DNAzyme‐Mediated Genetically Encoded Sensors for Ratiometric Imaging of Metal Ions in Living Cells

Genetically encoded fluorescent proteins (FPs) have been used for metal ion detection. However, their applications are restricted to a limited number of metal ions owing to the lack of available metal‐binding proteins or peptides that can be fused to FPs and the difficulty in transforming the binding of metal ions into a change of fluorescent signal. We report herein the use of Mg²⁺‐specific 10–23 or Zn²⁺‐specific 8–17 RNA‐cleaving DNAzymes to regulate the expression of FPs as a new class of ratiometric fluorescent sensors for metal ions. Specifically, we demonstrate the use of DNAzymes to suppress the expression of Clover2, a variant of the green FP (GFP), by cleaving the mRNA of Clover2, while the expression of Ruby2, a mutant of the red FP (RFP), is not affected. The Mg²⁺ or Zn²⁺ in HeLa cells can be detected using both confocal imaging and flow cytometry. Since a wide variety of metal‐specific DNAzymes can be obtained, this method can likely be applied to imaging many other metal ions, expanding the range of the current genetically encoded fluorescent protein‐based sensors.     

Target Self‐Enhanced Selectivity in Metal‐Specific DNAzymes

Highly selective recognition of metal ions by rational ligand design is challenging, and simple metal binding by biological ligands is often obscured by nonspecific interactions. In this work, binding‐triggered catalysis is used and metal selectivity is greatly increased by increasing the number of metal ions involved, as exemplified in a series of in vitro selected RNA‐cleaving DNAzymes. The cleavage junction is modified with a glycyl–histidine‐functionalized tertiary amine moiety to provide multiple potential metal coordination sites. DNAzymes that bind 1, 2, and 3 Zn²⁺ ions, increased their selectivity for Zn²⁺ over Co²⁺ ions from approximately 20‐, 1000‐, to 5000‐fold, respectively. This study offers important insights into metal recognition by combining rational ligand design and combinatorial selection, and it provides a set of new DNAzymes with excellent selectivity for Zn²⁺ ions.     

Target Self-Enhanced Selectivity in Metal-Specific DNAzymes

Highly selective recognition of metal ions by rational ligand design is challenging, and simple metal binding by biological ligands is often obscured by nonspecific interactions. In this work, binding-triggered catalysis is used and metal selectivity is greatly increased by increasing the number of metal ions involved, as exemplified in a series of in vitro selected RNA-cleaving DNAzymes. The cleavage junction is modified with a glycyl–histidine-functionalized tertiary amine moiety to provide multiple potential metal coordination sites. DNAzymes that bind 1, 2, and 3 Zn²⁺ ions, increased their selectivity for Zn²⁺ over Co²⁺ ions from approximately 20-, 1000-, to 5000-fold, respectively. This study offers important insights into metal recognition by combining rational ligand design and combinatorial selection, and it provides a set of new DNAzymes with excellent selectivity for Zn²⁺ ions.     

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.     

In vitro Selection of Chemically Modified DNAzymes

DNAzymes are in vitro selected DNA oligonucleotides with catalytic activities. RNA cleavage is one of the most extensively studied DNAzyme reactions. To expand the chemical functionality of DNA, various chemical modifications have been made during and after selection. In this review, we summarize examples of RNA-cleaving DNAzymes and focus on those modifications introduced during in vitro selection. By incorporating various modified nucleotides via polymerase chain reaction (PCR) or primer extension, a few DNAzymes were obtained that can be specifically activated by metal ions such as Zn²⁺ and Hg²⁺. In addition, some modifications were introduced to mimic RNase A that can cleave RNA substrates in the absence of divalent metal ions. In addition, single modifications at the fixed regions of DNA libraries, especially at the cleavage junctions, have been tested, and examples of DNAzymes with phosphorothioate and histidine-glycine modified tertiary amine were successfully obtained specific for Cu²⁺, Cd²⁺, Zn²⁺, and Ni²⁺. Labeling fluorophore/quencher pair right next to the cleavage junction was also used to obtain signaling DNAzymes for detecting various metal ions and cells. Furthermore, we reviewed work on the cleavage of 2′-5′ linked RNA and L-RNA substrates. Finally, applications of these modified DNAzymes as biosensors, RNases, and biochemical probes are briefly described with a few future research opportunities outlined at the end.     

Circular Polarized Light Activated Chiral Satellite Nanoprobes for the Imaging and Analysis of Multiple Metal Ions in Living Cells

Here, we construct a handedness‐dependent circular polarized light (CPL)‐activated chiral satellite assemblies formed from DNAzymes and spiny platinum modified with gold nanorods and upconversion nanoparticles (UCNPs), enabling the simultaneous quantitative analysis of multiple divalent metal ions in living cells. The chiral nanoprobes, in coordination with their corresponding divalent metal ions under 980 nm left circular polarized (LCP) light illumination, served as an in situ confocal bioimaging platform for the quantitation of the given intracellular metal ions. The limit of detection (LOD) of the chiral probes in living cells is 1.1 nmol/10⁶ cells, 1.02 nmol/10⁶ cells and 0.45 nmol/10⁶ cells for Zn²⁺, Mg²⁺, and Cu²⁺, respectively.     

1,8-萘酰亚胺为发色团的Zn2+荧光探针的合成及性能研究

合成了以1,8-萘酰亚胺为发色团,以联吡啶为离子受体的Zn²⁺荧光探针,并进行了表征及离子识别性能的研究。研究表明该化合物对Zn²⁺具有良好的识别性能,同时相对于Ca²⁺, Cd²⁺, Co²⁺, Cu²⁺, Hg²⁺, Fe³⁺, Mn²⁺, Ni²⁺, Pb²⁺等金属离子具有良好的选择性。     

Novel highly selective fluorescent chemosensors for Zn(II)

Two novel fluorescent Zn²⁺ chemosensors were synthesized in four steps from inexpensive starting materials. They exhibited very strong fluorescence responses to Zn²⁺ and had remarkably high selectivity to Zn²⁺ than other metal ions including Mg²⁺, Ca²⁺, Ni²⁺, Cu²⁺, and Cd²⁺. These two new molecules could be used as low-priced yet high-quality Zn²⁺ chemosensors.     

Imaging Endogenous Metal Ions in Living Cells Using a DNAzyme–Catalytic Hairpin Assembly Probe

DNAzymes are a promising platform for metal ion detection, and a few DNAzyme-based sensors have been reported to detect metal ions inside cells. However, these methods required an influx of metal ions to increase their concentrations for detection. To address this major issue, the design of a catalytic hairpin assembly (CHA) reaction to amplify the signal from photocaged Na⁺-specific DNAzyme to detect endogenous Na⁺ inside cells is reported. Upon light activation and in the presence of Na⁺, the NaA43 DNAzyme cleaves its substrate strand and releases a product strand, which becomes an initiator that trigger the subsequent CHA amplification reaction. This strategy allows detection of endogenous Na⁺ inside cells, which has been demonstrated by both fluorescent imaging of individual cells and flow cytometry of the whole cell population. This method can be generally applied to detect other endogenous metal ions and thus contribute to deeper understanding of the role of metal ions in biological systems.     

基于苯并噻唑Zn2+荧光探针及其细胞造影应用

设计合成基于苯并噻唑Zn²⁺荧光增强型探针BHP,在HEPES缓冲液中测其对Zn²⁺识别性能。实验结果表明,BHP对Zn²⁺有较高的选择性,对其他金属离子如Cd²⁺,Fe²⁺,Ni²⁺,Pb²⁺,Hg²⁺,Al³⁺,Mn²⁺,Ag⁺,Cu²⁺,Co²⁺,Na⁺,K⁺,Mg²⁺和Ca²⁺无明显荧光增强响应。BHP与Zn²⁺按1：1计量比配位,在生理条件下荧光强度不受pH值影响。在HeLa细胞中对Zn²⁺的造影表明BHP可用于生物体Zn²⁺检测。     

A New Fluorescent Chemosensor for Metal Ions Based upon 1,8‐Naphthalimide and 8‐Hydroxyquinoline

A new fluorescent chemosensor based upon 1,8‐naphthalimide and 8‐hydroxyquinoline was synthesized, and its fluorescent properties in the presence of different metal cations (Hg²⁺, Ag⁺, Zn²⁺, Fe²⁺, Cd²⁺, Pb²⁺, Ca²⁺, Cu²⁺, Mg²⁺, and Ba²⁺) were investigated. It displayed fluorescence quenching with some heavy and transition metal (HTM) ions, and the quenching strongly depended on the nature of HTM ions.     

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.     

Quantum yields and quantitative spectra of firefly bioluminescence with various bivalent metal ions

We measured quantitative spectra of firefly (Photinus pyralis) bioluminescence in the presence of Zn²⁺ and other bivalent metal ions to investigate the effects of these metal ions on luciferin‐luciferase reaction. We studied the dependence of the quantum yield and spectrum on quantity and kind of bivalent metal ions. Adding various amounts of Mg²⁺, Mn²⁺ and Ca²⁺ produced virtually no change in the quantum yields or the spectra of bioluminescence. In contrast, increasing amounts of ions such as Zn²⁺ and Cd²⁺ decreased quantum yields and changed the bioluminescence color from yellow‐green to red. Quantitative analysis showed that the sensitivities of the quantum yield and color to various metal ions were in the order of Hg²⁺>Zn²⁺, Cd²⁺>Ni²⁺, Co²⁺, Fe²⁺≫Mg²⁺, Mn²⁺, Ca²⁺. We propose that the changes in quantum yield and spectrum caused by the metal ions are due to their effect on luciferase that surrounds oxyluciferin during its radioactive decay. We also found that having more metal ions accelerated bioluminescence reactions. The sensitivity of the reaction rate had no correlation with those of the quantum yield and spectrum.     

Graphene–DNAzyme junctions: a platform for direct metal ion detection with ultrahigh sensitivity

Many metal ions are present in biology and in the human body in trace amounts. Despite numerous efforts, metal sensors with ultrahigh sensitivity (<a few picomolar) are rarely achieved. Here, we describe a platform method that integrates a Cu²⁺-dependent DNAzyme into graphene–molecule junctions and its application for direct detection of paramagnetic Cu²⁺ with femtomolar sensitivity and high selectivity. Since DNAzymes specific for other metal ions can be obtained through in vitro selection, the method demonstrated here can be applied to the detection of a broad range of other metal ions.     

Transition Metal Ions or Acid-induced Suppression of Photoinduced Proton Transfer and Electron Transfer Reaction in 5-(4-Fluorophenyl)-2-hydroxypyridine: A Molecule of Dual Mode Fluorosensitivity

The photophysical properties of 5-(4-fluorophenyl)-2-hydroxypyridine (FP2HP) at different pH and its fluorescence response toward different transition metal ions have been studied by steady-state absorption and emission spectroscopy in combination with quantum chemical calculations. Although keto-enol tautomerization is observed in the excited state, the molecule is weakly fluorescent due to the presence of electron-rich nitrogen atom and relatively electron-deficient fluorine atom, which may lead to photoinduced electron transfer process. In the presence of the transition metal ions, such as Zn²⁺, Cd²⁺, Hg²⁺, etc., the studied molecule exhibits changes in its absorption and emission properties. The present system shows fluorescence enhancement instead of usual quenching in presence of the transition metal ions, such as Fe²⁺ and Cu²⁺. Spectral observation leads to the interpretation that this structurally simple molecule can be effectively utilized as a chelation-enhanced fluorescence-based chemosensor for the detection of transition metal ions. The experimental findings corroborate well with theoretical calculations at Hartree–Fock level using 6-31G** and lanl2dz basis sets.     

New fluorescent chemosensor for Zn2+ ions on the basis of 3,3′-bis(dipyrrolylmethene)

Luminescence study of the reaction of 3,3′-methanediylbis(2,4,7,8,9-pentamethyldipyrrolylmethene) (H₂L) with a number of metal salts showed that this compound is an efficient fluorescent chemosensor for Zn²⁺ ions in organic solvents. The selectivity and sensitivity of H2L were estimated in various solvents in the presence of other metal cations (Na⁺, Mg²⁺, Co²⁺, Ni²⁺, Cu²⁺, Cd²⁺, Hg²⁺, Pb²⁺).     

DFT/MRCI assessment of the excited-state interplay in a coumarin-schiff Mg2+ fluorescent sensor

Fluorescent sensors with selectivity and sensitivity to metal ions are an active field in supramolecular chemistry for biochemical, analytical, and environmental problems. Mg²⁺ is one of the most abundant divalent ions in the cell, and it plays a critical role in many biological processes. Coumarin-based sensors are widely used as desirable fluorophore and binding moieties showing a remarkable sensitivity and fluorometric enhancement for Mg²⁺. In this work, density functional theory/multireference configuration interaction (DFT/MRCI) calculations were performed in order to understand the sensing behavior of the organic fluorescent sensor 7-hydroxy-4-methyl-8-((2-(pyridin-2-yl)hydrazono)methyl)-2H-chromen-2-one (PyHC) in ethanol to solvated Mg²⁺ ions. The computed optical properties reproduce well-reported experimental data. Our results suggest that after photoexcitation of the free PyHC, a photo-induced electron transfer (PET) mechanism may compete with the fluorescence decay to the ground state. In contrast, this PET channel is no longer available in the complex with Mg²⁺ making the emissive decay more efficient. © 2019 Wiley Periodicals, Inc.     

Highly selective fluorescent recognition of Zn2+ based on naphthalene macrocyclic derivative

A new macrocyclic chemosensor containing two naphthalene fluorophores has been synthesized. The fluorescent properties of this receptor has been studied in the presence of various metal ions such as Na⁺, Ag⁺, Cr³⁺, Mn²⁺, Fe³⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺ and Pb²⁺. When increasing concentrations of Zn²⁺ ions were introduced, the emission of L was drastically increased (EFE = 4.34). This special change was not observed when other metal ions were used; such highly selective fluorescent response indicates that this receptor can easily discriminate Zn²⁺ ions from other similar species. Model calculations at DFT level further suggest the possible interaction mode, and relatively steric position between the host and guest also influence the optical response.     

Salicylaldehyde hydrazones as fluorescent probes for zinc ion in aqueous solution of physiological pH

Salicylaldehyde hydrazones of 1 and 2 were synthesized and their potential as fluorescent probes for zinc ion was investigated in this paper. Both of the probes were found to show fluorescence change upon binding with Zn²⁺ in aqueous solutions, with good selectivity to Zn²⁺ over other metal ions such as alkali/alkali earth metal ions and heavy metal ions of Pb²⁺, Cd²⁺ and Hg²⁺. They showed 1:2 metal-to-ligand ratio when their Zn²⁺ complex was formed. By introducing pyrene as fluorophore, 2 showed interesting ratiometric response to Zn²⁺. Under optimal condition, 2 exhibited a linear range of 0-5.0 μM and detection limit of 0.08 μM Zn²⁺ in aqueous buffer, respectively. The detection of Zn²⁺ in drinking water samples using 2 as fluorescent probe was successful.     

Design and synthesis of a new fluorescent tripod for chemosensor applications

A new yellow-green fluorescent tripod based 1,8-naphthalimide has been synthesized and characterised. Its photophysical properties have been investigated in organic solvents of different polarity. The effect that the metal ions (Cd²⁺, Co²⁺, Zn²⁺, Mn²⁺, Mg²⁺, Ni²⁺, Pb²⁺, Cu²⁺, Ba²⁺, Fe³⁺ and Ag⁺) produce upon the fluorescent intensity of acetonitrile solutions of the tripod has been discussed viewing its potential applications as a detector for metal cations. The influence of protons on the fluorescence intensity of the tripod in DMF and methanol–water (1:4 v/v) solutions has also been investigated.