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.     

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.     

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.     

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.     

Orthogonal Activation of RNA‐Cleaving DNAzymes in Live Cells by Reactive Oxygen Species

RNA‐cleaving DNAzymes are useful tools for intracellular metal‐ion sensing and gene regulation. Incorporating stimuli‐responsive modifications into these DNAzymes enables their activities to be spatiotemporally and chemically controlled for more precise applications. Despite the successful development of many caged DNAzymes for light‐induced activation, DNAzymes that can be intracellularly activated by chemical inputs of biological importance, such as reactive oxygen species (ROS), are still scarce. ROS like hydrogen peroxide (H₂O₂) and hypochlorite (HClO) are critical mediators of oxidative stress‐related cell signaling and dysregulation including activation of immune system as well as progression of diseases and aging. Herein, we report ROS‐activable DNAzymes by introducing phenylboronate and phosphorothioate modifications to the Zn²⁺‐dependent 8–17 DNAzyme. These ROS‐activable DNAzymes were orthogonally activated by H₂O₂ and HClO inside live human and mouse cells.     

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.     

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.     

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.     

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.     

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.     

Near‐Infrared Photothermally Activated DNAzyme–Gold Nanoshells for Imaging Metal Ions in Living Cells

DNAzymes have enjoyed success as metal ion sensors outside cells. Their susceptibility to metal‐dependent cleavage during delivery into cells has limited their intracellular applications. To overcome this limitation, a near‐infrared (NIR) photothermal activation method is presented for controlling DNAzyme activity in living cells. The system consists of a three‐stranded DNAzyme precursor (TSDP), the hybridization of which prevents the DNAzyme from being active. After conjugating the TSDP onto gold nanoshells and upon NIR illumination, the increased temperature dehybridizes the TSDP to release the active DNAzyme, which then carries out metal‐ion‐dependent cleavage, resulting in releasing the cleaved product containing a fluorophore. Using this construct, detecting Zn²⁺ in living HeLa cells is demonstrated. This method has expanded the DNAzyme versatility for detecting metal ions in biological systems under NIR light that exhibits lower phototoxicity and higher tissue penetration ability.     

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.     

Graphene quantum dots with Zn2+ and Ni2+ conjugates can cleave supercoiled DNA

Graphene quantum dots (GQDs), inheriting the superb property of graphene oxide, possess smaller lateral size and high biocompatibility, thus having potential in biomedical applications. We previously discovered that GQDs, combining with Cu²⁺ ions, could cleave DNA primarily through an oxidative pathway; yet, oxidative DNA cleavage is not practically preferred in biology. In this work, we explore the DNA cleavage ability of GQDs with Zn²⁺ and Ni²⁺. Zn²⁺ and Ni²⁺ alone are incapable of cleaving supercoiled DNA, but when combining with the GQDs, Zn²⁺ and Ni²⁺ exhibit DNA cleavage activity. However, the activity of these two systems is much lower than that of GQDs/Cu²⁺, and GQDs/Ni²⁺ is less active than GQDs/Zn²⁺. The functional mechanism of GQDs/Ni²⁺ and GQDs/Zn²⁺ is different from that of GQDs/Cu²⁺. The GQDs play a key role in the two systems; the redox inactive Zn²⁺ and Ni²⁺ ions assist to generate the oxidative species that eventually lead to the DNA cleavage. The current results together with our previous result indicate that GQDs together with metal ions can cleave supercoiled DNA, and their cleavage activities depend on the properties of metal ions: for redox active metal ions, metal ions play key roles, for redox inactive metal ions, GQDs are dominant.     

Metal-Induced Fluorescence Quenching of Photoconvertible Fluorescent Protein DendFP

Sensitive and accurate detection of specific metal ions is important for sensor development and can advance analytical science and support environmental and human medical examinations. Fluorescent proteins (FPs) can be quenched by specific metal ions and spectroscopically show a unique fluorescence-quenching sensitivity, suggesting their potential application as FP-based metal biosensors. Since the characteristics of the fluorescence quenching are difficult to predict, spectroscopic analysis of new FPs is important for the development of FP-based biosensors. Here we reported the spectroscopic and structural analysis of metal-induced fluorescence quenching of the photoconvertible fluorescent protein DendFP. The spectroscopic analysis showed that Fe²⁺, Fe³⁺, and Cu²⁺ significantly reduced the fluorescence emission of DendFP. The metal titration experiments showed that the dissociation constants (K_d) of Fe²⁺, Fe³⁺, and Cu²⁺ for DendFP were 24.59, 41.66, and 137.18 μM, respectively. The tetrameric interface of DendFP, which the metal ions cannot bind to, was analyzed. Structural comparison of the metal-binding sites of DendFP with those of iq-mEmerald and Dronpa suggested that quenchable DendFP has a unique metal-binding site on the β-barrel that does not utilize the histidine pair for metal binding.     

Benzenesulfonamidoquinolino‐β‐cyclodextrin as a Cell‐Impermeable Fluorescent Sensor for Zn2+

A water‐soluble benzenesulfonamidoquinolino‐β‐cyclodextrin has been successfully synthesized in 30 % yield by incorporating a N‐(8‐quinolyl)‐p‐aminobenzenesulfonamide (HQAS) group to β‐cyclodextrin through a flexible linker. This compound exhibits a good fluorescence response in the presence of Zn²⁺ in water but gives poor fluorescence responses with other metal ions commonly present in a physiological environment under similar conditions. Fluorescence microscopic and two‐dimensional NMR experiments showed that benzenesulfonamidoquinolino‐β‐cyclodextrin could bind to the loose bilayer membranes. As a result, benzenesulfonamidoquinolino‐β‐cyclodextrin was found to act as an efficient cell‐impermeable Zn²⁺ probe, showing a specific fluorescent sensing ability to Zn²⁺‐containing damaged cells whilst exhibiting no response in the presence of healthy cells.