Ultrasensitive DNAzyme Beacon for Lanthanides and Metal Speciation

Splitting a DNAzyme enables a Na+-dependent FRET signal from the embedded aptamer

Recently, a few Na⁺-specific RNA-cleaving DNAzymes have been reported, and a Na⁺ aptamer was identified from the NaA43 and Ce13d DNAzymes. These DNAzymes and the embedded aptamer have been used for Na⁺ detection. In this work, we studied the Na⁺-dependent folding of the Ce13d DNAzyme using fluorescence resonance energy transfer (FRET). When a FRET donor and an acceptor were respectively labeled at the ends of the DNAzyme, Na⁺ failed to induce an obvious end-to-end distance change, suggesting a rigid global structure. To relax this rigidity, the Ce13d DNAzyme was systematically split at various sites on both the enzyme and the substrate strands. The Na⁺ binding activity of the split structures was characterized by 2-aminopurine fluorescence, enzymatic activity, Tb³⁺-sensitized luminescence, and DMS footprinting. Among the various constructs, the only one that retained Na⁺ binding was the split at the cleavage site, and this construct was further labeled with two dyes near the split site. This FRET result showed Na⁺-dependent folding with a K_d of 26 mM Na⁺. This study provides important structural information related to Na⁺ binding to this new aptamer, which might also be useful for future work in biosensor design.

Multi-metal-dependent nucleic acid enzymes

Nucleic acid enzymes require metal ions for activity, and many recently discovered enzymes can use multiple metals, either binding to the scissile phosphate or also playing an allosteric role.

Ultrasensitive DNAzyme-Based Ca2+ Detection Boosted by Ethanol and a Solvent-Compatible Scaffold for Aptazyme Design

Functional DNA includes aptamers and DNAzymes, and metal ions are often important for achieving the chemical functions of such DNA. Biosensors based on functional DNA have mainly been tested in aqueous buffers. By introducing organic solvents with much lower dielectric constants, the interaction between metal ions and DNA can be significantly enhanced, and this might affect the performance of DNA-based biosensors. In this work, the effect of ethanol on the activity of the EtNa DNAzyme was studied for Ca²⁺ detection. With 30 % ethanol, the sensor has a detection limit of 1.4 μm Ca²⁺ , which is a 16-fold improvement relative to that in water. This EtNa DNAzyme is unique because other tested DNAzymes are all inhibited by 50 % ethanol. Finally, by using the EtNa DNAzyme as a scaffold, the adenosine monophosphate (AMP) aptamer was inserted to construct an aptazyme, which allowed the measurement of AMP in ethanol. In summary, this study has reported the most sensitive DNA-based sensor for Ca²⁺ , and its sensitivity and selectivity can approach those of proteins or small-molecule ligands. This work also provides a way to measure aptamer binding in organic solvents.

Selective Heavy Element Sensing with a Simple Host-Guest Fluorescent Array

A simple three component array of host-fluorophore complexes is capable of sensitive and selective discrimination of heavy metal ions, including lanthanide and actinide salts in aqueous solution. Instead of applying optical sensors that only use "single-mode" detection, i.e., coordination of the metal to a specific ligand and monitoring the change in emission of an appended fluorophore, we exploit a series of host-fluorophore complexes that are affected by the presence of small amounts of metal ions in aqueous solution in different ways. Variable host-metal and host-guest-metal interactions lead to both turn-on and turn-off fluorescence sensing mechanisms, enhancing the discriminatory properties of the array. The limit of detection for certain metals is as low as 70 nM, and highly similar metals such as lanthanides and actinides can be easily distinguished at low micromolar concentrations in complex salt mixtures.

Two Completely Different Mechanisms for Highly Specific Na+ Recognition by DNAzymes

Our view of the interaction between Na⁺ and nucleic acids was changed by a few recently discovered Na⁺ -specific RNA-cleaving DNAzymes. In addition to nonspecific electrostatic interactions, highly specific recognition is also possible. Herein, two such DNAzymes, named EtNa and Ce13d, are compared to elucidate their mechanisms of Na⁺ binding. Mutation studies indicate that they have different sequence requirements. Phosphorothioate (PS) substitution at the scissile phosphate drops the activity of EtNa 140-fold, and it cannot be rescued by thiophilic Cd²⁺ or Mn²⁺ , whereas the activity of PS-modified Ce13d can be rescued. Na⁺ -dependent activity assays indicate that two Na⁺ ions bind cooperatively in EtNa, and each Na⁺ likely interacts with a nonbridging oxygen atom in the scissile phosphate, whereas Ce13d binds only one Na⁺ ion in a well-defined Na⁺ aptamer, and this Na⁺ ion does not directly interact with the scissile phosphate. Both DNAzymes display a normal pH-rate profile, with a single deprotonation reaction required for catalysis. For EtNa, Na⁺ fails to protect the conserved nucleotides from dimethyl sulfate attack, and no specific Na⁺ binding is detected by 2-aminopurine fluorescence, both of which are different from those observed for Ce13d. This work suggests that EtNa binds Na⁺ mainly through its scissile phosphate without significant involvement of the nucleotides in the enzyme strand, whereas Ce13d has a well-defined aptamer for Na⁺ binding. Therefore, DNA has at least two distinct ways to achieve highly selective Na⁺ binding.

Folding of the silver aptamer in a DNAzyme probed by 2-aminopurine fluorescence

The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag⁺ ions for activity. The Ag10c contains a well-defined Ag⁺ binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag⁺. The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand, one at a time. Ag⁺-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding. The measured K_d at the A9 position was 18 μM Ag⁺ with a Hill coefficient of 2.17, similar to those obtained from the previous cleavage activity based assays. However, labeling a 2AP at the A2 position inhibited the activity and folding. Compared to other metal ions, Ag⁺ has a unique sigmoidal folding profile indicative of multiple silver binding cooperatively. This suggests that Ag⁺ can induce a local folding in the enzyme loop and this folding is important for activity. This study provides important biophysical insights into this new DNAzyme, suggesting the possibility of designing folding-based biosensors for Ag⁺.

Kinetic Discrimination of Metal Ions Using DNA for Highly Sensitive and Selective Cr3+ Detection

Most metal sensors are designed for a strong binding affinity toward target metal ions, and the underlying principle relies on binding thermodynamics. The kinetic aspect of binding, however, was rarely explored for sensing. In this work, the binding kinetics of 19 common or toxic metal ions are compared based on a fluorescence quenching assay using DNA oligonucleotides as ligands. Among these metals, Cr³⁺ shows uniquely slow fluorescence quenching kinetics, and the quenched fluorescence cannot be recovered by EDTA or sulfide. Most other metals quenched fluorescence instantaneously and can be fully recovered by these metal chelators. Various factors such as DNA sequence and length, chelating agent, pH, and fluorophore type were studied to understand the binding mechanism, leading to a unique two-stage binding model for Cr³⁺. This system has a wide dynamic range of up to 50 μM Cr³⁺ and a low limit of detection of 80 nM. It is also useful for measuring Cr³⁺ in lake water. This work proposes a new metal sensor design by monitoring binding kinetics with Cr³⁺ being a primary example.

DNAzyme sensors for detection of metal ions in the environment and imaging them in living cells

The on-site and real-time detection of metal ions is important for environmental monitoring and for understanding the impact of metal ions on human health. However, developing sensors selective for a wide range of metal ions that can work in the complex matrices of untreated samples and cells presents significant challenges. To meet these challenges, DNAzymes, an emerging class of metal ion-dependent enzymes selective for almost any metal ion, have been functionalized with fluorophores, nanoparticles and other imaging agents and incorporated into sensors for the detection of metal ions in environmental samples and for imaging metal ions in living cells. Herein, we highlight the recent developments of DNAzyme-based fluorescent, colorimetric, SERS, electrochemical and electrochemiluminscent sensors for metal ions for these applications.

A Silver-Specific DNAzyme with a New Silver Aptamer and Salt-Promoted Activity

Most RNA-cleaving DNAzymes require a metal ion to interact with the scissile phosphate for activity. Therefore, few unmodified DNAzymes work with thiophilic metals because of their low affinity for phosphate. Recently, an Ag⁺-specific Ag10c DNAzyme was reported via in vitro selection. Herein, Ag10c is characterized to rationalize the role of the strongly thiophilic Ag⁺. Systematic mutation studies indicate that Ag10c is a highly conserved DNAzyme and its Ag⁺ binding is unrelated to C-Ag⁺-C interaction. Its activity is enhanced by increasing Na⁺ concentrations in buffer. At the same metal concentration, activity decreases in the following order: Li⁺ > Na⁺ > K⁺. Ag10c binds one Na⁺ ion and two Ag⁺ ions for catalysis. The pH-rate profile has a slope of ∼1, indicating a single deprotonation step. Phosphorothioate substitution at the scissile phosphate suggests that Na⁺ interacts with the pro-R_p oxygen of the phosphate, and dimethyl sulfate footprinting indicates that the DNAzyme loop is a silver aptamer binding two Ag⁺ ions. Therefore, Ag⁺ exerts its function allosterically, while the scissile phosphate interacts with Na⁺, Li⁺, Na⁺, or Mg²⁺. This work suggests the possibility of isolating thiophilic metal aptamers based on DNAzyme selection, and it also demonstrates a new Ag⁺ aptamer.

A rapid and visual turn-off sensor for detecting copper (II) ion based on DNAzyme coupled with HCR-based HRP concatemers

To solve the requirement of on-site, rapid, and visual detection of copper (II) (Cu2+) in aqueous solution, a turn-off sensor for detecting copper (II) ion was developed based on Cu2+-dependent DNAzyme as the recognition element and hybridization chain reaction (HCR)-based horseradish peroxidase (HRP) concatemers as the signal amplifier and the signal report element. The detection unit, which was composed of the immobilized Cu2+-dependent DNAzyme coupled with HCR-based HRP concatemers via Waston-Crick base pairing, could catalyze hydrogen peroxide (H2O2) via TMB, generating obvious green color and turning yellow after sulfuric acid termination with optical absorption at 450 nm. Upon Cu2+ addition, the substrate strand of the Cu2+-dependent DNAzyme concatenated with the HCR-based HRP complex was irreversibly cleaved, efficiently causing dramatic reduction of the detection signal. Under optimal conditions, the detection signal decreased with the concentration of Cu2+ in 5 min, exhibiting a linear calibration from 0.05 to 3 μM with a detection limit of 8 nM. The sensor also displayed a high selectivity for Cu2+ given the specificity and anti-interference of the detection unit, and this system was applicable for monitoring Cu2+ in real water samples. Generally speaking, the proposed sensor exhibits good potential in environment surveys.

Theranostic DNAzymes

DNAzymes are catalytically active DNA molecules that are obtained via in vitro selection. RNA-cleaving DNAzymes have attracted significant attention for both therapeutic and diagnostic applications due to their excellent programmability, stability, and activity. They can be designed to cleave a specific mRNA to down-regulate gene expression. At the same time, DNAzymes can sense a broad range of analytes. By combining these two functions, theranostic DNAzymes are obtained. This review summarizes the progress of DNAzyme for theranostic applications. First, in vitro selection of DNAzymes is briefly introduced, and some representative DNAzymes related to biological applications are summarized. Then, the applications of DNAzyme for RNA cleaving are reviewed. DNAzymes have been used to cleave RNA for treating various diseases, such as viral infection, cancer, inflammation and atherosclerosis. Several formulations have entered clinical trials. Next, the use of DNAzymes for detecting metal ions, small molecules and nucleic acids related to disease diagnosis is summarized. Finally, the theranostic applications of DNAzyme are reviewed. The challenges to be addressed include poor DNAzyme activity under biological conditions, mRNA accessibility, delivery, and quantification of gene expression. Possible solutions to overcome these challenges are discussed, and future directions of the field are speculated.

A new AgNC fluorescence regulation mechanism caused by coiled DNA and its applications in constructing molecular beacons with low background and large signal enhancement

A AgNC fluorescence interference strategy caused by a coiled DNA sequence (A) and its applications in target DNA detection (B).

Integrating Deoxyribozymes into Colorimetric Sensing Platforms

Biosensors are analytical devices that have found a variety of applications in medical diagnostics, food quality control, environmental monitoring and biodefense. In recent years, functional nucleic acids, such as aptamers and nucleic acid enzymes, have shown great potential in biosensor development due to their excellent ability in target recognition and catalysis. Deoxyribozymes (or DNAzymes) are single-stranded DNA molecules with catalytic activity and can be isolated to recognize a wide range of analytes through the process of in vitro selection. By using various signal transduction mechanisms, DNAzymes can be engineered into fluorescent, colorimetric, electrochemical and chemiluminescent biosensors. Among them, colorimetric sensors represent an attractive option as the signal can be easily detected by the naked eye. This reduces reliance on complex and expensive equipment. In this review, we will discuss the recent progress in the development of colorimetric biosensors that make use of DNAzymes and the prospect of employing these sensors in a range of chemical and biological applications.

Giant Catalytic DNA Particles for Simple and Intuitive Detection of Pb(2.)

DNAzymes have been extensively studied as biosensors because of their unique functionality of cleaving substrate in the presence of metal ion cofactors. However, there are only a few reports on visual detection using gold nanoparticles. Here, we synthesized the DNAzyme microparticle (DzMP) (~1 μm) via rolling circle amplification for detection of Pb(2+) without the help of other materials. Then, the substrate strands were labeled with two different fluorophores (6-carboxyfluorescein and Cy5) to visualize the DzMPs and to monitor the separation of substrate strands. Because of their large size, the decline in the number of fluorescent particles in the presence of Pb(2+) could be successfully demonstrated by a fluorescence microscopy, presenting a new platform for heavy metal detection.

A highly specific sodium aptamer probed by 2-aminopurine for robust Na+ sensing

Sodium is one of the most abundant metals in the environment and in biology, playing critical ecological and physiological roles. Na⁺ is also the most common buffer salt for nucleic acids research, while its specific interaction with DNA has yet to be fully studied. Herein, we probe a highly selective and robust Na⁺ aptamer using 2-aminopurine (2AP), a fluorescent adenine analog. This aptamer has two DNA strands derived from the Ce13d DNAzyme. By introducing a 2AP at the cleavage site of the substrate strand, Na⁺ induces ∼40% fluorescence increase. The signaling is improved by a series of rational mutations, reaching >600% with the C₁₀A₂₀ double mutant. This fluorescence enhancement suggests relaxed base stacking near the 2AP label upon Na⁺ binding. By replacing a non-conserved adenine in the enzyme strand by 2AP, Na⁺-dependent fluorescence quenching is observed, suggesting that the enzyme loop folds into a more compact structure upon Na⁺ binding. The fluorescence changes allow for Na⁺ detection. With an optimized sequence, a detection limit of 0.4 mM Na⁺ is achieved, reaching saturated signal in less than 10 s. The sensor response is insensitive to ionic strength, which is critical for Na⁺ detection.

An Amperometric Immunosensor Based on an Ionic Liquid and Single-Walled Carbon Nanotube Composite Electrode for Detection of Tetrodotoxin in Pufferfish

An amperometric immunosensor based on a composite electrode of single-walled carbon nanotubes and ionic liquid n-octylpyridinum afluorophosphate (SWCNT-ILE) was developed for the determination of tetrodotoxin (TTX). Compared with the glassy carbon electrode (GCE), the electrode combined advantages of carbon nanotubes and ionic liquid, which exhibited the excellent antifouling ability of p-nitrophenol (PNP) so that it remarkably improved the stability of the p-nitrophenyl phosphate-based sensor. Combining the enzyme-linked immune sorbent assay (ELISA) by alkaline phosphatase (AP) and magnetic particles immobilized with antigens, a real-time assay of tetrodotoxin was developed by amperometric immunosensors. Under the optimium condition, the developed sensor demonstrated a linear range of tetrodotoxin from 2 to 45 ng/mL with a low detection limit of 5 ng/mL. Furthermore, the amperometric immunosensor was applied to determine TTX in real samples and could be used as an effective and sensitive sensor for direct detection of tetrodotoxin within 20 min.

Modulating luminescence of Tb(3+) with biomolecules for sensing heparin and its contaminant OSCS

The detection of heparin (Hep) and its contaminant oversulfated chondroitin sulfate (OSCS) is of great importance in clinics but remains challenging. Here, we report a sensitive and selective time-resolved luminescence (TRL) biosensing system for Hep by modulating the photoluminescence of Tb(3+) with guanine-rich ssDNA and Hep-specific AG73 peptide (RKRLQVQLSIRT). With the developed system, Hep including both unfractionated Hep (UFH) and the low molecular weight Hep (LMWH) has been successfully detected with a satisfactory detection limit. Owing to the highly specific interaction between Hep and AG73 peptide, major interfering substances in Hep detection, such as Hep analogs of chondrotin sulfate (Chs) and hyaluronic acid (HA), did not interfere with Hep detection. The established TRL sensing system was then successfully used for monitoring Hep metabolism in living rats by microdialysis. Moreover, the proposed TRL sensing system was further applied to analyze OSCS contaminant in Hep with heparinases treatment by exploring the inhibition effects of OSCS on the activity of heparinases. As low as 0.002% of OSCS in Hep was identified.

A Selective Na(+) Aptamer Dissected by Sensitized Tb(3+) Luminescence

A previous study of two RNA-cleaving DNAzymes, NaA43 and Ce13d, revealed the possibility of a common Na(+) aptamer motif. Because Na(+) binding to DNA is a fundamental biochemical problem, the interaction between Ce13d and Na(+) was studied in detail by using sensitized Tb(3+) luminescence spectroscopy. Na(+) displaces Tb(3+) from the DNAzyme, and thus quenches the emission from Tb(3+) . The overall requirement for Na(+) binding includes the hairpin and the highly conserved 16-nucleotide loop in the enzyme strand, along with a few unpaired nucleotides in the substrate. Mutation studies indicate good correlation between Na(+) binding and cleavage activity, thus suggesting a critical role of Na(+) binding for the enzyme activity. Ce13d displayed a Kd of ∼20 mm with Na(+) (other monovalent cations: 40-60 mm). The Kd values for other metal ions are mainly due to non-specific competition. With a single nucleotide mutation, the specific Na(+) binding was lost. Another mutant improved Kd to 8 mm with Na(+) . This study has demonstrated a Na(+) aptamer with important biological implications and analytical applications. It has also defined the structural requirements for Na(+) binding and produced an improved mutant.

DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays

Zinc oxide (ZnO) is a highly important material, and Zn(2+) is a key metal ion in biology. ZnO and Zn(2+) interconvert via dissolution and hydrolysis/condensation. In this work, we explore their interactions with DNA, which is important for biointerface, analytical, and bioinorganic chemistry. Fluorescently labeled DNA oligonucleotides were adsorbed by a low concentration (around 5 μg/mL) of ZnO nanoparticles, near the solubility limit. Right after mixing, fluorescence quenching occurred, indicating DNA adsorption. Then, fluorescence recovered, attributable to ZnO dissolution. The dissolution rate followed A5 > T5 > C5. Dissolution was slower with longer DNA. The adsorption affinity was also measured by a displacement assay to be G5 > C5 > T5 > A5, suggesting that tightly adsorbed DNA can retard ZnO dissolution. Electrostatic interactions are important for DNA adsorption because ZnO is positively charged at neutral pH, and a high salt concentration inhibits DNA adsorption. Next, in situ formation of ZnO from Zn(2+) was studied. First, titrating Zn(2+) into a fluorescently labeled oligonucleotide at pH 7.5 resulted in an abrupt fluorescence quenching beyond 0.2 mM Zn(2+). At pH 6, quenching occurred linearly with the Zn(2+) concentration, suggesting the effect of Zn(2+) precipitation at pH 7.5. Second, a Zn(2+)-dependent DNA-cleaving DNAzyme was studied. This DNAzyme was inhibited at higher than 2 mM Zn(2+), attributable to Zn(2+) precipitation and adsorption of the DNAzyme. This paper has established the interplay between DNA, Zn(2+), and ZnO. This understanding can avoid misinterpretation of DNA assay results and adds knowledge to DNA immobilization.

Biochemical and Biophysical Understanding of Metal Ion Selectivity of DNAzymes

This review summarizes research into the metal-binding properties of catalytic DNAzymes, towards the goal of understanding the structural properties leading to metal ion specificity. Progress made and insight gained from a range of biochemical and biophysical techniques are covered, and promising directions for future investigations are discussed.

In Vitro Selection of a DNAzyme Cooperatively Binding Two Lanthanide Ions for RNA Cleavage

Trivalent lanthanide ions (Ln(3+)) were recently employed to select RNA-cleaving DNAzymes, and three new DNAzymes have been reported so far. In this work, dysprosium (Dy(3+)) was used with a library containing 50 random nucleotides. After six rounds of in vitro selection, a new DNAzyme named Dy10a was obtained and characterized. Dy10a has a bulged hairpin structure cleaving a RNA/DNA chimeric substrate. Dy10a is highly active in the presence of the five Ln(3+) ions in the middle of the lanthanide series (Sm(3+), Eu(3+), Gd(3+), Tb(3+), and Dy(3+)), while its activity descends on the two sides. The cleavage rate reaches 0.6 min(-1) at pH 6 with just 200 nM Sm(3+), which is the fastest among all known Ln(3+)-dependent enzymes. Dy10a binds two Ln(3+) ions cooperatively. When a phosphorothioate (PS) modification is introduced at the cleavage junction, the activity decreases by >2500-fold for both the Rp and Sp diastereomers, and thiophilic Cd(2+) cannot rescue the activity. The pH-rate profile has a slope of 0.37 between pH 4.2 and 5.2, and the slope was even lower at higher pH. On the basis of these data, a model of metal binding is proposed. Finally, a catalytic beacon sensor that can detect Ho(3+) down to 1.7 nM is constructed.

An Efficient Lanthanide-Dependent DNAzyme Cleaving 2'-5'-Linked RNA

RNA can form two types of linkage. In addition to the predominant 3'-5' linkage, 2'-5'-linked RNA is also important in biology, medicine, and prebiotic studies. Here, in vitro selection was used to isolate a DNAzyme that specifically cleaves 2'-5' RNA by using Ce(3+) as the metal cofactor, but leaves the 3'-5' counterpart intact. This Ce5 DNAzyme requires trivalent light lanthanide ions and shows a rate of 0.16 min(-1) in the presence of 10 μm Ce(3+) ; the activity decreases with heavier lanthanide ions. This is the fastest DNAzyme reported for this reaction, and it might enable applications in chemical biology. As a proof-of-concept, using this DNAzyme, the reactions between phosphorothioate-modified RNA and strongly thiophilic metals (Hg(2+) and Tl(3+) ) were studied as a function of pH.

An Ultrasensitive Light-up Cu(2+) Biosensor Using a New DNAzyme Cleaving a Phosphorothioate-Modified Substrate

Cu(2+) is a very important metal ion in biology, environmental science, and industry. Developing biosensors for Cu(2+) is a key topic in analytical chemistry. DNAzyme-based sensors are highly attractive for their excellent sensitivity, stability, and programmability. In the past decade, a few Cu(2+) biosensors were reported using DNAzymes with DNA cleavage or DNA ligation activity. However, they require unstable ascorbate or imidazole activation. So far, no RNA-cleaving DNAzymes specific for Cu(2+) are known. In this work, a phosphorothioate (PS) RNA-containing library was used for in vitro selection, and a few new Cu(2+)-specific RNA-cleaving DNAzymes were isolated. Among them, a DNAzyme named PSCu10 was studied further. It has only eight nucleotides in the enzyme loop with a cleavage rate of 0.1 min(-1) in the presence of 1 μM Cu(2+) at pH 6.0 (its optimal pH). Between the two diastereomers of the PS RNA chiral center, the R(p) isomer is 37 times more active than the S(p) one. Among the other divalent metal ions, only Hg(2+) can cleave the substrate due to its extremely high thiophilicity. A catalytic beacon sensor was designed with a detection limit of 1.6 nM Cu(2+) and extremely high selectivity. PSCu10 is specific for Cu(2+), and it has no cleavage in the presence of ascorbate, which reduces Cu(2+) to Cu(+).

A DNAzyme requiring two different metal ions at two distinct sites

Most previously reported RNA-cleaving DNAzymes require only a single divalent metal ion for catalysis. We recently reported a general trivalent lanthanide-dependent DNAzyme named Ce13d. This work shows that Ce13d requires both Na⁺ and a trivalent lanthanide (e.g. Ce³⁺), simultaneously. This discovery is facilitated by the sequence similarity between Ce13d and a recently reported Na⁺-specific DNAzyme, NaA43. The Ce13d cleavage rate linearly depends on the concentration of both metal ions. Sensitized Tb³⁺ luminescence and DMS footprinting experiments indicate that the guanines in the enzyme loop are important for Na⁺-binding. The Na⁺ dissociation constants of Ce13d measured from the cleavage activity assay, Tb³⁺ luminescence and DMS footprinting are 24.6, 16.3 and 47 mM, respectively. Mutation studies indicate that the role of Ce³⁺ might be replaced by G₂₃ in NaA43. Ce³⁺ functions by stabilizing the transition state phosphorane, thus promoting cleavage. G₂₃ competes favorably with low concentration Ce³⁺ (below 1 μM). The G₂₃-to-hypoxanthine mutation suggests the N1 position of the guanine as a hydrogen bond donor. Together, Ce13d has two distinct metal binding sites, each fulfilling a different role. DNAzymes can be quite sophisticated in utilizing metal ions for catalysis and molecular recognition, similar to protein metalloenzymes.

A New Na(+)-Dependent RNA-Cleaving DNAzyme with over 1000-fold Rate Acceleration by Ethanol

Enzymes working in organic solvents are important for analytical chemistry, catalysis, and mechanistic studies. Although a few protein enzymes are highly active in organic solvents, little is known regarding nucleic acid-based enzymes. Herein, we report the first RNA-cleaving DNAzyme, named EtNa, that works optimally in concentrated organic solvents containing only monovalent Na(+). The EtNa DNAzyme has a rate of 2.0 h(-1) in 54% ethanol (with 120 mM NaCl and no divalent metal ions), and a Kd of 21 mm Na(+). It retains activity even in 72% ethanol as well as in DMSO. With 4 mm Na(+), the rate in 54% ethanol is >1000-fold higher than that in water. We also demonstrated the use of EtNa to measuring the ethanol content in alcoholic drinks. In total, this DNAzyme has three unique features: divalent metal independent activity, Na(+) selectivity among monovalent metals, and acceleration by organic solvents.

DNA Catalysis: The Chemical Repertoire of DNAzymes

Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.

Identification of the Same Na(+)-Specific DNAzyme Motif from Two In Vitro Selections Under Different Conditions

We report an investigation of the functional relationship between two independently selected RNA-cleaving DNAzymes, NaA43, and Ce13, through in vitro selection. The NaA43 DNAzyme was obtained through a combination of gel-based and column-based in vitro selection in the presence of Na(+) and reported to be highly selective for Na(+) over other metal ions. The Ce13 DNAzyme was isolated via a gel-based method in the presence of Ce(4+) and found to be active with trivalent lanthanides, Y(3+) and Pb(2+). Despite completely different activities reported for the two DNAzymes, they share a high level of sequence similarity (~60% sequence identity). In this work, we systematically analyzed the activity of both DNAzymes to elucidate their potential functional relationship. We found that Na(+) is an obligate cofactor of the Ce13 DNAzyme and lanthanides cannot initiate the cleavage reaction in the absence of Na(+). Hence, we conclude that the Ce13 DNAzyme is a variant of the NaA43 DNAzyme that catalyzes reaction in the presence Na(+) and also utilizes lanthanides in a potentially allosteric manner. These results have identified a new DNAzyme motif that is not only remarkably Na(+)-specific, but also allows for design of novel allosteric DNAzymes for different biotechnological applications.

Searching for a DNAzyme Version of the Leadzyme

The leadzyme refers to a small ribozyme that cleaves a RNA substrate in the presence of Pb(2+). In an optimized form, the enzyme strand contains only two unpaired nucleotides. Most RNA-cleaving DNAzymes are much longer. Two classical Pb(2+)-dependent DNAzymes, 8-17 and GR5, both contain around 15 nucleotides in the enzyme loop. This is also the size of most RNA-cleaving DNAzymes that use other metal ions for their activity. Such large enzyme loops make spectroscopic characterization difficult and so far no high-resolution structural information is available for active DNAzymes. The goal of this work is to search for DNAzymes with smaller enzyme loops. A simple replacement of the ribonucleotides in the leadzyme by deoxyribonucleotides failed to produce an active enzyme. A Pb(2+)-dependent in vitro selection combined with deep sequencing was then performed. After sequence alignment and DNA folding, a new DNAzyme named PbE22 was identified, which contains only 5 nucleotides in the enzyme catalytic loop. The biochemical characteristics of PbE22 were compared with those of the leadzyme and the two classical Pb(2+)-dependent DNAzymes. The rate of PbE22 rises with increase in Pb(2+) concentration, being 1.7 h(-1) in the presence of 100 μM Pb(2+) and reaching 3.5 h(-1) at 500 µM Pb(2+). The log of PbE22 rate rises linearly in a pH-dependent fashion (20 µM Pb(2+)) with a slope of 0.74. In addition, many other abundant sequences in the final library were studied. These sequences are quite varied in length and nucleotide composition, but some contain a few conserved nucleotides consistent with the GR5 structure. Interestingly, some sequences are active with Pb(2+) but none of them were active with even 50 mM Mg(2+), which is reminiscent of the difference between the GR5 and 8-17 DNAzymes.

Desulfurization Activated Phosphorothioate DNAzyme for the Detection of Thallium

Thallium (Tl) is a highly toxic heavy metal situated between mercury and lead in the periodic table. While its neighbors have been thoroughly studied for DNA-based sensing, little is known about thallium detection. In this work, in vitro selection of RNA-cleaving DNAzymes is carried out using Tl(3+) as the target metal cofactor. Both normal DNA and phosphorothioate (PS)-modified DNA are tested for this purpose. While no Tl(3+)-dependent DNAzymes are obtained, a DNA oligonucleotide containing a single PS-modified RNA nucleotide is found to cleave by ∼7% by Tl(3+) at the RNA position. The remaining 93% are desulfurized. By hybridization of this PS-modified oligonucleotide with the Tm7 DNAzyme, the cleavage yield increases to ∼40% in the presence of Tl(3+) and Er(3+). Tm7 is an Er(3+)-dependent RNA-cleaving DNAzyme. It cleaves only the normal substrate but is completely inactive using the PS-modified substrate. Tl(3+) desulfurizes the PS substrate to the normal substrate to be cleaved by Tm7 and Er(3+). This system is engineered into a catalytic beacon for Tl(3+) with a detection limit of 1.5 nM, which is below its maximal contamination limit defined by the U.S. Environmental Protection Agency (10 nM).