In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme

Orthogonal Demethylase-Activated Deoxyribozyme for Intracellular Imaging and Gene Regulation

The epigenetic modification of nucleic acids represents a versatile approach for achieving high-efficient control over gene expression and transcription and could dramatically expand their biosensing and therapeutic applications. Demethylase-involved removal of N6-methyladenine (m⁶A) represents one of the vital epigenetic reprogramming events, yet its direct intracellular evaluation and as-guided gene regulation are extremely rare. The endonuclease-mimicking deoxyribozyme (DNAzyme) is a catalytically active DNA that enables the site-specific cleavage of the RNA substrate, and several strategies have imparted the magnificent responsiveness to DNAzyme by using chemical and light stimuli. However, the epigenetic regulation of DNAzyme has remained largely unexplored, leaving a significant gap in responsive DNA nanotechnology. Herein, we reported an epigenetically responsive DNAzyme system through the in vitro selection of an exquisite m⁶A-caged DNAzyme that could be specifically activated by FTO (fat mass and obesity-associated protein) demethylation for precise intracellular imaging-directed gene regulation. Based on a systematic investigation, the active DNAzyme configuration was potently disrupted by the site-specific incorporation of m⁶A modification and subsequently restored into the intact DNAzyme structure via the tunable FTO-specific removal of m⁶A-caging groups under a variety of conditions. This orthogonal demethylase-activated DNAzyme amplifier enables the robust and accurate monitoring of FTO and its inhibitors in live cells. Moreover, the simple demethylase-activated DNAzyme facilitates the assembly of an intelligent self-adaptive gene regulation platform for knocking down demethylase with the ultimate apoptosis of tumor cells. As a straightforward and scarless m⁶A removal strategy, the demethylase-activated DNAzyme system offers a versatile toolbox for programmable gene regulation in synthetic biology.

Simultaneous and ultra-sensitive detection of Cu2+ and Mg2+ in wine and beer based on dual DNA tweezers and entropy-driven three-dimensional DNA nanomachine

Simultaneous and ultra-sensitive detection strategy of Cu²⁺ and Mg²⁺ in wine and beer was developed based on dual DNA tweezers and entropy-driven three-dimensional DNA nanomachine. The dual DNAzyme can simultaneously respond to two kinds of metal ions and cause two kinds of "turn-on" fluorescent signals. The working principle of this strategy was indirectly proven. In addition, some key experimental parameters were also optimized. Under the optimum conditions, the limit of detection was 10 pM for Cu²⁺ and 2 nM for Mg²⁺ respectively which was significantly improved by entropy driven amplification. This strategy also showed good selectivity and specificity. It was successfully used to detect of Cu²⁺ and Mg²⁺ in wine and beer with 5.26% to 9.12% of relative standard deviation and 90.4% to 110.5% of recoveries.

A MnO2 nanosheet-mediated photo-controlled DNAzyme for intracellular miRNA cleavage to suppress cell growth

Certain miRNAs, called oncomiRs, play a causal role in the onset and maintenance of cancer when overexpressed, thus, representing a potential new class of targets for therapeutic intervention. RNA-cleaving DNAzymes, mainly aimed at mRNA, have shown potential as therapeutic agents for various diseases. However, it's rarely reported that a DNAzyme was used for intracellular miRNA cleavage to suppress cell growth. Herein, we have developed a MnO₂ nanosheet-mediated photo-controlled DNAzyme (NPD) for intracellular miRNA cleavage to suppress cell growth. MnO₂ nanosheets adsorb photocaged DNAzymes, protect them from enzymatic digestion, and efficiently deliver them into cells. In the presence of intracellular glutathione (GSH), MnO₂ nanosheets are reduced to Mn²⁺ ions, which serve as cofactors of the 8-17 DNAzyme for miRNA cleavage. Once the DNAzyme is activated by light, it can cyclically cleave endogenous miR-21 inside cells, which would suppress cancer cell migration and invasion, and finally induce cancer cell apoptosis.

Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications

Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.

A responsive pure DNA hydrogel for label-free detection of lead ion

It is of great significance to develop facile and economical strategies for on-site detection and treatment of toxic metal ions. Stimulus-responsive DNA hydrogel materials have been increasingly used for convenient detection of metal ions due to their advantages such as simplicity, portability, and ease of storage. However, these methods still require encapsulation of signal tags by labeling or embedding. In this paper, a one-step preparation of Pb²⁺-responsive pure DNA hydrogel material was designed to realize a new label-free strategy for Pb²⁺ biosensing. The Pb²⁺-dependent DNAzyme strand and substrate strand were introduced to fabricate the DNA hydrogel. The presence of Pb²⁺ in the sample activates the enzyme strand in the hydrogel skeleton and triggers the cleavage of the substrate, thereby destroy the hydrogel structure. DNA fragments released by the collapsed hydrogel were readily measured as signal output for quantifying Pb²⁺ concentrations with a minimum detection limit of 7.7 nM. We successfully eliminated the need for embedding or labeling of signal molecules by using the DNA molecules that construct hydrogels as the signal output. And the newly developed method for label-free detection of Pb²⁺ based on pure DNA hydrogel is simple, easy readout, and cost-effective. By adjusting the DNAzyme and substrate sequences, label-free analysis of other metal ions can also be achieved. We expect that our strategy can be applied to the field detection of toxic metal ions.

Zn2+-dependent DNAzymes that cleave all combinations of ribonucleotides

Although several DNAzymes are known, their utility is limited by a narrow range of substrate specificity. Here, we report the isolation of two zinc-dependent DNAzymes, ZincDz1 and ZincDz2, which exhibit compact catalytic core sequences with highly versatile hydrolysis activity. They were selected through in vitro selection followed by deep sequencing analysis. Despite their sequence similarity, each DNAzyme showed different Zn²⁺-concentration and pH-dependent reaction profiles, and cleaved the target RNA sequences at different sites. Using various substrate RNA sequences, we found that the cleavage sequence specificity of ZincDz2 and its highly active mutant ZincDz2-v2 to be 5'-rN↓rNrPu-3'. Furthermore, we demonstrated that the designed ZincDz2 could cut microRNA miR-155 at three different sites. These DNAzymes could be useful in a broad range of applications in the fields of medicine and biotechnology.

DNAzymes for amine and peptide lysine acylation

DNAzymes were previously identified by in vitro selection for a variety of chemical reactions, including several biologically relevant peptide modifications. However, finding DNAzymes for peptide lysine acylation is a substantial challenge. By using suitably reactive aryl ester acyl donors as the electrophiles, here we used in vitro selection to identify DNAzymes that acylate amines, including lysine side chains of DNA-anchored peptides. Some of the DNAzymes can transfer a small glutaryl group to an amino group. These results expand the scope of DNAzyme catalysis and suggest the future broader applicability of DNAzymes for sequence-selective lysine acylation of peptide and protein substrates.

Review of recent progress on DNA-based biosensors for Pb2+ detection

Lead (Pb) is a highly toxic heavy metal of great environmental and health concerns, and interestingly Pb²⁺ has played important roles in nucleic acids chemistry. Since 2000, using DNA for selective detection of Pb²⁺ has become a rapidly growing topic in the analytical community. Pb²⁺ can serve as the most active cofactor for RNA-cleaving DNAzymes including the GR5, 17E and 8-17 DNAzymes. Recently, Pb²⁺ was found to promote a porphyrin metalation DNAzyme named T30695. In addition, Pb²⁺ can tightly bind to various G-quadruplex sequences inducing their unique folding and binding to other molecules such as dyes and hemin. The peroxidase-like activity of G-quadruplex/hemin complexes was also used for Pb²⁺ sensing. In this article, these Pb²⁺ recognition mechanisms are reviewed from fundamental chemistry to the design of fluorescent, colorimetric, and electrochemical biosensors. In addition, various signal amplification mechanisms such as rolling circle amplification, hairpin hybridization chain reaction and nuclease-assisted methods are coupled to these sensing methods to drive up sensitivity. We mainly cover recent examples published since 2015. In the end, some practical aspects of these sensors and future research opportunities are discussed.

A new Pb2+-specific DNAzyme by revisiting the catalytic core of 10-23 DNAzyme

10-23 DNAzyme is a catalytic DNA molecule from in vitro selection, the 15-mer catalytic core was investigated for more DNAzyme variants by block deletions. DNAzyme DZM01 was selected with metal ion dependence of Pb²⁺ ≫ Mn²⁺, with no activity in the presence of Mg²⁺ (20 mM), Ca²⁺ (20 mM), Zn²⁺ (20 mM, pH 6). The unique binding properties of Pb²⁺ with nucleic acids might be responsible for the formation of the catalytic core, which is different from that of other divalent metal ions. More DNAzyme variants are expected to be derived for specific metal ion dependence by various nucleobase sequences and modifications.

Zn2+ -Dependent DNAzymes: From Solution Chemistry to Analytical, Materials and Therapeutic Applications

Since 1994, deoxyribozymes or DNAzymes have been in vitro selected to catalyze various types of reactions. Metal ions play a critical role in DNAzyme catalysis, and Zn²⁺ is a very important one among them. Zn²⁺ has good biocompatibility and can be used for intracellular applications. Chemically, Zn²⁺ is a Lewis acid and it can bind to both the phosphate backbone and the nucleobases of DNA. Zn²⁺ undergoes hydrolysis even at neutral pH, and the partially hydrolyzed polynuclear complexes can affect the interactions with DNA. These features have made Zn²⁺ a unique cofactor for DNAzyme reactions. This review summarizes Zn²⁺ -dependent DNAzymes with an emphasis on RNA-/DNA-cleaving reactions. A key feature is the sharp Zn²⁺ concentration and pH-dependent activity for many of the DNAzymes. The applications of these DNAzymes as biosensors for Zn²⁺ , as therapeutic agents to cleave intracellular RNA, and as chemical biology tools to manipulate DNA are discussed. Future studies can focus on the selection of new DNAzymes with improved performance and detailed biochemical characterizations to understand the role of Zn²⁺ , which can facilitate practical applications of Zn²⁺ -dependent DNAzymes.

DNAzyme Sensor for the Detection of Ca2+ Using Resistive Pulse Sensing

DNAzymes are DNA oligonucleotides that can undergo a specific chemical reaction in the presence of a cofactor. Ribonucleases are a specific form of DNAzymes where a tertiary structure undergoes cleavage at a single ribonuclease site. The cleavage is highly specificity to co-factors, which makes them excellent sensor recognition elements. Monitoring the change in structure upon cleavage has given rise to many sensing strategies; here we present a simple and rapid method of following the reaction using resistive pulse sensors, RPS. To demonstrate this methodology, we present a sensor for Ca²⁺ ions in solution. A nanoparticle was functionalised with a Ca²⁺ DNAzyme, and it was possible to follow the cleavage and rearrangement of the DNA as the particles translocate the RPS. The binding of Ca²⁺ caused a conformation change in the DNAzyme, which was monitored as a change in translocation speed. A 30 min assay produced a linear response for Ca²⁺ between 1–9 μm, and extending the incubation time to 60 min allowed for a concentration as low as 0.3 μm. We demonstrate that the signal is specific to Ca²⁺ in the presence of other metal ions, and we can quantify Ca²⁺ in tap and pond water samples.

Characterization of a DNA-hydrolyzing DNAzyme for generation of PCR strands of unequal length

I-R3 DNAzyme is a small, highly active catalytic DNA for DNA hydrolysis. In here, we designed two cis-structure DNAzymes (I-R3N and I-R3S) based on the different locates of the joint linker between I-R3 and its substrate. Data demonstrated that both DNAzymes were highly dependent on Zn²⁺, and worked at a narrow range around pH 7.0. They exhibited strong anti-interference with Mg²⁺ and Ca²⁺, but inhibited by Na⁺ and K⁺. Moreover, single and multiple-site mutations were generated within the catalytic core to carry out a comprehensive mutational study of I-R3 motif, in which most nucleotides were highly conserved and the nucleotides A5, T11 and T8 were identified as the mutational hotspots. Furthermore, an efficient variant A5G was obtained and its reaction condition was optimized. Finally, we constructed A5G to the 3' end of a single-stranded DNA (ssDNA) and applied it for asymmetrical PCR amplification to produce a single and double-stranded DNA mixture, in which A5G within ssDNA can self-cleave to generate a shorter desired ssDNA by denaturing gel separation. This would provide a new non-chemical modification approach for preparation of the expected ssDNA for in vitro selection of DNAzymes.

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.

Dynamic DNA Assemblies in Biomedical Applications

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

Selection of a metal ligand modified DNAzyme for detecting Ni2

Nickel is a highly important metal, and the detection of Ni²⁺ using biosensors is a long-stand analytical challenge. DNA has been widely used for metal detection, although no DNA-based sensors were reported for Ni²⁺. DNAzymes are DNA-based catalysts, and they recruit metal ions for catalysis. In this work, in vitro selection of RNA-cleaving DNAzymes was carried out using a library containing a region of 50 random nucleotides in the presence of Ni²⁺. To increase Ni²⁺ binding, a glycyl-histidine-functionalized tertiary amine moiety was inserted at the cleavage junction. A representative DNAzyme named Ni03 showed a high cleavage yield with Ni²⁺ and it was further studied. After truncation, the optimal sequence of Ni03l could bind one Ni²⁺ or two Co²⁺ for catalysis, while other metal ions were inactive. Its cleavage rates for 100 μM Ni²⁺ reached 0.63 h^-1 at pH 8.0. A catalytic beacon biosensor was designed by labeling a fluorophore and a quencher on the Ni03l DNAzyme. Fluorescence enhancement was observed in the presence of Ni²⁺ with a detection limit of 12.9 μM. The sensor was also tested in spiked Lake Ontario water achieving a similar sensitivity. This is another example of using single-site modified DNAzyme for sensing transition metal ions.

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.

Catalytic Nucleic Acids: Biochemistry, Chemical Biology, Biosensors, and Nanotechnology

Since the initial discovery of ribozymes in the early 1980s, catalytic nucleic acids have been used in different areas. Compared with protein enzymes, catalytic nucleic acids are programmable in structure, easy to modify, and more stable especially for DNA. We take a historic view to summarize a few main interdisciplinary areas of research on nucleic acid enzymes that may have broader impacts. Early efforts on ribozymes in the 1980s have broken the notion that all enzymes are proteins, supplying new evidence for the RNA world hypothesis. In 1994, the first catalytic DNA (DNAzyme) was reported. Since 2000, the biosensor applications of DNAzymes have emerged and DNAzymes are particularly useful for detecting metal ions, a challenging task for enzymes and antibodies. Combined with nanotechnology, DNAzymes are key building elements for switches allowing dynamic control of materials assembly. The search for new DNAzymes and ribozymes is facilitated by developments in DNA sequencing and computational algorithms, further broadening our fundamental understanding of their biochemistry.

Nucleic Acid Catalysis under Potential Prebiotic Conditions

Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.

Sensitivity of a classic DNAzyme for Pb2+ modulated by cations, anions and buffers

Both cations and anions in salt strongly affect the activity of a classic Pb²⁺ specific DNAzyme, which in turn can affect the sensitivity of related biosensors.

Cationic copolymer enhances 8–17 DNAzyme and MNAzyme activities

Cationic copolymer acts as a chaperone to facilitate multiple strand assembly and enhance nucleic acid enzyme activities.

DNAzyme–gold nanoparticle-based probes for biosensing and bioimaging

The design and applications of DNAzyme–gold nanoparticle-based probes in biosensing and bioimaging are summarized here.

Insights into DNA catalysis from structural and functional studies of the 8-17 DNAzyme

The review examines functional knowledge gathered over two decades of research on the 8-17 DNAzyme, focusing on three aspects: the structural requirements for catalysis, the role of metal ions and the participation of general acid-base catalysis.

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.

The Two Classic Pb2+ -Selective DNAzymes Are Related: Rational Evolution for Understanding Metal Selectivity

In 1994, the first DNAzyme named GR5 was reported, which specifically requires Pb²⁺ for its RNA cleavage activity. Three years later, the 8-17 DNAzyme was isolated. The 8-17 DNAzyme and the related 17E DNAzyme are also most active with Pb²⁺ , although other divalent metals can work as well. GR5 and 17E have the same substrate sequence, and their catalytic loops in the enzyme strands also have a few similar and conserved nucleotides. Considering these, we hypothesized that 17E might be a special form of GR5. To test this hypothesis, we performed systematic rational evolution experiments to gradually mutate GR5 toward 17E. By using the activity ratio in the presence of Pb²⁺ and Mg²⁺ for defining these two DNAzymes, the critical nucleotide was identified to be T₁₂ in 17E for metal specificity. In addition, G₉ in GR5 is a position not found in most 17E or 8-17 DNAzymes, and G₉ needs to be added to rescue GR5 activity if T₁₂ becomes a cytosine. This study highlights the links between these two classic and widely used DNAzymes, and offers new insight into the sequence-activity relationship related to metal selectivity.

Highly Sensitive RNA-Cleaving DNAzyme Sensors from Surface-to-Surface Product Enrichment

The engineering of easy-to-use biosensors with ultra-low detection sensitivity remains a major challenge. Herein, we report a simple approach for creating such sensors through the use of an RNA-cleaving DNAzyme (RcD) and a strategy designed to concentrate its cleavage product significantly. The assay uses micron-sized beads loaded with a target-responsive RcD and a paper strip containing a microzone covered with a DNA oligonucleotide capable of capturing the cleavage product of the RcD through Watson-Crick hybridization. Placing the beads and the paper strip in a target-containing test sample allows the bead-bound RcD molecules to undergo target-induced RNA cleavage, releasing a DNA fragment that is captured by the paper strip. This strategy, though simple, is very effective in achieving high levels of detection sensitivity, being able to enrich the concentration of the cleavage product by three orders of magnitude. It is also compatible with both fluorescence-based and colorimetric reporting mechanisms. This work provides a simple platform for developing ultrasensitive biosensors that take advantage of the widely available RcDs as molecular recognition elements.

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.

Repeated Reuse of Deoxyribozyme-Based Logic Gates

Deoxyribozymes (DNAzymes) have demonstrated a significant capacity for biocomputing and hold promise for information processing within advanced biological devices if several key capabilities are developed. One required capability is reuse-having DNAzyme logic gates be cyclically, and controllably, activated and deactivated. We designed an oligonucleotide-based system for DNAzyme reuse that could (1) remove previously bound inputs by addition of complementary oligonucleotides via toe-hold mediated binding and (2) diminish output signal through the addition of quencher-labeled oligonucleotides complementary to the fluorophore-bound substrate. Our system demonstrated, for the first time, the ability for DNAzymes to have their activity toggled, with activity returning to 90-125% of original activity. This toggling could be performed multiple times with control being exerted over when the toggling occurs, with three clear cycles observed before the variability in activity became too great. Our data also demonstrated that fluorescent output of the DNAzyme activity could be actively removed and regenerated. This reuse system can increase the efficiency of DNAzyme-based logic circuits by reducing the number of redundant oligonucleotides and is critical for future development of reusable biodevices controlled by logical operations.

Functionalization of 8-17 DNAzymes modulates catalytic efficiency and divalent metal ion preference

8-17 and 17E DNAzyme are being explored as biosensors for metal ions and RNA motifs of interest, more sensitive and efficient DNAzymes are required to meet the practical applications. Their similarity in the catalytic cores and differences in catalytic efficiency and metal ion dependence initiated great interest about the contribution of the catalytic residues. Functionalization of four adenine residues in the catalytic cores of 8-17 DNAzyme and 17E was conducted with amino, guanidinium, and imidazolyl groups. In the bulge loops of 8-17 and 17E, N⁶-(3-aminopropyl)-2'-deoxyadenosine (residue 1) at A15 led to new DNAzymes 8-17DZ-A15-1 and 17E-A15-1, with much more efficient cleavage ability in the Ca²⁺-mediated reaction and the greater preference for Ca²⁺ over Mg²⁺ than 8-17 DNAzyme and 17E, respectively, especially with a concentration-dependent increase of the selectivity, which is different from most DNAzymes with the similar dependence on both Mg²⁺ and Ca²⁺. With this kind of post-selection modification on 8-17 DNAzymes, for the first time, the catalytic efficiency and metal ion selectivity could be positively modulated. It is also helpful for the catalyic mechanistic studies of these DNAzymes, especially, the role of the unconserved A15 should be emphasized.

Metal-Dependent DNAzymes for the Quantitative Detection of Metal Ions in Living Cells: Recent Progress, Current Challenges, and Latest Results on FRET Ratiometric Sensors

Many different metal ions are involved in various biological functions including metallomics and trafficking, and yet there are currently effective sensors for only a few metal ions, despite the first report of metal sensors for calcium more than 40 years ago. To expand upon the number of metal ions that can be probed in biological systems, we and other laboratories employ the in vitro selection method to obtain metal-specific DNAzymes with high specificity for a metal ion and then convert these DNAzymes into fluorescent sensors for these metal ions using a catalytic beacon approach. In this Forum Article, we summarize recent progress made in developing these DNAzyme sensors to probe metal ions in living cells and in vivo, including several challenges that we were able to overcome for this application, such as DNAzyme delivery, spatiotemporal control, and signal amplification. Furthermore, we have identified a key remaining challenge for the quantitative detection of metal ions in living cells and present a new design and the results of a Förster resonance energy transfer (FRET)-based DNAzyme sensor for the ratiometric quantification of Zn2+ in HeLa cells. By converting existing DNAzyme sensors into a ratiometric readout without compromising the fundamental catalytic function of the DNAzymes, this FRET-based ratiometric DNAzyme design can readily be applied to other DNAzyme sensors as a major advance in the field to develop much more quantitative metal-ion probes for biological systems.

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 (H₂ O₂ ) 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 H₂ O₂ and HClO inside live human and mouse cells.

Misfolding of a DNAzyme for ultrahigh sodium selectivity over potassium

Herein, the excellent Na+ selectivity of a few RNA-cleaving DNAzymes was exploited, where Na+ can be around 3000-fold more effective than K+ for promoting catalysis. By using a double mutant based on the Ce13d DNAzyme, and by lowering the temperature, increased 2-aminopurine (2AP) fluorescence was observed with addition of both Na+ and K+. The fluorescence increase was similar for these two metals at below 10 mM, after which K+ took a different pathway. Since 2AP probes its local base stacking environment, K+ can be considered to induce misfolding. Binding of both Na+ and K+ was specific, since single base mutations could fully inhibit 2AP fluorescence for both metals. The binding thermodynamics was measured by temperature-dependent experiments revealing enthalpy-driven binding for both metals and less coordination sites compared to G-quadruplex DNA. Cleavage activity assays indicated a moderate cleavage activity with 10 mM K+, while further increase of K+ inhibited the activity, also supporting its misfolding of the DNAzyme. For comparison, a G-quadruplex DNA was also studied using the same system, where Na+ and K+ led to the same final state with only around 8-fold difference in Kd. This study provides interesting insights into strategies for discriminating Na+ and K+.

A Novel Small RNA-Cleaving Deoxyribozyme with a Short Binding Arm

Deoxyribozymes capable of catalyzing sequence-specific RNA cleavage have found broad applications in biotechnology, DNA computing and environmental sensing. Among these, deoxyribozyme 8–17 is the most common small DNA motif capable of catalyzing RNA cleavage. However, the extent to which other DNA molecules with similar catalytic motifs exist remains elusive. Here we report a novel RNA-cleaving deoxyribozyme called 10–12opt that functions with an equally small catalytic motif and an unusually short binding arm. This deoxyribozyme contains a 14-nucleotide catalytic core that preferentially catalyzes RNA cleavage at UN dinucleotide junctions (k_obs = 0.9 h⁻¹ for UU cleavage). Surprisingly, the left binding arm contains only three nucleotides and forms two canonical base pairs with the RNA substrate. Mutational analysis reveals that a riboguanosine residue 3-nucleotide downstream of cleavage site must not form canonical base pairing for the optimal catalysis, and this nucleobase likely participates in catalysis with its carbonyl O6 atom. Furthermore, we demonstrate that deoxyribozyme 10–12opt can be utilized to cleave certain microRNA sequences which are not preferentially cleaved by 8–17. Together, these results suggest that this novel RNA-cleaving deoxyribozyme forms a distinct catalytic structure than 8–17 and that sequence space may contain additional examples of DNA molecules that can cleave RNA at site-specific locations.

An investigation of solid-state nanopores on label-free metal-ion signalling via the transition of RNA-cleavage DNAzyme and the hybridization chain reaction

Recent advances have proven solid-state nanopores as a powerful analysis platform that enables label-free and separation-free single-molecule analysis. However, the relatively low resolution still limits its application because many chemicals or targets with small sizes could not be recognized in a label-free condition. In this paper, we provide a possible solution that uses solid-state nanopores for small species signaling via the transition of huge DNA assembly products. DNAzyme responding to metal ions and the hybridization chain reaction (HCR) generating nanopore-detectable dsDNA concatamers are used as the transition model set. By the two-step DNAzyme-HCR transition, Pb2+ that was too tiny to be sensed was successfully recognized by the nanopore. The whole process happened in a completely homogeneous solution without any chemical modification. During condition optimization, we also discussed one possible application challenge that may affect the HCR signal-background distinction. Solid-state nanopores provide a potential solution to this challenge due to its ability to profile product length or even 3D structure information.

Growing prospects of DNA nanomaterials in novel biomedical applications

As an important genetic material for life, DNA has been investigated widely in recent years, especially in interdisciplinary fields crossing nanomaterials and biomedical applications. It plays an important role because of its extraordinary molecular recognition capability and novel conformational polymorphism. DNA is also a powerful and versatile building block for the fabrication of nanostructures and nanodevices. Such DNA-based nanomaterials have also been successfully applied in various aspects ranging from biosensors to biomedicine and special logic gates, as well as in emerging molecular nanomachines. In this present mini-review, we briefly overview the recent progress in these fields. Furthermore, some challenges are also discussed in the conclusions and perspectives section, which aims to stimulate broader scientific interest in DNA nanotechnology and its biomedical applications.

Enhancing Catalytic Activity of Uranyl-Dependent DNAzyme by Flexible Linker Insertion for More Sensitive Detection of Uranyl Ion

The uranyl-dependent DNAzyme 39E cleaves its nucleic acid substrate in the presence of uranyl ion (UO₂²⁺). It has been widely utilized in many sensor designs for selective and sensitive detection of UO₂²⁺ in the environment and inside live cells. In this work, by inserting a flexible linker (C3 Spacer) into one critical site (A₂₀) of the 39E catalytic core, we successfully enhanced the original catalytic activity of 39E up to 8.1-fold at low UO₂²⁺ concentrations. Applying such a modified DNAzyme (39E-A₂₀-C3) in a label-free fluorescent sensor for UO₂²⁺ detection achieved more than 1 order of magnitude sensitivity enhancement over using native 39E, with the UO₂²⁺ detection limit improved from 2.6 nM (0.63 ppb) to 0.19 nM (0.047 ppb), while the high selectivity to UO₂²⁺ over other metal ions was fully preserved. The method was also successfully applied for the detection of UO₂²⁺-spiked environmental water samples to demonstrate its practical usefulness.

A stimuli-responsive DNAzyme displaying Boolean logic-gate responses

Introducing a desired stimuli-responsive function into catalytically active biomacromolecules is potentially useful in developing molecular tools for various bio-applications. In this paper, we discuss the development of a stimuli-responsive DNAzyme (catalytic deoxyribozyme) capable of displaying Boolean logic-gate responses.

A hybridization-triggered DNAzyme cascade assay for enzyme-free amplified fluorescence detection of nucleic acids

An enzyme-free and ultrasensitive fluorescence assay for the detection of nucleic acids was successfully established by a hybridization-triggered DNAzyme cascade (HTDC).

A simple mix-and-read bacteria detection system based on a DNAzyme and a molecular beacon

A simple improved mix-and-read method for the detection of bacteria is developed based on a DNAzyme and a molecular beacon.