⁺, Zn²⁺, Ag⁺ and Pb²⁺. Moreover, it presented a fluorescent switch function when EDTA was added to the compound‐Cu²⁺ complex in examined systems.