A novel aptasensor based on HCR and G-quadruplex DNAzyme for fluorescence detection of Carcinoembryonic Antigen

In this paper, a rationally designed aptasensing platform based on Hybridization Chain Reaction (HCR) and G-quadruplex DNAzyme for the fluorescence detection of Carcinoembryonic Antigen (CEA) has been developed. In the presence of target CEA, the aptamer sequence in Aptamer Probe (AP) specifically bound to CEA, resulting in the AP conformation change and thus releasing initiator, which triggered the autonomous cross-opening of Hairpin 1 (H1) and Hairpin 2 (H2) that yielded extended nicked double-stranded DNA via HCR. Upon the addition of hemin, G-rich segments at the end of H1 and H2 self-assembled into the peroxidase-mimicking hemin/G-quadruplex DNAzymes, which catalyzed the hydrogen peroxide-mediated oxidation of thiamine to achieve fluorescence detection of CEA. The HCR product, and the formation and catalytic performance of DNAzyme were characterized by agarose gel electrophoresis, UV-vis spectroscopy and fluorescence spectroscopy, respectively. Under optimal conditions, the fluorescent aptasensor showed a linear relationship ranging from 0.25 to 1.5 nM toward CEA with a detection limit of 0.2 nM. In addition, this aptasensor exhibited high selectivity for CEA without being affected by other interfering proteins, such as IgG, AFP and PSA. Furthermore, this proposed aptasensor was successfully applied to CEA analysis in diluted human serum samples. It is believed that this strategy has a promising potential in biochemical analysis and clinic application.

Single and Bilayer Polyacrylamide Hydrogel-Based Microcapsules for the Triggered Release of Loads, Logic Gate Operations, and Intercommunication between Microcapsules

A method to assemble loaded stimuli-responsive DNA-polyacrylamide hydrogel-stabilized microcapsules is presented. The method involves coating substrate-loaded CaCO₃ microparticles, functionalized with nucleic acid promoter units, and cross-linking DNA-modified polyacrylamide chains on the microcapsules, using the hybridization chain reaction (HCR) to yield the DNA-cross-linked hydrogel coating. Dissolution of the CaCO₃ particles generated the substrate-loaded hydrogel-protected microcapsules. The microcapsule-hydrogel shells include engineered stimuli-responsive oligonucleotide cross-linkers that control the stiffness of the hydrogel shells, allowing the triggered release of the loads. One approach includes the incorporation of cofactor-dependent DNAzyme units into the cross-linked hydrogel layers (cofactor = Mg²⁺ ions, Zn²⁺ ions, or histidine) as stimuli-responsive units. Cleavage of the cross-linking DNAzyme substrates by the respective cofactors yields hydrogel coatings with a reduced stiffness and higher porosity that allow the release of the loads. A further approach involved the application of the HCR process to assemble the bilayer hydrogel microcapsules that are unlocked by two cooperative triggers. Bilayer microcapsules consisting of a K⁺ ions-stabilized G-quadruplex/18-crown-6-ether (CE) responsive layer and a Mg²⁺ ion DNAzyme-responsive layers are presented. Unlocking and locking of the G-quadruplex cross-linked layer by 18-crown-6-ether and K⁺ ions, respectively, in the presence of Mg²⁺ ions allow the switchable controlled release of the load. In addition, the intercommunication of two kinds of stimuli-responsive bilayer hydrogel microcapsules carrying two different loads (tetramethylrhodamine-dextran, TMR-D, and CdSe/ZnS quantum dots) is demonstrated. The intercommunication process involves the stimuli-triggered generation of "information transfer" strands from one microcapsule to another that activate the release of the loads.

Enzyme-Guided Selection and Cascaded Emergence of Nanostructured Constitutional Dynamic Networks

Enzymes (endonucleases) are coupled to constitutional dynamic networks to stimulate the selection of a constituent and cascaded emergence of a new network. This is exemplified with the EcoRI-dictated depletion of a network and selection of a constituent that activates the cascaded emergence of a new network. The new network is further depleted by HindIII to a selected constituent that can be coupled to the cascaded emergence of a dynamic network. In addition, upon subjecting a [3 × 3] constitutional dynamic network to endonucleases EcoRI and HindIII, the programmed hierarchical selection of [2 × 2] constitutional dynamic networks followed by the biocatalytic selection of a constituent for the subsequent emergence of new networks is demonstrated.

Multifunctional DNA Polymer-Assisted Upconversion Therapeutic Nanoplatform for Enhanced Photodynamic Therapy

Although considerable clinical attempts on various kinds of cancers have been made, photodynamic therapy (PDT) still suffers from attenuated therapeutic effects because of the developed resistance of cancer cells. As a novel antiapoptosis protein, survivin has been demonstrated to be selectively overexpressed in a great number of human malignancies and plays a significant part in cancer progression and therapeutic resistance. Herein, we present an upconversion nanoplatform for enhanced PDT by DNAzyme-mediated gene silencing of survivin. In our system, a long single-stranded DNA (ssDNA) with a repetitive aptamer (AS1411) and survivin-targeted DNAzyme was fabricated by rolling circle amplification (RCA) and adsorbed on the upconversion nanoparticles (UCNPs) by electrostatic attraction. The multivalence of the ssDNA endows the upconversion nanoplatform with high recognition and loading capacity of photosensitizers and DNAzymes. When the nanoplatform is targeted internalized into cancer cells, PDT can be triggered by near-infrared (NIR) light to generate reactive oxygen species (ROS) for killing the cancer cells. Moreover, the encoded DNAzyme can efficiently inhibit the gene expression of survivin, providing the potential to enhance the efficiency of PDT. This study thus highlights the promise of an upconversion photodynamic nanoplatform for admirable combination therapy in cancer.

RNA-Cleaving NAzymes: The Next Big Thing in Biosensing?

Nucleic acid enzymes (NAzymes) are nucleic acid molecules with catalytic activity. A subset, the RNA-cleaving NAzyme, is characterized by its substrate of choice: an RNA unit. These enzymes have been used for diverse applications, including biosensor development, akin to their protein counterparts. Owing to their function as both biorecognition elements and signal generators, robust bioassays based entirely on NAzyme molecules have been developed. Additionally, unique mechanisms for integration with other biorecognition elements and signal generation methods have been explored to realize ultrasensitive, specific, and user-friendly biosensors. Furthermore, NAzyme-based bioassays have already broken into the in vitro diagnostics market, with more promise in the pipeline.

Amplified electrochemical determination of UO22+ based on the cleavage of the DNAzyme and DNA-modified gold nanoparticle network structure

A superior electrochemical biosensor was designed for the determination of UO₂²⁺ in aqueous solution by integration of DNAzyme and DNA-modified gold nanoparticle (DNA-AuNP) network structure. Key features of this method include UO₂²⁺ inducing the cleavage of the DNAzyme and signal amplification of DNA-AuNP network structure. In this electrochemical method, the DNA-AuNP network structure can be effectively modified on the surface of gold electrode and then employed as an ideal signal amplification unit to generate amplified electrochemical response by inserting a large amount of electrochemically active indicator methylene blue (MB). In the presence of UO₂²⁺, the specific sites on DNA-AuNP network structure can be cleaved by UO₂²⁺, releasing the DNA-AuNP network structure with detectable reduction of electrochemical response intensity. The electrochemical response intensity is related to the concentration of UO₂²⁺. The logarithm of electrochemical response intensity and UO₂²⁺ concentration showed a wide linear range of 10~100 pM, and the detection limit reached 8.1 pM (S/N = 3). This method is successfully used for determination of UO₂²⁺ in water samples. Graphical abstract Fabricated DNAzyme network structure for enhanced electrical signal. Numerical experiments show that the current signal decreases as the concentration of UO₂²⁺ increases. It can be seen that the biosensors could be used to detect UO₂²⁺ in aqueous solution effectively.

Modeling Gene Expression Instability by Programmed and Switchable Polymerization/Nicking DNA Nanomachineries

Models for gene expression instability by noncanonical DNA-nanostructures are introduced. The systems consist of a promoter-template scaffold that acts as a polymerization/nicking machinery that models, in the presence of polymerase/Nt.BbvCI and dNTPs, the autonomous synthesis of displaced strands mimicking the native "genes". Incorporation of noncanonical DNA structures into the scaffolds consisting of Sr²⁺-ion-stabilized G-quadruplexes, T-A·T triplexes, or ATP-aptamer complexes results in the perturbation of the polymerization/nicking DNA machineries and the synthesis of displaced strands-"genes" exhibiting other structures. By the dissociation of the noncanonical blockage units, the regeneration of the synthesis of the original intact displaced strands-"genes" is demonstrated. The study introduces conceptual means to eliminate destructive gene expression instability pathways.

Sensitive Detection of Nucleic Acids Using Subzyme Feedback Cascades

The development of Subzymes demonstrates how the catalytic activity of DNAzymes can be controlled for detecting nucleic acids; however, Subzymes alone lack the sensitivity required to detect low target concentrations. To improve sensitivity, we developed a feedback system using a pair of cross-catalytic Subzymes. These were individually tethered to microparticles (MP) and separated by a porous membrane rendering them unable to interact. In the presence of a target, active PlexZymes^® cleave a first Subzyme, which separates a first DNAzyme from its MP, allowing the DNAzyme to migrate through the membrane, where it can cleave a second Subzyme. This releases a second DNAzyme which can now migrate through the membrane and cleave more of the first Subzyme, thus initiating a cross-catalytic cascade. Activated DNAzymes can additionally cleave fluorescent substrates, generating a signal, and thereby, indicating the presence of the target. The method detected 1 fM of DNA homologous to the ompA gene of Chlamydia trachomatis within 30 min, demonstrating a 10,000-fold increase in sensitivity over PlexZyme detection alone. The Subzyme cascade is universal and can be triggered by any target by modifying the target sensing arms of the PlexZymes. Further, it is isothermal, protein-enzyme-free and shows great potential for rapid and affordable biomarker detection.

Heme•G-Quadruplex DNAzymes: Conditions for Maximizing Their Peroxidase Activity

Catalytic DNAs (DNAzymes) with peroxidase-like activity have great potential in bioanalytical chemistry [1], owing to numerous advantages that DNA enzymes offer over conventional protein enzymes, including structural simplicity, low cost, thermal stability, and straightforward handling and preparation. Maximizing the efficiency of the peroxidase activity of such DNAzymes is a subject in need of review. In this chapter, we discuss the optimal experimental conditions for the peroxidase activity of these DNAzymes and describe general procedures for their utilization.

Nucleic-Acid Structures as Intracellular Probes for Live Cells

The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.

A simple and programmed DNA tweezer probes for one-step and amplified detection of UO22

A simple DNA tweezer was proposed for one-step and amplified detection of UO₂²⁺ based on DNAzyme catalytic cleavage. The two arms of DNA tweezers are close in the original form. Thus, the fluorescent signal of fluorophore at the end of arm is dramatically quenched. However, the structure of DNA tweezers can be changed from "close" to "open" in the presence of UO₂²⁺, resulting the strong fluorescent signal. The linear range was obtained in the range of 0.1 nM to 60 nM and the limit of detection was 25 pM with the amplification of DNAzyme catalytic cleavage reaction. Importantly, the whole detection process is very simple and only one operation step is required. In addition, it shows great potential and promising prospects for uranyl detection in practical application.

Development of a Novel DNA Oligonucleotide Targeting Low-Density Lipoprotein Receptor

Low-density lipoprotein receptor (LDL-R) is a cell surface receptor protein expressed in a variety of solid cancers, including lung, colon, breast, brain, and liver, and therefore it opens up opportunities to deliver lysosome-sensitive anti-cancer agents, especially synthetic nucleic acid-based therapeutic molecules. In this study, we focused on developing novel nucleic acid molecules specific to LDL-R. For this purpose, we performed in vitro selection procedure via systematic evolution of ligands by exponential enrichment (SELEX) methodologies using mammalian cell-expressed human recombinant LDL-R protein as a target. After 10 rounds of selections, we identified a novel DNA oligonucleotide aptamer, RNV-L7, that can bind specifically to LDL-R protein with high affinity and specificity (KD = 19.6 nM). Furthermore, flow cytometry and fluorescence imaging assays demonstrated efficient binding to LDL-R overexpressed human cancer cells, including Huh-7 liver cancer cells and MDA-MB-231 breast cancer cells, with a binding affinity of ∼200 nM. Furthermore, we evaluated the functional potential of the developed LDL-R aptamer RNV-L7 by conjugating with a previously reported miR-21 targeting DNAzyme for inhibiting miR-21 expression. The results showed that the miR-21 DNAzyme-RNV-L7 aptamer chimera efficiently reduced the expression of miR-21 in Huh-7 liver cancer cells. As currently there are no reports on LDL-R aptamer development, we think that RNV-L7 could be beneficial toward the development of targeted cancer therapeutics.

Plasmonic Biosensor Controlled by DNAzyme for On-Site Genetic Detection of Pathogens

On-site predetection of pathogens could significantly decrease of a disease outbreak or national loss in most of the countries. However, conventional detection techniques are limited in use for on-site detection due to the necessity of specialized skill or equipment. Therefore, it is necessary to develop a new technique that can predetect pathogens in the field without special skills or equipment. Here, a DNAzyme strategy to control a plasmonic biosensor for rapid and simple visual detection of Salmonella choleraesuis is adopted. Multicomponent DNAzyme formed by target addition can cleave the linker effectively at 50 °C. Linker cleavage induces dispersion of two DNA-immobilized gold nanoparticles and color change. Under optimized assay conditions, the target could be detected via visual discrimination sensitively and specifically. Moreover, the biosensor shows the possibility of practical use with contaminants and a 16S rRNA real target. As a result, the proposed plasmonic biosensor can visually detect S. choleraesuis without unstable enzymes, a specialized technique, or equipment. Therefore, these advantages could allow that this biosensor would be used for on-site predetection to lower the risk of transmission of infectious diseases.

A Smart, Autocatalytic, DNAzyme Biocircuit for in Vivo, Amplified, MicroRNA Imaging

DNAzymes have been recognized as promising transducing agents for visualizing endogenous biomarkers, but their inefficient intracellular delivery and limited amplification capacity (including insufficient cofactor supply) preclude their extensive biological application. Herein, an autocatalytic DNAzyme (ACD) biocircuit is constructed for amplified microRNA imaging in vivo based on a hybridization chain reaction (HCR) and DNAzyme biocatalysis, sustained by a honeycomb MnO₂ nanosponge (hMNS). The hMNS not only delivers DNA probes, but also supplies Mn²⁺ as a DNAzyme cofactor and magnetic resonance imaging (MRI) agent. Through the subsequent cross-activation of HCR and DNAzyme amplicons, the ACD amplifies the limited signal resulting from miRNA recognition. The hMNS/ACD system was used to image microRNA in vivo, thus demonstrating its great promise in cancer diagnosis.

Engineering a DNAzyme-Based Operon System for the Production of DNA Nanoscaffolds in Living Bacteria

The ability to create nanoscaffolds within living cells using DNA has the potential to become a powerful tool in synthetic biology. However, to date, genetically encoded DNA nanostructures are limited to simple architecture due to the lack of genetic parts that can produce multiple ssDNAs in a single bacterium. Here, we develop a system that overcomes this challenge by using a single oligo gene mimicking operons. This was achieved by converting a noncoding RNA into a long ssDNA that self-cleaves into multiple ssDNAs using R3-DNAzymes (DNAzyme-based operon). We demonstrate the ability to apply the DNAzyme-based operon to produce a four-ssDNA crossover nanostructure (25 nm) that recruits split YFPs when properly assembled. This system enables the formation of more complex DNA nanostructures in vivo and thus paves the way to further integrate the field of DNA nanotechnology into living bacteria for basic biology, bioengineering, and medicine applications.

Microfluidic Particle Dam for Visual and Quantitative Detection of Lead Ions

Lead contamination in drinking water is a primary concern in public health, but it is difficult to monitor by end-users. Here, we provide a rapid and power-free microfluidic particle dam which enables visual quantification of lead ions (Pb²⁺) by the naked eye. GR-5 DNAzyme with extended termini can connect magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) by DNA hybridization, forming "MMPs-GR-5-PMPs". When Pb²⁺ is present, GR-5 is cleaved, resulting in an increasing number of free PMPs. To visually count the free PMPs, the solution is loaded to a capillary-driven microfluidic device that consists of a magnetic separator to remove the MMPs-GR-5-PMPs, followed by a particle dam that traps and accumulates the free PMPs into a visual bar with growing length proportional to the concentration of lead. The device achieved a limit of detection at 2.12 nM (0.44 ppb), high selectivity (>20,000-fold) against other metal ions, high tolerance to different pH and water hardness, and is compatible with tap water with a high recovery rate, enabling visual quantification and user-friendly interface for rapid screening of water safety.

Nucleic acid-cleaving catalytic DNA for sensing and therapeutics

DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.

Fluorometric determination of lead(II) by using aptamer-functionalized upconversion nanoparticles and magnetite-modified gold nanoparticles

A fluorescent nanoprobe for Pb(II) has been developed by employing aptamer-functionalized upconversion nanoparticles (UCNPs) and magnetic Fe₃O₄-modified (MNPs) gold nanoparticles (GNPs). First, aptamer-functionalized UCNPs and aptamer-functionalized magnetic GNPs were synthesized to obtained the fluorescent nanoprobe. The particles were combined by adding a complementary ssDNA. In the absence of Pb(II), the UCNPs, MNPs and GNPs are linked via complementary base pairing. This led to a decrease in the green upconversion fluorescence peaking at 547 nm (under 980 nm excitation). In the presence of Pb(II), the dsDNA between UCNPs and MNPs-GNPs is cleaved, and fluorescence recovers. This effect allows Pb(II) to be quantified, with a wide working range of 25-1400 nM and a lower detection limit of 5.7 nM. The nanoprobe gave satisfactory results when analyzing Pb(II) in tea and waste water. Graphical abstractSchematic representation of fluorescent nanoprobe based on fluorescence resonance energy transfer (FRET) between upconversion nanoparticles (UCNPs) and gold nanoparticles (GNPs)-Fe₃O₄ magnetic nanoparticles (MNPs) for detection of Pb²⁺.

Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics

Purpose

To systematically evaluate human rod opsin (hRHO) mRNA for potential target sites sensitive to posttranscriptional gene silencing (PTGS) by hammerhead ribozyme (hhRz) or RNA interference (RNAi) in human cells. To develop a comprehensive strategy to identify and optimize lead candidate agents for PTGS gene therapeutics.

Methods

In multidisciplinary RNA drug discovery, computational mRNA accessibility and in vitro experimental methods using reverse transcription–polymerase chain reaction (RT-PCR) were used to map accessibility in full-length hRHO transcripts. HhRzs targeted predicted accessible and inaccessible sites and were screened for cellular knockdown using a bicistronic reporter construct. Lead hhRz and RNAi PTGS agents were rationally optimized for target knockdown in human cells.

Results

Systematic screening of hRHO mRNA targeting agents resulted in lead candidate identification of a novel hhRz embedded in an RNA scaffold. Rational optimization strategies identified a minimal 725 hhRz as the most active agent. Recently identified tertiary accessory elements did not enhance activity. A 725-short-hairpin RNA (shRNA) agent exerts log-order knockdown. Silent modulation of the 725-hhRz target site in hRHO mRNA resulted in resistance to knockdown.

Conclusions

Combining rational RNA drug design with cell-based screening allowed rapid identification of lead agents targeting hRHO. Optimization strategies identified the agent with highest intracellular activity. These agents have therapeutic potential in a mutation-independent strategy for adRP, or other degenerations where hRHO is a target. This approach can be broadly applied to any validated target mRNA, regardless of the disease.

Translational Relevance

This work establishes a platform approach to develop RNA biologicals for the treatment of human disease.

A "signal-on" electrochemical biosensor based on DNAzyme-driven bipedal DNA walkers and TdT-mediated cascade signal amplification strategy

In this work, a dual amplified signal enhancement approach based on coupling deoxyribozyme (DNAzyme)-driven bipedal DNA walkers (BDW) and terminal deoxynucleotidyl transferase (TdT)-mediated DNA elongation signal amplifications has been developed for highly sensitive and label-free electrochemical detection of thrombin in human serums. In presence of thrombin, the BDW complex, which is comprised from the target thrombin and two DNAzyme-containing probes, can exhibit autonomous cleavage behavior on the surface of the substrate DNA (SD) modified electrode, and remove the cleaved DNA fragment from the electrode surface. Subsequently, the TdT can catalyze the elongation of the SD with free 3'-OH termini and formation of many G-quadruplex sequence replicates with the presence of 2'-deoxyaguanosine-5'-triphosphate (dGTP) and adenosine 5'-triphosphate (dATP) at a molar ratio of 6:4. These G-quadruplex sequences bind hemin and generate drastically amplified current response for sensitive detection of thrombin in a "signal-on" and completely label-free fashion. Under optimized conditions, the response peak current was linear with the concentration of thrombin in the range from 0.5 pM to 100000 pM with detection limit of 0.31 pM. This research provides us a sustainable idea for the hyphenated multiple amplification strategies and a stable and effective method for the detection of protein biomarkers.

Improved performances of catalytic G-quadruplexes (G4-DNAzymes) via the chemical modifications of the DNA backbone to provide G-quadruplexes with double 3'-external G-quartets

Here we report on the design of a new catalytic G-quadruplex-DNA system (G4-DNAzyme) based on the modification of the DNA scaffold to provide the DNA pre-catalyst with two identical 3'-ends, known to be more catalytically proficient than the 5'-ends. To this end, we introduced a 5'-5' inversion of polarity site in the middle of the G4-forming sequences AG₄A and AG₆A to obtain d(^3'AGG^5'-^5'GGA^3') (or AG₂-G₂A) and d(^3'AGGG^5'-^5'GGGA^3') (or AG₃-G₃A) that fold into stable G4 whose tetramolecular nature was confirmed via nuclear magnetic resonance (NMR) and circular dichroism (CD) investigations. Both AG₂-G₂A and AG₃-G₃A display two identical external G-quartets (3'-ends) known to interact with the cofactor hemin with a high efficiency, making the resulting complex competent to perform hemoprotein-like catalysis (G4-DNAzyme). A systematic comparison of the performances of modified and unmodified G4s lends credence to the relevance of the modification exploited here (5'-5' inversion of polarity site), which represents a new chemical opportunity to improve the overall activity of catalytic G4s.

A DNAzyme based knockdown model for Fragile-X syndrome in zebrafish reveals a critical window for therapeutic intervention

INTRODUCTION

FXS is the leading cause of intellectual disabilities in males and a major monogenic cause of ASD (Autism spectrum disorders). It occurs due to the loss of FMRP, whose role in early development is not well understood. In this study, we have used a novel DNAzyme based approach to create a larval model of FXS in zebrafish with specific focus on the early developmental window.

METHODS

Fmr1specific DNAzymes were electroporated into embryos to create the knockdown. Changes in RNA and protein levels of FMRP and relevant biomarkers were measured in the 0-7dpf window. Behavioral tests to measure anxiety, cognitive impairments and irritability in the larvae were conducted at the 7dpf stage. Drug treatment was carried out at various time points in the 0-7dpf window to identify the critical window for pharmacological intervention.

RESULTS

The DNAzyme based knockdown approach led to a significant knockdown of FMRP in the zebrafish embryos, accompanied by increased anxiety, irritability and cognitive impairments at 7dpf, thus creating a robust larval model of FXS. Treatment with the Mavoglurant was able to rescue the behavioral phenotypes in the FXS larvae, and found to be more efficacious in the 0-3dpf window.

DISCUSSION

The results from this study have revealed that a) a DNAzyme based knockdown approach can be used to create robust larval zebrafish model of disease, in a high-throughput manner and b) optimal window for therapeutic intervention for FXS as well as other pediatric diseases with a monogenic cause can be identified using such a model.

A Dual-Sensing DNA Nanostructure with an Ultrabroad Detection Range

Despite considerable interest in the development of biosensors that can measure analyte concentrations with a dynamic range spanning many orders of magnitude, this goal has proven difficult to achieve. We describe here a modular biosensor architecture that integrates two different readout mechanisms into a single-molecule construct that can achieve target detection across an extraordinarily broad dynamic range. Our dual-mode readout DNA biosensor combines an aptamer and a DNAzyme to quantify adenosine triphosphate (ATP) with two different mechanisms, which respond to low (micromolar) and high (millimolar) concentrations by generating distinct readouts based on changes in fluorescence and absorbance, respectively. Importantly, we have also devised regulatory strategies to fine-tune the target detection range of each sensor module by controlling the target-sensitivity of each readout mechanism. Using this strategy, we report the detection of ATP at a dynamic range spanning 1-500 000 μM, more than 5 orders of magnitude, representing the largest dynamic range reported to date with a single biosensor construct.

Catalytic hairpin assembly-based double-end DNAzyme cascade-feedback amplification for sensitive fluorescence detection of HIV-1 DNA

In this work, a simple all-nucleic acid cascade-feedback amplification strategy for homogeneous and protein enzyme-free fluorescence detection of HIV-1 related DNA (HIV-1 DNA) has been proposed by integrating catalytic hairpin assembly (CHA) circuit with double-end Mg²⁺-dependent DNAzyme autocatalytic feedback amplification. Here, the active double-end DNAzyme assemblies were derived from target-catalyzed CHA circuit, which further circularly cleaved the ribonucleotide-containing quenched fluorogenic hairpin substrates to generate distinctly amplified fluorescence signal. Meanwhile, the released quencher-labeled fragments as target DNA analogues were also able to autocatalyze CHA-DNAzyme reaction process, thus improving the determination sensitivity of HIV-1 DNA. The result demonstrated that the fluorescence intensity increment of double-end DNAzyme was over 3 times higher than that of single-end DNAzyme. The sensing method displayed a good linear range from 1 pM to 2 nM with a detectable minimum concentration of 1 pM and high specificity towards different mismatched target DNAs. Moreover, the practical application potential of the proposed method for target DNA detection in complex biological matrices was also assessed. Considering the appealing feature of programmable nucleic acids in CHA-DNAzyme sensing platform, the current strategy may provide a prospective design for detection of broad-spectrum nucleic acid biomarkers.

Controlled assembly of AIEgens based on a super-quadruplex scaffold for detection of plasma membrane proteins

Quantification of plasma membrane proteins (PMPs) is crucial for understanding the fundamentals of cellular signaling systems and their related diseases. In this work, a super-quadruplex scaffold was designed to regulate assembly of oligonucleotide-grafted AIEgens for detection of PMPs. The nonfluorescence oligonucleotide-grafted AIEgen (Oligo-AIEgen) was firstly synthesized by attaching the AIEgen to 3'-terminus of the oligonucleotide through click chemistry. Meanwhile, the tetramolecular hairpin-conjugated super-quadruplex (THP-G4) as cleavage element and signal enhancement scaffold composited of three elements: a substrate sequence of DNAzyme in the loop region, partial hybridization region in the stem, and six guanine nucleotides to form G-quadruplex. Once the DNAzyme was anchored on the specific PMPs through aptamer-protein recognition, the substrate sequence on the loop of THP-G4 was cleaved by DNAzyme with the aid of cofactor Mn^II, resulting in the conformation switch of THP-G4 to the activated G-quadruplex scaffold. The latter could assemble Oligo-AIEgens to generate aggregation-induced emission (AIE) enhancement, resulting in a simple and sensitive strategy for detection of membrane proteins. Moreover, the DNAzyme continuously cut the next THP-G4 to achieve recycling amplification. Under the optimized conditions, this AIE-based strategy exhibited good linear relationship with the logarithm of MUC1 concentration from 0.01 to 10 μg mL^-1 with the limit of detection down to 4.3 ng mL^-1. The G4-assembled AIEgens provides a universal platform for detecting various biomolecules and a proof-of concept for AIE biosensing.

Triggered Interconversion of Dynamic Networks Composed of DNA-Tetrahedra Nanostructures

Constitutional dynamic networks (CDNs) consisting of DNA tetrahedra allow the dynamically triggered adaptive control over the compositions and structures of the constituents. In one system, a CDN consisting of four tetrahedra constituents is orthogonally triggered by two alternative triggers, T₁ or T₂, to reconfigure into two different CDNs, revealing adaptive control-over the tetrahedra compositions in the two CDNs. In the presence of the counter triggers T₁' or T₂', the parent CDN is regenerated. In the second system, the assembly of a CDN consisting of four dimeric tetrahedra exhibiting variable sizes and shapes is described. The orthogonal triggering of the CDN by two different triggers T₃ or T₄, leads to the adaptive reconfiguration of the CDN into new equilibrated CDNs exhibiting control-over the compositions and shapes of the dimeric tetrahedra comprising the CDNs. Mg²⁺-ion-dependent DNAzyme units conjugated to the tetrahedra nanostructures and complementary electrophoretic experiments provide means to quantitatively evaluate the compositions of the different CDN systems. By the functionalization of the four-tetrahedra-based CDN system with two fluorophor donor-acceptor pairs and the orthogonal reconfiguration of the CDN in the presence of two alternative triggers, the control-over the FRET functions of the CDN systems is demonstrated.

Aptazymes: Expanding the Specificity of Natural Catalytic Nucleic Acids by Application of In Vitro Selected Oligonucleotides

Aptazymes are synthetic molecules composed of an aptamer domain and a catalytic active nucleic acid unit, which may be a ribozyme or a DNAzyme. In these constructs the aptamer domain serves as a molecular switch that can regulate the catalytic activity of the ribozyme or DNAzyme subunit. This regulation is triggered by binding of the aptamers target molecule, which causes significant structural changes in the aptamer and thus in the entire aptazyme. Therefore, aptazymes function similar to allosteric enzymes, whose catalytic activity is regulated by binding of ligands (effectors) to allosteric sites due to alteration of the three-dimensional structure of the active site of the enzyme. In case of aptazymes, the allosteric site is composed of an aptamer. Aptazymes can be designed for different applications and have already been used in analytical assays as well as for the regulation of gene expression.

Bioanalytical Application of Peroxidase-Mimicking DNAzymes: Status and Challenges

DNAzymes with peroxidase-mimicking activity are a new class of catalytically active DNA molecules. This system is formed as a complex of hemin and a G-quadruplex structure created by oligonucleotides rich in guanine. Considering catalytic activity, this DNAzyme mimics horseradish peroxidase, the enzyme most commonly used for signal generation in bioassays. Because DNAzymes exhibit many advantages over protein enzymes (thermal stability, easy and cheap synthesis and purification) they can successfully replace HRP in bioanalytical applications. HRP-like DNAzymes have been applied in the detection of several DNA sequences. Many amplification techniques have been conjugated with DNAzyme systems, resulting in ultrasensitive bioassays. On the other hand, the combination of aptamers and DNAzymes has led to the development of aptazymes for specific targets. An up-to-date summary of the most interesting DNAzyme-based assays is presented here. The elaborated systems can be used in medical diagnosis or chemical and biological studies.

Target-induced formation of multiple DNAzymes in solid-state nanochannels: Toward innovative photoelectrochemical probing of telomerase activity

Solid-state nanochannels have great potentials in the vibrant field of photoelectrochemical (PEC) bioanalysis. This work herein demonstrates the innovative use of DNA-decorated nanoporous anodic alumina (NAA) nanochannels for sensitive PEC bioanalysis of telomerase (TE) activity. Specifically, telomerase primer sequences (TS) were initially immobilized within the NAA nanochannels and then extended by TE in the presence of deoxyribonucleoside triphosphates (dNTPs). The as formed single-strand DNA was then directed to hybrid with many partially matched single-strand assisting DNA (aDNA), leading to the formation of multiple DNAzymes by the unmatched parts and the subsequent DNAzyme-stimulated biocatalytic precipitation (BCP) within the nanochannels. Because the inhibited signals of the photoelectrode could be correlated with TE-enabled TS extension, an innovative nanochannels PEC bioanalysis could be realized for probing TE activity. This work features the ingenious use of DNA-associated nanochannels for PEC bioanalysis of TE activity. Given the versatile functions of DNA molecules, the extension of this strategy easily allows for addressing numerous other targets of interest. Also, we envision this work could inspire more interest for the further development of nanochannels PEC bioanalysis.

A sensitive and radiolabeling-free method for pseudouridine detection

Existing methodologies for detecting Pseudouridine (Ψ) mostly use CMCT labeling or radiolabeling. Described herein is a sensitive and quantitative method for Ψ detection that does not need this labelling. This approach combines the selectivity of a 10-23 DNAzyme, which can distinguish Ψ from uridine (U), with rolling circle amplification (RCA) to increase the sensitivity of the assay.

One-step label-free chemiluminescent assay for determination of exonuclease III activity towards hairpin oligonucleotides

Fast label-free chemiluminescent assay for determination of exonuclease III (ExoIII) activity measured towards hairpin oligonucleotide substrates was developed. The designed substrates consisted of EAD2 aptamer to hemin which was associated with DNA sequence complementary to 5'-terminus fragment of EAD2. In the presence of ExoIII the associated sequence of the hairpin stem was digested, producing EAD2 aptamer which reacted with hemin with the formation of peroxidase-mimicking DNAzyme (PMDNAzyme). The catalytic activity of the produced PMDNAzyme was measured towards luminol/H₂O₂. Under the optimized conditions the limit of detection and sensitivity of the one-step chemiluminescent assay of ExoIII were 7.3 nM and 1.7 × 10⁸ M^-1, respectively. The coefficient of variation (CV) was lower than 6%.

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.

An Origami Paper-Based Device Printed with DNAzyme-Containing DNA Superstructures for Escherichia coli Detection

Rapid detection of pathogenic bacteria is extremely important for public health and safety. Here, we describe for the first time an integrated origami paper-based analytical device (PAD) incorporating cell lysis, molecular recognition, amplification and visual detection of Escherichia coli (E. coli). The device features three components: paper for its ability to extract protein molecules nonspecifically from cells, DNA superstructures for their ability to immobilize RNA-cleaving DNAzymes (RCDs) but undergo target-induced RNA cleavage on paper, and isothermal rolling circle amplification (RCA) for its ability to amplify each cleavage event into repetitive sequence units that can be detected by naked eye. This device can achieve detection of E. coli K12 with a detection limit of as low as 103 CFU·mL-1 in a total turnaround time of 35 min. Furthermore, this device allowed the sensitive detection of E. coli in complex sample matrices such as juice and milk. Given that more specific RCDs can be evolved for diverse bacteria, the integrated PAD holds great potential for rapid, sensitive and highly selective detection of pathogenic bacteria in resource-limited settings.

Inhibition of proliferation and migration of tumor cells through phenylboronic acid-functionalized polyamidoamine-mediated delivery of a therapeutic DNAzyme Dz13

BACKGROUND

The phenylboronic acid-functionalized polyamidoamine (PP) was employed as a gene carrier for Dz13 delivery, inducing an obvious anticancer response.

MATERIALS AND METHODS

The Dz13 condensation ability of PP was evaluated through gel retardation assay. The cellular uptake mechanism of PP/Dz13 nanoparticles was studied using confocal laser scanning microscope and flow cytometer. The inhibition ability of cell proliferation, migration and invasion was investigated through MTT assay, flow cytometry, wound healing and Transwell migration assays, using hepatocarcinoma cell line HepG2 as a model. Finally, Western blotting analysis was used to detect the signaling pathway associated with the inhibition of cell apoptosis and migration induced by Dz13 delivery.

RESULTS

The carrier PP could efficiently condense Dz13 into stable nanoparticles at mass ratios of >1.5. The hydrodynamic diameter and zeta potential of PP/Dz13 nanoparticles were measured to be 204.77 nm and +22.00 mV at a mass ratio of 10.0, respectively. The nanoparticles could realize an efficient cellular uptake in sialic acid-dependent endocytosis manner. Moreover, the nanoparticles exhibited an obvious antiproliferation effect through the induction of cell apoptosis and cell cycle arrest due to the cleavage of c-Jun mRNA. Besides, the suppression of cell migration and invasion could be achieved after the PP/Dz13 transfection, attributing to the decreased expression level of MMP-2 and MMP-9.

CONCLUSION

The PP provided a potential delivery system to achieve the tumor-targeting gene therapy.

Rapid and sensitive determination of bisphenol A using aptamer and split DNAzyme

Despite the increasing concern regarding bisphenol A (BPA) as an endocrine disrupting chemical (EDC) upon environmental or human exposure, development of simple method for BPA detection has been hampered, due to the lack of a stable bioreceptor and signal generator. Here, we report a nucleic acid-based rapid and sensitive method for BPA detection, which constitutes a ssDNA aptamer and ssDNAzyme. When the peroxidase-like DNAzyme sequence was split into two parts (one incorporated into the anti-BPA aptamer as a target recognition element and the other into the complementary sequence as a bait), the presence of BPA hindered the association of the split DNA sequence, leading to a reduced signal in the DNAzyme-triggered chemiluminescence (CL). Thus, this NA-based CL measurement permitted the detection of BPA at as low as 5 nM with a broad dynamic range of five orders and with high selectivity towards BPA over other EDCs with structural similarity. With the development of aptamers, our detection method is expected to facilitate studies to monitor EDCs with high simplicity and sensitivity in the field of environmental science.

An enzyme-free and label-free signal-on aptasensor based on DNAzyme-driven DNA walker strategy

Herein, a signal-on electrochemical aptasensor for highly sensitive detection of thrombin (TB) was constructed based on the DNAzyme-driven DNA walker strategy. We developed a new dual functional hairpin DNA (HP) containing a substrate sequence of the Mg²⁺-dependent DNAzyme (in the loop region) and the G-quadruplex forming segment (in the stem region). The DNA walker (TBA₂-DWs), containing a TB aptamer and an enzymatic sequence, was introduced onto gold electrode (GE) by aptamers-target specific recognition, and thus initiated the enzymatic sequences to hybridize with the substrate sequence. Then, the DNA walker could repeatedly bind and cleave HP in the assistance of Mg²⁺, unlocking many active G-quadruplex forming sequences. Finally, hemin can further bind the G-quadruplex to form G-quadruplex/hemin complexes and generate enhanced current output. The aptasensor for TB assay showed a linear detection range from 1 pM to 60000 pM with a lower detection limit of 0.58 pM. And more, the proposed detection strategy was enzyme-free and label-free.

Development of Novel antimiRzymes for Targeted Inhibition of miR-21 Expression in Solid Cancer Cells

MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the regulation of gene expression. Previous reports showed an over-expression of miRNA-21 (miR-21) in various cancer cells, and its up-regulation is closely related to cancer initiation, proliferation and metastasis. In this work, we envisioned the development of novel antimiRzymes (anti-miRNA-DNAzyme) that are capable of selectively targeting and cleaving miR-21 and inhibit its expression in cancer cells using the DNAzyme technique. For this purpose, we have designed different antimiRzyme candidates by systematically targeting different regions of miR-21. Our results demonstrated that RNV541, a potential arm-loop-arm type antimiRzyme, was very efficient (90%) to suppress miR-21 expression in U87MG malignant glioblastoma cell line at 200 nM concentration. In addition, RNV541 also inhibited miR-21 expression (50%) in MDA-MB-231 breast cancer cell line. For targeted delivery, we conjugated RNV541 with a transferrin receptor (TfR) targeting aptamer for TfR-mediated cancer cell delivery. As expected, the developed chimeric structure efficiently delivered the antimiRzyme RNV541 into TfR positive glioblastoma cells. TfR aptamer-RNV541 chimeric construct showed 52% inhibition of miR-21 expression in U87MG glioblastoma cells at 2000 nM concentration, without using any transfection reagents, making it a highly desirable strategy to tackle miR-21 over-expressed malignant cancers. Although these are in vitro based observations, based on our results, we firmly believe that our findings could be beneficial towards the development of targeted cancer therapeutics where conventional therapies face several challenges.

A general scheme for fluorometric detection of multiple oligonucleotides by using RNA-cleaving DNAzymes: application to the determination of microRNA-141 and H5N1 virus DNA

A widely applicably method is described for fluorometric determination of targets such as microRNA and viral DNA. It is making use of a Mg(II)-dependent DNAzyme and a G-quadruplex. In the absence of analyte, an inactive DNAzyme is formed by the hybridization of split DNAzymes and substrate. On addition of target analyte, the end of each strand of the split DNAzymes bind the analyte. This leads to the generation of an active DNAzyme. In the presence of Mg(II), the activated DNAzyme is formed and can cleave the substrate strand. Hence, the caged G-quadruplex sequences will be released. These released G-quadruplexes combine with thioflavin T to generate a G-quadruplex/thioflavin T complex and thereby cause amplified fluorescence. The method shows a 70 pM detection limit for H5N1 and works over a wide linear range 1 nM to 400 nM. Conceivably, this detection scheme has a wide scope in that it may be applied to other assays for microRNAs and DNAs by variation of the type of DNAzyme. Graphical abstract Schematic presentation of target detection: the DNAzyme cannot cleave the substrate strand when target is absent. Once the target is added, the active DNAzyme can cleave the substrate strand in the presence of Mg²⁺, resulting in significant fluorescence enhancement when the release of the caged G-quadruplex sequences binding with 2-[4-(dimethylamino)phenyl]-3,6-dimethylbenzothiazolium chloride (ThT).

DNAzyme-Functionalized R-Phycoerythrin as a Cost-Effective and Environment-Friendly Fluorescent Biosensor for Aqueous Pb2+ Detection

The sensitive detection of Pb²⁺ is of significant importance for food safety, environmental monitoring, and human health care. To this end, a novel fluorescent biosensor, DNAzyme-functionalized R-phycoerythrin (DNAzyme-R-PE), was presented for Pb²⁺ analysis. The biosensor was prepared via the immobilization of Iowa Black^® FQ-modified DNAzyme–substrate complex onto the surface of SPDP-functionalized R-PE. The biosensor produced a minimal fluorescence signal in the absence of Pb²⁺. However, Pb²⁺ recognition can induce the cleavage of substrate, resulting in a fluorescence restoration of R-PE. The fluorescence changes were used to measure sensitively Pb²⁺ and the limit of detection was 0.16 nM with a linear range from 0.5–75 nM. Furthermore, the proposed biosensor showed excellent selectivity towards Pb²⁺ even in the presence of other metal ions interferences and was demonstrated to successfully determine Pb²⁺ in spiked lake water samples.

A "turn-off" SERS aptasensor based DNAzyme-gold nanorod for ultrasensitive lead ion detection

It is great significance to precisely monitor lead (II) ions (Pb²⁺) for environment protection and human health monitoring. We designed a sensitive detection strategy for sensitive and selective determination of Pb²⁺, based on a Pb²⁺-specific DNAzyme as the catalytic unit, Cy3-labeled DNA modified gold nanorods (AuNRs) as SERS reporter. Firstly, AuNRs surface were employed as a platform for the immobilization of thiolated probe DNA, and then hybridized with DNAzyme catalytic beacons. By taking advantage of DNAzyme digest, a molecular beacon, causes a "turn-off" SERS signal by disrupting the labeled probes. Under the optical conditions, the DNAzyme-AuNRs sensor system exhibited high sensitivity, acceptable stability and reproducibility with a wide linear range from 0.5 to 100 nM (R² = 0.9973), and an ultra-low detection limit of 0.01 nM. The proposed strategy has additional advantages of being less time-consuming, low-cost and remote query, and avoids the interference of some metals such as Fe³⁺, Cd²⁺, Ba²⁺, Cu²⁺, Zn²⁺. The SERS biosensor system has been successfully applied for detecting Pb²⁺ in real samples with a satisfactory result. The result indicated that the proposed sensing strategy not only enriches SERS platform of monitoring Pb²⁺ but also exhibits potential for the point-of-care diagnostic application of the clinical screening in complicated biological samples.

Nonviolent Self-Catabolic DNAzyme Nanosponges for Smart Anticancer Drug Delivery

The development of self-assembled DNA nanomedicine requires a facile and accurate DNA degradation strategy for precisely programmable drug release. Conventional DNA catabolic strategies are restrained with the fragile and unclear enzymatic reactions that might lead to inefficient and uncontrollable digestion of DNA scaffolds and thus might bring undesirable side effects to the sophisticated biosystems. Herein we reported a versatile self-sufficient DNAzyme-driven drug delivery system consisting of the rolling circle polymerized DNAzyme-substrate scaffolds and the encapsulated pH-responsive ZnO nanoparticles (NPs). The full DNAzyme nanosponges (NSs) were also encoded with multivalent tandem aptamer sequences to facilitate their efficient delivery into cancer cells, where the acidic endo/lysosomal microenvironment stimulates the dissolution of ZnO into Zn²⁺ ions as DNAzyme cofactors and therapeutic reactive oxygen species generators. The supplement Zn²⁺ cofactors mediated the nonviolent DNAzyme-catalyzed cleavage of DNA scaffolds for precise and efficient drug administrations with synergistically enhanced therapeutic performance. The facile design of DNAzyme, together with their cost-effective and intrinsic robust features, is anticipated to provide extensive insights for the development of DNA-based therapeutic platforms by activating the specific intracellular biocatalytic reactions. As an intelligent and nonviolent self-driven drug delivery platform, the present DNAzyme NS system could be engineered with more therapeutic sequences and agents and was anticipated to show exceptional promise and versatility for applications in biomedicine and bioengineering.

Self-Assembly of Functional Nucleic Acid-Based Colorimetric Competition Assay for the Detection of Immunoglobulin E

In this work, we have developed a simple and rapid colorimetric assay for the detection of immunoglobulin E (IgE) using functional nucleic acids (FNAs) and a solid-phase competition enzyme-linked immunosorbent assay (ELISA). The FNAs including aptamer of recombinant IgE, G-quadruplex and its complementary fragments were immobilized on 96-well microplates to achieve recognition and detection of IgE in biological samples. The G-quadruplex DNAzyme catalyzed 2,2'-Azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS)-hemin-H2O2 system was used to improve the sensitivity of colorimetric assay. In the presence of IgE, the hairpin structure and G-quadruplex would be destroyed, resulting in the inactivation of DNAzyme and subsequent reduction of its absorbance. This cost-effective approach detected IgE in the linear range from 5.0 pg/mL to 500 ng/mL, with the limit of detection (LOD) of 2.0 pg/mL, under optimal conditions. Moreover, the developed method was successfully applied to the rapid detection of IgE in human urine, indicating a great potentiality of this approach in clinical diagnosis and other biomedical applications.

A Universal Paper-Based Electrochemical Sensor for Zero-Background Assay of Diverse Biomarkers

This paper describes a universal paper-based electrochemical sensing platform that uses a paper modified with signal molecule-labeled DNA and a screen-printed electrode along with target recognition solutions to achieve the detection of multiple types of biomarkers. These assays rely on the target-induced synthesis of Mg²⁺-dependent DNAzyme for catalyzing the cleavage of substrate DNA from paper, which have been demonstrated by using microRNA recognition probe for miR-21, a phosphorylated hairpin probe for alkaline phosphatase, and a DNA aptamer for carcinoembryonic antigen assays, respectively. Taking advantages of the high specific target-triggered polymerization/nicking and DNAzyme-catalyzed signal amplification, the present assays enable highly sensitive and selective detection of these targets with zero-background. These assays can also be applied to detect target in spiked serum samples, demonstrating the potential for point-of-care detection of clinical samples.

A quencher-free DNAzyme beacon for fluorescently sensing uranyl ions via embedding 2-aminopurine

DNAzyme-based fluorescent probes have provided valuable protocols for detecting uranium, one of the most common radioactive contaminants in the environment, with ultra-high selectivity and sensitivity. Designing novel DNAzyme beacons to update the mode of fluorescence reporting and/or quenching will continuously enhance "turn-on" sensing performance as well as promote actual application of the biological probes. In this work, we developed a novel quencher-free DNAzyme beacon by embedding fluorescent 2-aminopurine for rapid detection of uranyl ion. 2-aminopurine is able to substitute adenine and keep strong fluorescence in single-stranded DNA whereas being quenched in the hybridized double-stranded DNA by the base-stacking interaction. The combination of such trait of 2-aminopurine and cleavage reaction of DNAzyme in the presence of target co-factors possesses two main advantages for ion sensing: simplicity for avoidance of extra quencher groups and high performance because of superiority of DNAzyme essence. The experimental conditions including embedding site, pH and salt concentration of buffer solutions, and the amount ratio of enzyme strand to substrate strand used to form DNAzymes were systematically optimized to inspire the highest performance of the biological beacon. Thus, a detection limit of 9.6 nM, a wide linear range from 5 nM to 400 nM (R² = 0.997), and selectivity of more than 400 000-fold over other metal ions were achieved by the novel DNAzyme probes. The highly sensitive, selective and quencher-free DNAzyme probes accommodated a simple and cost-efficient alternative to current fluorescent counterparts, holding a great potential for further application in practical ion assay.

A dynamic, ultra-sensitive and "turn-on" strategy for fluorescent detection of uranyl based on DNAzyme and entropy-driven amplification initiated circular cleavage amplification

A uranyl detection strategy with ultra-sensitivity was developed based on entropy-driven amplification and DNAzyme circular cleavage amplification. The cleavage of UO₂²⁺-specific DNAzyme produces a DNA fragment to initiate the entropy-driven amplification. Two DNA sequences released from the entropy-driven amplification are partly complementary. They can form an entire enzyme strand (E-DNA) of Mg²⁺-specific DNAzyme. The formed E-DNA can circularly cleave FAM-labeled probes on gold nanoparticles (AuNPs), causing the leaving of FAM from AuNPs and recovery of fluorescent signal. A linear relationship was obtained in the range from 30 pM to 5 nM between fluorescence intensity and concentration of UO₂²⁺. The limit of detection was low to 13 pM. This method showed a promising future for practical application in real water samples.

G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing

G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.

Visual Detection of Cucumber Green Mottle Mosaic Virus Based on Terminal Deoxynucleotidyl Transferase Coupled with DNAzymes Amplification

A simple, rapid, and sensitive visual detection method for observing cucumber green mottle mosaic virus was reported based on the template-independent polymerization activity of terminal deoxynucleotidyl transferase (TdT), coupled with the cascade amplification of Mg²⁺-dependent DNAzyme and hemin/G-quadruplex DNAzyme. Briefly, the hybridized dsDNA of T1/P1 was cut into two parts at its position of 5′-AA↓CG↑TT-3′ by the restricted enzyme AcII. The longer, newborn fragment originating from P1 was tailed at its 3’-end by oligo dG, and an intact enzymatic sequence of Mg²⁺-dependent DNAzyme was generated. The substrate sequence in the loop segment of the hairpin probe (HP) hybridized with the newborn enzymatic sequence and was cleaved into two parts in the presence of Mg²⁺. The locked G-quadruplex sequence in the stem segment of the HP was released, which catalyzed the oxidation of ABTS^2- in the presence of H₂O₂, and the resulting solution turned green. A correlation between the absorbance and concentration of T1 was obtained in a range from 0.1 pM to 2 nM, with a detection limit of 0.1 pM. In addition to promoting a lower detection limit and shorter monitoring time, this method also demonstrated an excellent selectivity to single or double nucleotide changes. Therefore, the designed strategy provided a rapid and efficient platform for viral inspection and plant protection.

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.

Colorimetric Aptasensor Based on Truncated Aptamer and Trivalent DNAzyme for Vibrio parahemolyticus Determination

In this work, after optimizing the original aptamer sequence by truncation and site-directed mutagenesis, a simple and sensitive colorimetric aptasensor was established for detecting the widespread food-borne pathogen Vibrio parahemolyticus ( V. parahemolyticus). The detection strategy was based on the competition for an V. parahemolyticus specific aptamer between its complementary DNA (cDNA) and V. parahemolyticus. The aptamer-conjugated magnetic nanoparticles (MNPs) were used as capture probes, and the G-quadruplex (G4) DNAzyme was employed as the signal amplifying element. Under optimal conditions, a wide linear detection range (from 10² to 10⁷ cfu/mL) was available, and the detection limit could be as low as 10 cfu/mL. This method was also used to detect V. parahemolyticus in contaminated salmon samples, and the results showed good consistency with those obtained from standard plate counting method. Therefore, this novel aptasensor could be a good candidate for sensitive and selective detection of V. parahemolyticus without complicated operations.

Electrochemical analysis of 8-hydroxy-2'-deoxyguanosine with enhanced sensitivity based on exonuclease-mediated functional nucleic acid

In this work, an electrochemical method for sensitive analysis of 8-hydroxy-2'-deoxyguanosine, a key biomarker that is widely used to study oxidative injury-related diseases, is proposed based on exonuclease-mediated functional nucleic acid. In the design, exonuclease can not only distinguish the existence of target, but also suppress the background noise, thus the sensitivity can be enhanced. Moreover, DNAzyme designed in the functional nucleic acid can further improve the sensitivity of the analysis during signal generation process. Therefore, exonuclease-mediated functional nucleic acid may ensure high sensitivity of the assay. Further studies reveal that the detection of 8-hydroxy-2'-deoxyguanosine can be achieved with a linearity from 0.01 nM to 7.0 μM and a detection limit of 6.82 pM. The new method has also been successfully applied to the determination of 8-OHdG in urine with good results, indicating its great potential for practical use.