A Dual-Enzyme-Assisted Three-Dimensional DNA Walking Machine Using T4 Polynucleotide Kinase as Activators and Application in Polynucleotide Kinase Assays

Enzyme-Programmed Self-Assembly of Nanoparticles

Nanoparticles are a hot topic in the field of nanomaterial research due to their excellent physical and chemical properties. In recent years, DNA-directed nanoparticle self-assembly technology has been widely applied to the development of numerous complex nanoparticle superstructures. Due to the inherent stability and surface electric repulsion of nanoparticles, it is difficult to make nanoparticle superstructures respond to molecular signals in the external environment. In fact, enzyme-programmed molecular systems are developed to allow diverse functions, including logical operations, signal amplification, and dynamic assembly control. Therefore, combining enzyme-controlled DNA systems may endow nanoparticle assembly systems with more flexibility in program design, allowing them to respond to a variety of external signals. In this review, we summarize the basic principles of enzyme-controlled DNA/nanoparticle self-assembly and introduce its applications in heavy metal detection, gene expression, proteins inside living cells, cancer cell therapy, and drug delivery. With the continuous development of new nanoparticle materials and the increasing functionality of enzyme DNA circuits, enzyme-directed DNA/nanoparticle self-assembled probe technology is expected to see significant future development.

RNA-Cleaving DNAzyme-Based Amplification Strategies for Biosensing and Therapy

Since their first discovery in 1994, DNAzymes have been extensively applied in biosensing and therapy that act as recognition elements and signal generators with the outstanding properties of good stability, simple synthesis, and high sensitivity. One subset, RNA-cleaving DNAzymes, is widely employed for diverse applications, including as reporters capable of transmitting detectable signals. In this review, the recent advances of RNA-cleaving DNAzyme-based amplification strategies in scaled-up biosensing are focused, the application in diagnosis and disease treatment are also discussed. Two major types of RNA-cleaving DNAzyme-based amplification strategies are highlighted, namely direct response amplification strategies and combinational response amplification strategies. The direct response amplification strategies refer to those based on novel designed single-stranded DNAzyme, and the combinational response amplification strategies mainly include two-part assembled DNAzyme, cascade reactions, CHA/HCR/RCA, DNA walker, CRISPR-Cas12a and aptamer. Finally, the current status of DNAzymes, the challenges, and the prospects of DNAzyme-based biosensors are presented.

Construction and Application of DNAzyme-based Nanodevices

The development of stimuli-responsive nanodevices with high efficiency and specificity is very important in biosensing, drug delivery, and so on. DNAzymes are a class of DNA molecules with the specific catalytic activity. Owing to their unique catalytic activity and easy design and synthesis, the construction and application of DNAzymes-based nanodevices have attracted much attention in recent years. In this review, the classification and properties of DNAzyme are first introduced. The construction of several common kinds of DNAzyme-based nanodevices, such as DNA motors, signal amplifiers, and logic gates, is then systematically summarized. We also introduce the application of DNAzyme-based nanodevices in sensing and therapeutic fields. In addition, current limitations and future directions are discussed.

CRISPR/Cas13a-assisted AMP generation for SARS-CoV-2 RNA detection using a personal glucose meter

Herein, we described a washing- and label-free clustered regularly interspaced short palindromic repeats (CRISPR)/LwaCas13a-based RNA detection method utilizing a personal glucose meter (PGM), which relies on the trans-cleavage activity of CRISPR/Cas13a and kinase reactions. In principle, the presence of target RNA activates the trans-cleavage of CRISPR/Cas13a, generating 2',3'-cyclic phosphate adenosine, which is converted to adenosine monophosphate (AMP) by the T4 polynucleotide kinase. Subsequently, the AMP is converted to adenosine diphosphate (ADP) through phosphorylation by a myokinase; ADP is then used as a substrate in the cascade enzymatic reaction promoted by pyruvate kinase and hexokinase. The overall reaction leads to the continuous conversion of glucose to glucose-6-phosphate, resulting in a reduction of glucose concentration proportional to the level of target RNA, which can therefore be indirectly measured with a PGM. By employing this novel strategy, severe acute respiratory syndrome coronavirus-2 RNA can be successfully detected with excellent specificity. In addition, we were able to overcome non-specific responses of CRISPR/Cas13a and distinguish single nucleotide polymorphisms by introducing a single-base mismatch in the complementary RNA. Our study provides an alternative coronavirus disease 2019 detection technology that is affordable, accessible, and portable with a fast turnaround time and excellent selectivity.

Electrochemiluminescence resonance energy transfer biosensing platform between g-C3N4 nanosheet and Ru-SiO2@FA for dual-wavelength ratiometric detection of SARS-CoV-2 RdRp gene

Rational detection of syndrome coronavirus 2 (SARS-CoV-2) is crucial to prevention, control, and treatment of disease. Herein, a dual-wavelength ratiometric electrochemiluminescence (ECL) biosensor based on resonance energy transfer (RET) between g-C₃N₄ nanosheets and Ru-SiO₂@folic acid (FA) nanomaterials was designed to realize ultrasensitive detection of SARS-CoV-2 virus (RdRp gene). Firstly, the unique g-C₃N₄ nanosheets displayed very intense and stable ECL at 460 nm, then the triple helix DNA was stably and vertically bound to g-C₃N₄ on electrode by high binding affinity between ssDNA and g-C₃N₄. Meanwhile, trace amounts of target genes were converted to a large number of output by three-dimensional (3D) DNA walker multiple amplification, and the output bridged a multifunctional probe Ru-SiO₂@FA to electrode. Ru-SiO₂@FA not only showed high ECL at 620 nm, but also effectively quenched g-C₃N₄ ECL. As a result, ECL decreased at 460 nm and increased at 620 nm, which was used to design a rational ECL biosensor for detection of SARS gene. The results show that the biosensor has excellent detection sensitivity for RdRp gene with a dynamic detection range of 1 fM to 10 nM and a limit of detection (LOD) of 0.18 fM. The dual-wavelength ratio ECL biosensor has inestimable value and application prospects in the fields of biosensing and clinical diagnosis.

Split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive detection of 17β-estradiol

DNA walker machines, as one of the dynamic DNA nanodevices, have attracted extensive interest in the field of analysis due to their inherent superiority. Herein, we reported a split aptamer remodeling-initiated target-self-service 3D-DNA walker for ultrasensitive, specific, and high-signal-background ratio determination of 17β-estradiol (E2) in food samples. Two split probes (STWS-a and STWS-b) were rationally designed that can undergo structural reassembled to serve as walking strands (STWS) under the induction of the target. Meanwhile, an intact E6-DNAzyme region was formed and activated at the tail of STWS. The activated E6-DNAzyme then continuously drives the 3D-DNA walker for signal amplification and specific detection of E2. Under optimal conditions, the proposed DNA walker-based biosensor exhibited excellent linearity in the range of 1 pM to 50 nM with a low limit of detection (LOD) of 0.28 pM, and good precision (2.7%) for 11 replicate determinations of 1 nM of E2. Furthermore, the developed DNA walker-based biosensor achieved excellent sensitive analysis of E2 in the complex food matrix with recoveries of 95.6-106.5%. This newly proposed split aptamer-based strategy has the advantages of ultrasensitive, high signal-to-background ratio, and high stability. Noteworthy, the successful operation of the DNA walker initiated by the split aptamer expands the principles of DNA walker design and provides a universal signal amplification platform for trace analysis.

Sensitive Autocatalytic Hybridization Circuit for Reliable In Situ Intracellular Polynucleotide Kinase Imaging

Exploring the characteristic functions of polynucleotide kinase (PNK) could substantially promote the elucidation of PNK-related mechanistic pathways. Yet, the sensitive and reliable detection of intracellular PNK still presents a challenging goal. Herein, we propose a simple autocatalytic hybridization circuit (AHC) for in situ intracellular imaging of PNK with high reliability. The AHC amplifier consists of two mutually activated hybridization chain reaction (HCR) modules for magnified signal transduction. The PNK is transduced into initiator I by phosphorylation and cleavage of mediator H_p. Initiator I activates the initial HCR-1 module, leading to the formation of long dsDNA nanowires that carry numerous initiator T. Then, T-initiated feedback HCR-2 module generates branched products that contain plentiful initiator I, thus realizing an autocatalytic HCR amplification reaction. Simultaneously, the HCR-2 module is also assembled as a versatile signal transduction unit for generating the amplified readout. Based on the mutually sustained accumulation of two initiators for the reciprocal activation of two reaction modules, continuous signal amplification and assembly of high-molecular-weight copolymers endow the AHC system with high sensitivity and robustness for the PNK assay. Moreover, the PNK-sensing AHC system achieves reliable imaging of intracellular PNK, thus showing great potential to decipher the correlation between PNK and related diseases.

An Autocatalytic DNA Circuit Based on Hybridization Chain Assembly for Intracellular Imaging of Polynucleotide Kinase

Polynucleotide kinase (PNK) plays an essential role in various cellular events by regulating phosphorylation processes, and abnormal homeostasis of PNK could cause many human diseases. Herein, we proposed an autocatalytic hybridization system (AHS) through the elaborate integration of hybridization chain assembly (HCA) and catalytic DNA assembly (CDA) that enables a highly efficient positive feedback amplification. The PNK-targeting AHS biosensor is composed of three modules: a recognition module, an HCA amplification module, and a CDA autocatalytic module. In the presence of PNK, the recognition module could transform the PNK input into an exposed nucleic acid initiator (I). Then the initiator strand I could trigger the autonomous HCA process in the amplification module, and the resulted HCA products could reassemble the split CDA trigger strand T, subsequently inducing the CDA process in the autocatalytic module to form abundant DNA duplex products. Consequently, the embedded initiator strand I was liberated from the CDA duplex product to autonomously trigger the new rounds of HCA circuit. The rational integration and cooperative cross-activation between the HCA and CDA module could prominently accelerate the reaction and realize the exponential amplification efficiency by initiator regeneration. As a result, the self-sustainable AHS amplifier could implement the sensitive detection of PNK in vitro and in biological samples and further fulfill accurate monitoring of the intracellular PNK activity and the effective screening of PNK inhibitors. This work paves a way for exploiting highly efficient artificial DNA circuits to analyze low-abundance biomarkers, holding great potential in biochemical research and clinical diagnosis.

Ultra-specific fluorescence detection of DNA modifying enzymes by dissipation system

Abnormal expression of DNA modifying enzymes (DMEs) is linked to a variety of diseases including cancers. It is desirable to develop accurate methods for DME detection. However, the substrate-based probe for target DMEs is disturbed by various non-target DMEs that have similar activity resulting in a loss of specificity. Here we utilized dissipative DNA networks to develop an ultra-specific fluorescence assay for DME, absolutely distinguishing between target and non-target enzymes. Unlike the conventional sensors in which the discrimination of target and non-target relies on signal intensity, in our system, target DMEs exhibit featured fluorescence oscillatory signals, while non-target DMEs show irreversible 'one-way' fluorescence increase. These dissipation-enabled probes (DEPs) exhibit excellent generality for various types of DMEs including DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1), polynucleotide kinase (T4 PNK), and methyltransferase (Dam). DEPs provide a novel quantification mode based on area under curve which is more robust than those intensity-based quantifications. The detection limits of APE1, T4 PNK, and Dam reach 0.025 U/mL, 0.44 U/mL, and 0.113 U/mL, respectively. DEPs can accurately identify their corresponding DMEs with excellent specificity in cell extracts. Fluorescence sensors based on DEPs herein represent a conceptually new class of methods for enzyme detection, which can be easily adapted to other sensing platforms such as electrochemical sensors.

Through the Eyes of Creators: Observing Artificial Molecular Motors

Inspired by molecular motors in biology, there has been significant progress in building artificial molecular motors, using a number of quite distinct approaches. As the constructs become more sophisticated, there is also an increasing need to directly observe the motion of artificial motors at the nanoscale and to characterize their performance. Here, we review the most used methods that tackle those tasks. We aim to help experimentalists with an overview of the available tools used for different types of synthetic motors and to choose the method most suited for the size of a motor and the desired measurements, such as the generated force or distances in the moving system. Furthermore, for many envisioned applications of synthetic motors, it will be a requirement to guide and control directed motions. We therefore also provide a perspective on how motors can be observed on structures that allow for directional guidance, such as nanowires and microchannels. Thus, this Review facilitates the future research on synthetic molecular motors, where observations at a single-motor level and a detailed characterization of motion will promote applications.

Types and Applications of Nicking Enzyme-Combined Isothermal Amplification

Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.

Primer-template conversion-based cascade signal amplification strategy for sensitive and accurate detection of polynucleotide kinase activity

Here, a primer-template conversion-based cascade signal amplification strategy is described for the sensitive detection of polynucleotide kinase (PNK) activity. This strategy integrated rolling circle amplification (RCA) and multiple-repeated-strand displacement amplification (MRSDA) with G-quadruplex based fluorescence lighting-up assay. A delicate dumbbell-shaped DNA probe with 5'-hydroxyl terminus was designed, in which G-quadruplex and half recognition site of nicking enzyme Nb.BbvCI were encoded in two loops respectively. Under the action of PNK, the 5' terminus on dumbbell probe was firstly phosphorylated, and then the dumbbell was cyclized with the catalyzation of T4 ligase to become the RCA template. The RCA process produced multiple copies of the prolonged primer. After that, under the assistance of nicking enzyme Nb.BbvCI, a primer-template conversion occurred, which converted the primer and template of RCA into the template and primer of the subsequent MRSDA, respectively. The MRSDA generated multiple repeated ssDNA sequences which possessed G-quadruplexes for outputting signal by lighting-up fluorescence of thioflavin T (ThT). The cascade signal amplification of RCA and MRSDA provided high detection sensitivity, and the target-dependence of template in cascade signal amplification led to a low background. The method showed excellent detection limit of 0.2 × 10^-6 U μL^-1 in buffer and 5 cells in cell lysate sample. Moreover, this method displayed favorable selectivity when interfering proteins were present. The developed strategy has good practical potential for PNK activity detection in clinical diagnosis and medical research.

Microchamber-Free Digital Flow Cytometric Analysis of T4 Polynucleotide Kinase Phosphatase Based on Single-Enzyme-to-Single-Bead Space-Confined Reaction

Digital bioassays have attracted extensive attention in biomedical applications due to their ultrahigh sensitivity. However, traditional digital bioassays require numerous microchambers such as droplets or microwells, which restricts their application scope. Herein, we propose a microchamber-free flow cytometric method for the digital quantification of T4 polynucleotide kinase phosphatase (T4 PNKP) based on an unprecedented phenomenon that each T4 PNKP molecule-catalyzed reaction can be spatially self-confined on a single microbead, which ultimately enables the one-target-to-one-fluorescence-positive microbead digital signal transduction. The digital signal-readout mode can clearly detect T4 PNKP concentrations as low as 1.28 × 10^-10 U/μL, making it most sensitive method to date. Significantly, T4 PNKP can be specifically distinguished from other phosphatases and nucleases in complex samples by digitally counting the fluorescence-positive microbeads, which cannot be realized by traditional bulk measurement-based methods. Taking advantage of the novel space-confined enzymatic feature of T4 PNKP, this digital mechanism can use T4 PNKP as the enzyme label to fabricate digital sensing systems toward various biomolecules such as digital enzyme-linked immunosorbent assay (ELISA). Therefore, this work not only enlarges the toolbox for high-sensitivity biomolecule detection but also opens new gates to fabricate next-generation digital assays.

A DNAzyme-driven random biped DNA walking nanomachine for sensitive detection of uracil-DNA glycosylase activity

Highly specific and ultrasensitive detection of uracil-DNA glycosylase (UDG) activity is of great significance for maintaining genomic integrity and medical research of related diseases. Here, we constructed a random DNA walking nanomachine based on a DNAzyme for UDG activity detection on the AuNP (Au nanoparticle) surface. When UDG is present, the U bases in the Y structure are removed, resulting in AP sites, which will be cleaved by Endo-IV to generate a 3' concave end for Exo-III, causing the locking strand of the DNAzyme to be completely hydrolyzed by the Exo-III and release the walking strand to randomly pair with the substrate strand on the AuNP surface; then, the walking strand exerts its cleavage activity with the assistance of Mg2+ to cleave the substrate strand and keep the fluorophore 6-carboxyfluorescein (FAM) away from the surface of the AuNP, which restores the fluorescence signal of this system. In this way, sensitive detection of UDG can be realized, and the detection limit is as low as 3.69 × 10-6 U mL-1. In addition, we found that this method is highly specific to UDG and can be used to detect UDG specifically in complex samples, which has certain application prospects in biomedical research and clinical diagnosis related to UDG.

Hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a for lipopolysaccharide analysis

In this work, hydrazone ligation assisted DNAzyme walking nanomachine is explored to couple with CRISPR-Cas12a trans-cleavage. Hydrazone ligation with high efficiency can mediate signal input which can be induced by target binding, thereby regulating the performance of DNAzyme walking nanomachine. The product strand from DNAzyme walking nanomachine can further activate the trans-cleavage of Cas12a. So, cascade signal amplification can be achieved to enhance the sensitivity for target detection. Subsequently, hydrazone ligation assisted DNAzyme walking nanomachine coupled with CRISPR-Cas12a has been further developed as a biosensor to analyze lipopolysaccharides. The developed biosensor exhibits a linear range from 0.05 ng/mL to 10⁶ ng/mL and a lowest limit of detection of 7.31 fg/mL. This research provides a new mode for the signal output of DNAzyme walking nanomachine, so as to sensitively analyze different biomolecules.

DNAzyme Walker for Homogeneous Detection of Enterovirus EV71 and CVB3

When dealing with infectious pathogens, the risk of contamination or infection in the process of detecting them is nonnegligible. Separation-free detection will be beneficial in operation and safety. In this work, we proposed a DNAzyme walker for homogeneous and isothermal detection of enterovirus. The DNAzyme is divided into two inactivate subunits. When the subunit-conjugated antibody binds to the target virus, the activity of the DNAzyme recovers as a result of spatial proximity. The walker propels, and the fluorescence recovers. The final fluorescence intensity of the reaction mixture is related to the concentration of the target virus. The detection limit of this proposed method is 6.6 × 10⁴ copies/mL for EV71 and 4.3 × 10⁴ copies/mL for CVB3, respectively. Besides, this method was applied in detection of EV71 in clinical samples with a satisfactory result. The entire experiment is easy to operate, and the proposed method has great potential for practical use.

A "turn-on" and proximity ligation assay dependent DNA tweezer for one-step amplified fluorescent detection of DNA

A "turn-on" and proximity ligation assay dependent DNA tweezer was proposed for one-step amplified fluorescent detection of DNA. Target DNA can anneal with capture probe to form an entire long sequence. The formed long sequence can circularly open the hairpin, resulting the "turn-on" of DNA tweezers. A good linear relationship was shown from 40 pM to 20 nM with limit of detection of 10 pM. In addition, it has been successfully utilized to analysis DNA in human serum, representing a great and practical application future.

Three-dimensional bipedal DNA walker enabled logic gates responding to telomerase and miRNA

In this work, we have developed a simple and reliable platform for simultaneous analysis of telomerase and miRNA. A three-dimensional bipedal DNA walking strategy is designed utilizing gold nanoparticles and MnO2 nanosheets. Given the merits of fast, sensitive and selective analysis, the developed method has great potential application in early clinical diagnosis.

Chemoselective ligation assisted DNA walker for analysis of double targets

Chemoselective ligation assisted DNA walker with input and output of double signals, has been constructed through simultaneous assistance of oxime chemistry and alkyne-azide cycloaddition. The constructed DNA walker has been further developed as a biosensor with lipopolysaccharide (LPS) and 5-hydroxymethyl-2-furaldehyde (HMF) as targets. The biosensor owns one-to-one mapping functionality and can sensitively distinguish all cases of two targets through the unique output signal feature. Moreover, the biosensor can simultaneously analyze LPS and HMF. This work provides a new insight for analysis of double targets based on chemoselective ligation assisted DNA walker.

An enzyme-powered, three-dimensional lame DNA walker

Molecular machines constructed by three-dimensional (3-D) DNA walker have emerged as a hot topic in applications such as novel biosensors, cargo delivery platforms and intracellular imaging. Herein, we first propose a lame DNA walker that can randomly and autonomously move on microsphere-based 3-D track. The stochastic lame walker has a long leg mainly responsible for persistent movement and a short leg cutting substrates rapidly. Its motion is propelled by a nicking endonuclease cleavage of hybridized DNA tracks. Kinetic and persistent study show that the lame DNA walker enables reaction equilibrium at 30 min, need a cleat domain of at least 14 nucleotides and can persistently move on 3-D tracks with an average rate of 6.467 × 10^-11 M s^-1. We also demonstrate that the lame walker can be used to detect target DNA in the detection range of 10 pM-5 nM with high specificity by toehold exchange mechanism. This work will further expand the performance of 3-D DNA walkers and substantially contributes to the improved understanding of DNA walking systems.

Paper-Based Bipolar Electrode Electrochemiluminescence Platform for Detection of Multiple miRNAs

This paper introduces a novel potential-resolved paper-based biosensor for simultaneous detection of multiple microRNAs (miRNAs) (taking miRNA-155 and miRNA-126 as examples) based on the bipolar electrode (BPE) electrochemiluminescence (ECL) strategy. The proposed multiple-channel paper-based sensing microfluidic platform was prepared by wax-printing technology, screen-printing method, and in situ Au nanoparticles (AuNPs) growth to form hydrophilic areas, hydrophobic boundaries, waterproof electronic bridge, driving electrode regions, and parallel bipolar electrode regions. CdTe quantum dots (QDs)-H2 and Au@g-C₃N₄ nanosheets (NSs)-DNA1 were used as dual electrochemiluminescence signal probes, and carboxylated Fe₃O₄ magnetic nanoparticles existed as carriers. CdTe QDs-H2/S₂O₈^2- and Au@g-C₃N₄ NSs-DNA1/S₂O₈^2- could exhibit two strong and stable ECL emissions at a drive voltage of 9 and 12 V, respectively, which can be used as effective potential-resolved signal tags. In addition, the proposed three-dimensional (3D) DNA nanomachine model and the target miRNA cycle strategy were used to achieve double amplification of electrochemiluminescence intensity. More importantly, the combination of the bipolar electrode system and the potential-resolved multitarget electrochemiluminescence method can greatly reduce the spatial interference between substances. The prepared ECL biosensor showed a favorable linear response for the detection of miRNA-155 and miRNA-126 with relatively low detection limits of 5.7 and 4.2 fM, respectively. With excellent sensitivity, the strategy may provide an efficient method for clinical application, especially in detection of trace multiple targets.

Electrochemical DNA Sensors Based on MoS2-AuNPs for Polynucleotide Kinase Activity and Inhibition Assay

The determination of T4 polynucleotide kinase (PNK) activity and the screening of PNK inhibitors are critical to disease diagnosis and drug discovery. Numerous electrochemical strategies have been developed for the sensitive measurement of PNK activity and inhibition. However, they often suffer from additional labels and multiple steps of the detection process for the electrochemical readout. Herein, we have demonstrated an electrochemical DNA (E-DNA) sensor for the one-step detection of PNK with "signal-on" readout with no need for additional labels. In our design, the highly switchable double-stranded DNA (dsDNA) probes are immobilized on the gold nanoparticle-decorated molybdenum disulfide nanomaterial (MoS₂-AuNPs), which possesses large surface area and high conductivity for elevating the signal gain in the PNK detection. This signal-on E-DNA sensor integrated with MoS₂-AuNPs exhibits a much higher sensitivity than that without MoS₂-AuNPs, showing a detection limit of 2.18 × 10^-4 U/mL. Furthermore, this assay shows high selectivity, with the ability to discriminate PNK from other enzymes and proteins, and can be utilized to screen inhibitors. The proposed sensor is easy to operate with one-step readout and robust for PNK detection in the biological matrix and shows great potential for point-of-care in clinical diagnostics and drug screening.

Three-Dimensional DNA Nanomachine Combined with Toehold-Mediated Strand Displacement Reaction for Sensitive Electrochemical Detection of MiRNA

MicroRNA (miRNA) serves as an ideal biomarker for diagnosis, prognosis, and therapy of various human cancers. The rationally designed three-dimensional (3D) DNA nanomachine was constructed on the matrixes of magnetic beads, and the high density of gold nanoparticles (AuNPs) on each magnetic bead and further enlargement of the AuNPs lead to the anchoring of numerous DNA walkers and signal probes on the AuNPs. With the combination of toehold-mediated strand displacement reaction (SDR), amplified electrochemical detection of miRNA is performed. The existence of miRNA triggers the toehold-mediated SDR and the released DNA walker probe is hybridized with the ferrocene (Fc)-tagged signal probe. The cleavage of the duplex by the nicking endonuclease detaches the signal probe from the magnetic nanocomposites. The oxidation current of Fc moieties was found to be inversely proportional to the concentrations of miRNA-182 between 1.0 fM and 2 pM. The assay is highly selective for discrimination of miRNAs with similar sequences. The feasibility of the method for sensitive detection of the expression levels of miRNA-182 from serum samples of glioma patients at different stages was demonstrated. The sensing protocol holds great promise for early diagnosis and prognosis of the cancer cases with abnormal miRNA expression.

Novel Luminescent Nanostructured Coordination Polymer: Facile Fabrication and Application in Electrochemiluminescence Biosensor for microRNA-141 Detection

A series of novel luminescent nanostructured coordination polymers (Ce-Ru-NCPs) with tunable morphologies have been successfully synthesized on a large scale at room temperature by a facile and rapid solution-phase method using Ce³⁺ and tris(4,4'-dicarboxylicacid-2,2'-bipyridyl) ruthenium(II) dichloride (Ru(dcbpy)₃²⁺). Among them, the flowerlike Ce-Ru-NCP shows good cathodic electrochemiluminescence (ECL) characteristics. The ECL efficiency of the Ce-Ru-NCP/S₂O₈^2- system is about 2.34 times that of the classic tris(2,2'-bipyridyl) ruthenium(II) dichloride/S₂O₈^2- (Ru(bpy)₃²⁺/S₂O₈^2-) system. Hence, we report a sensitive ECL biosensor for microRNA-141 (miRNA-141) detection based on the flowerlike Ce-Ru-NCP as a cathodic ECL luminophore and a bipedal three-dimensional (3D) DNA walking machine as a signal amplifier. Through the bipedal 3D DNA walking machine, trace targets can be converted to substantial secondary targets (marked with the quencher dopamine), and a significant quenching effect on the ECL signal is achieved. As a result, the proposed biosensor exhibits a relatively good sensitivity for miRNA-141 detection and shows a dynamic range from 1.0 × 10^-16 to 1.0 × 10^-6 mol·L^-1 with a limit of detection (LOD) of 33 amol·L^-1 (S/N = 3). The Ce-Ru-NCP with tunable morphologies and high ECL efficiency, intensity, and stability possesses potential applications in ECL analysis.

An interparticle relatively motional DNA walker and its sensing application

DNA molecular machines are DNA self-assemblies that perform quasi-mechanical movement at the micro-nano scale, and have attracted increasing attention in the fields of biosensing, drug delivery and biocomputing. Herein, we report the concept and operation of an interparticle relatively motional DNA walker. The walker is composed of walking particles (WPs) and track particles (TPs). The WPs and TPs are obtained by respective functionalization of locked walking strands containing DNAzyme sequences and fluorophore-labelled track strands containing substrate sequences onto gold nanoparticles (AuNPs). Triggered by the target that specifically unlocks the walking strand, the liberated walking strands cooperatively hybridize with the track strands. The track strand gets cleaved by the DNAzyme, accompanied by the fluorophore release. The adjacent walking strand on the WP subsequently hybridizes to the next track strand, inducing the relative motion of the WP around the TP. After walking along the surface of one TP, the WP can continue to interact with another TP. As a result of the improved moving freedom and area, the interparticle motional mode induces high continuity and achieves large signal accumulation. Taking Zika virus RNA fragments (ZIKV-RNA) as a model target, the DNA walker shows a high sensitivity with a detection limit of 118 pM, and can reliably detect the target in biological fluids due to the stability of its components. The constructed DNA walker provides a new type of free and robust motion mode between particles and holds potential in clinical diagnosis.

DNAzyme-Powered Three-Dimensional DNA Walker Nanoprobe for Detection Amyloid β-Peptide Oligomer in Living Cells and in Vivo

Amyloid β-peptide oligomer (AβO) is widely acknowledged as the promising biomarker for the diagnosis of Alzheimer's disease (AD). In this work, we designed a three-dimensional (3D) DNA walker nanoprobe for AβO detection and real-time imaging in living cells and in vivo. The presence of AβO triggered the DNAzyme walking strand to cleave the fluorophore (TAMRA)-labeled substrate strand modified on the gold nanoparticle (AuNP) surface and release TAMRA-labeled DNA fragment, resulting in the recovery of fluorescent signal. The entire process was autonomous and continuous, without external fuel strands or protease, and finally produced plenty of TAMRA fluorescence, achieving signal amplification effect. The nanoprobe enabled the quantitative detection of AβO in vitro, and the limit of detection was 22.3 pM. Given the good biocompatibility of 3D DNA walker nanoprobe, we extended this enzyme-free signal amplification method to real-time imaging of AβO. Under the microscope, nanoprobe accurately located and visualized the distribution of AβO in living cells. Moreover, in vivo imaging results showed that our nanoprobe could be used to effectively distinguish the AD mice from the wild-type mice. This nanoprobe with the advantages of great sensitivity, high specificity, and convenience, provides an outstanding prospect for AD's early diagnosis development.

A nanoplatform based on metal-organic frameworks and coupled exonuclease reaction for the fluorimetric determination of T4 polynucleotide kinase activity and inhibition

A nanoplatform based on metal-organic frameworks (MOFs) and lambda exonuclease (λ exo) for the fluorimetric determination of T4 polynucleotide kinase (T4 PNK) activity and inhibition is described. Fe-MIL-88 was selected as the nanomaterial because of its significant preferential binding ability to single-stranded DNA (ssDNA) over double-stranded DNA (dsDNA) and its quenching property. The synthesized Fe-MIL-88 was characterized by transmission electron microscope, scanning electron microscope, and X-ray photoelectron spectroscopy. In the presence of T4 PNK, FAM-labeled dsDNA (FAM-dsDNA) is phosphorylated on its 5'-terminal. λ exo then recognizes and cleaves the phosphorylated strand yielding FAM-labeled ssDNA (FAM-ssDNA). The fluorescence of the produced FAM-ssDNA is quenched due to Fe-MIL-88's absorbing on FAM-ssDNA. On the contrary, in the absence of T4 PNK, the phosphorylation and cleavage processes cannot take place. Therefore, the fluorescence of FAM-dsDNA still remains. The fluorescence intensity is detected at the maximum emission wavelength of 524 nm using the maximum excitation wavelength of 488 nm. The assay of T4 PNK based on the fluorescence quenching of FAM-ssDNA achieves a linear relationship in the range 0.01-5.0 U mL^-1 with a detection limit of 0.0089 U mL^-1 in buffer. The assay exhibits excellent performance for T4 PNK activity determination in a complex biological matrix. The results also reveal the ability of the assay for T4 PNK inhibitor screening. Graphical abstract Schematic presentation of a nanoplatform based on Fe-MIL-88 and coupled exonuclease reaction for the fluorimetric determination of T4 polynucleotide kinase activity. FAM-ssDNA, FAM-labeled single-stranded DNA; cDNA, complementary DNA; λ exo, lambda exonuclease;T4 PNK, T4 polynucleotide kinase.

Isothermal cross-boosting extension–nicking reaction mediated exponential signal amplification for ultrasensitive detection of polynucleotide kinase

A novel nucleic acid-based isothermal signal amplification strategy, named cross-boosting extension–nicking reaction (CBENR) is developed and successfully used for rapid and ultrasensitive detection of polynucleotide kinase (PNK) activity.

An enzyme-initiated DNAzyme motor for RNase H activity imaging in living cell

A signal amplification strategy based on an enzyme-initiated DNAzyme motor for sensitive imaging of RNase H activity in living cell.

Label-free fluorescence DNA walker for protein analysis based on terminal protection and dual enzyme assisted cleavage induced G-quadruplex/berberine conformation

Development of a simple, fast, cost-efficient and sensitive approach for accurate protein analysis is of high significance due to its potential application in disease diagnosis and biomedicine research.

Binding-Induced 3D-Bipedal DNA Walker for Cascade Signal Amplification Detection of Thrombin Combined with Catalytic Hairpin Assembly Strategy

As an important biomarker, thrombin (TB) is a major player in thrombosis and hemostasis and has attracted increasing attention involving its determination. Herein a universal and ultrasensitive fluorescence biosensor based on a binding-induced 3D-bipedal DNA walker and catalytic hairpin assembly (CHA) strategy has been proposed for cascade signal amplification detection of thrombin. In this study, we designed two proximity probes (foot 1 and foot 2) which include a specific affinity ligand for TB binding and a Pb²⁺-dependent DNAzyme tail sequence. In the presence of TB, the simultaneous binding of TB to foot 1 (F1) and foot 2 (F2) via TB aptamer (TBA) brings the tail sequences into close proximity and the melting temperature for tail sequences and track DNA is increased, allowing the Pb²⁺-dependent DNAzyme to cleave the track DNA into two short fragments which have lower affinities for the DNAzyme and, finally, leading to the release of trigger DNA (T-DNA) for subsequent CHA reaction. In the meantime, the dissociated DNA walkers (F1 and F2) explore adjacent unwound track DNA, and the walking procedure is conducted. Unlike the conventional unipedal DNA walkers that anchor foot DNA and track DNA on the same sensing surface, the proposed 3D-bipedal DNA walking machine can not only increase the local concentration of track DNA but can also improve the walking efficiency and expand the range of the walkers to some extent due to the two free feet. Moreover, with the advantages of superior sensitivity and excellent specificity, this biosensing platform exhibits a huge potential in practical application in biomedical research and clinical diagnosis.

Versatile Electrochemiluminescence and Photoelectrochemical Detection of Glutathione Using Mn2+ Substitute Target by DNA-Walker-Induced Allosteric Switch and Signal Amplification

Glutathione (GSH) serves vital functions in biological systems and associates with various human diseases. In this work, a versatile electrochemiluminence (ECL) and a photoelectrochemical (PEC) "signal on" biosensing platform were developed for a sensitive assay of GSH by a Mn²⁺-powered DNAzyme amplification strategy combined with DNA-walker-triggered allosteric conversion. First, MnO₂ nanosheets were reduced to Mn²⁺ by GSH; then, Mn²⁺ as a substitute target triggered DNAzyme-assisted cleavage-cycling amplification to generate numerous DNA output (s3). Meanwhile, the DNA molecular machine was introduced to bridge signal probes for versatile biosensing, which included hairpin DNA as a track and an arm as a walker. The presence of DNA output (s3) activated the swing arm to hybridize with hairpin DNA and then cut it by Nt.BbvCI, which initiated autonomous walking of the arm for forming a large number of streptavidin (SA) aptamers. Thus, a large number of CdS:Mn-SA tags as versatile signal probes was linked to the electrode by specific SA-aptamer binding, generating highly enhanced ECL and PEC signals for sensitive detection of the target. The present biosensing system take advantage of metal ion-based DNAzyme amplification, a DNA walker machine, multi-signals of QDs, and specificity of aptamers, which can provide a universal and efficient biosensing method for detecting various targets. The designed strategy demonstrated good performance for a GSH assay in human serum samples, showing more promising applications than other reported methods.

Highly ordered 3D electrochemical DNA biosensor based on dual orientation controlled rolling motor and graftable tetrahedron DNA

Herein, a robust and highly ordered three-dimensional electrochemical DNA (3D E-DNA) biosensor was proposed, and its orientation was controlled from top down by poly adenine oligonucleotides (polyA-ODNs)-mediated rolling motor (PRM) and graftable tetrahedron DNA (GTD). The GTD with a grafting domain was immobilized on the electrode surface to construct a well-organized sensing interface and controlled the orientation and distribution of the whole system at the "bottom" of this biosensor. The polyA-ODNs regulated the direction and density of the leg DNA attached on PRM at the "top" of the biosensor. The motion was achieved through the target induced cyclic cleaving, which triggered the motor rolling rather than walk. Impressively, the duplex strand DNA (dsDNA) formed after grafting, as a girder, provided a stable support to the soft long single strand (ssDNA), which facilitated the formation of the catalytic center, elevated the efficiency of the rolling cleavage. Under the optimal conditions, the designed biosensor exhibited a lower limit of 0.17 nM and wide linear range from 0.5 nM to 1.5 μM for adenosine rapid detection. Unique dual orientation regulated characteristics of the system increased the probability hybridization enormously and improved the motion efficiency significantly, which offered new avenue of DNA nanomachines development in biosensor platform.

Click DNA cycling in combination with gold nanoparticles loaded with quadruplex DNA motifs enable sensitive electrochemical quantitation of the tuberculosis-associated biomarker CFP-10 in sputum

An electrochemical aptamer-based assay is described for the determination of CFP-10 which is an early secretary biomarker of Mycobacterium tuberculosis. CFP-10 is specifically captured by its aptamer and then induces a DNA cross-linking click reaction, the release of CFP-10, and an amplification cycle of repeated CFP-10 release. This mechanism (with dual amplification via DNA click and target release cycle) causes more and more CFP-10 Apt strands on the electrode surface to expose their 5' overhang and to hybridize with the DNA complexes linked to the gold nanoparticles (AuNPs). Consequently, large amounts of AuNPs, each loaded with a number of quadruplex DNA motifs, can be bound on the electrode surface and remarkably enhance the signal. Under optimal conditions, the method has a detection limit as low as 10 pg.mL^-1 of CFP-10. The method was successfully applied to the diagnosis of M. tuberculosis in sputum. Graphical abstract Schematic representation of an electrochemical CFP-10 (10-kDa culture filtrate protein) assay using click DNA cycling in combination with gold nanoparticles loaded with quadruplex DNA motifs. Click chemistry reaction between Dibenzocyclooctyne (DBCO)-DNA and azido-DNA can liberate the CFP-10 antigen for the next cycle, which can be viewed as the first amplification step. G-quadruplex-based DNAzyme is formed due to the guanine-rich sequences of DNA S1, which can be viewed as the second amplification step.

Two-layer three-dimensional DNA walker with highly integrated entropy-driven and enzyme-powered reactions for HIV detection

Here, we propose a new two-layer three-dimensional (3-D) DNA walker sensor with highly integrated entropy-driven and enzyme-powered reactions for the first time. The 3-D DNA walker sensor is constructed by assembling densely carboxyfluorescein-labeled single strand oligonucleotides (inner-layer tracks) and nucleic acid complex S (outer-layer tracks) on a microparticle. In the presence of the target, outer and inner tracks are activated in turn, thereby releasing a great deal of the signal reporters for signal reading. As a result, our 3-D DNA walker sensor can realize the target detection in the range from 2 pM to 5 nM within one hour. Besides, the specific walker sensor can clearly distinguish even one-base mismatched target analogue. More importantly, our walker sensor can also test the target in human serum samples in the concentrations as low as 0.1 nM, which provides a bridge between real sample detection and clinical application. Certainly, this smart strategy could also be generalized to any target of interest by proper design.

A DNA functionalized porphyrinic metal-organic framework as a peroxidase mimicking catalyst for amperometric determination of the activity of T4 polynucleotide kinase

An electrochemical method is described for the sensitive detection of the activity of the enzyme T4 polynucleotide kinase (PNK) by using a DNA functionalized porphyrinic metal-organic framework (L/(Fe-P)n-MOF). In the presence of PNK, the hairpin oligonucleotide (HP1) becomes phosphorylated, and the trigger is released by lambda exonuclease (λ exo). The trigger DNA hybridizes with hairpin probe (immobilized on the gold electrode) to form a nicking endonuclease cleavage site. Thus, a single-strand capture probe is employed to hybridize with L/(Fe-P)n-MOF. The (Fe-P)n-MOF is a peroxidase mimicking material with high catalytic efficiency. By using this amplification strategy, an electrochemical signal is procured that allows for the determination of T4 PNK in the 1.0 mU·mL^-1 to 1.0 U·mL^-1 with a detection limit of 0.62 mU·mL^-1. The method is selective and can be used to screen for enzyme inhibitors. Conceivably, the (Fe-P)n-MOF can also be used to detect other analytes via its peroxidase-mimicking activity. Graphical abstract Schematic presentation of T4 polynucleotide kinase (PNK) detection. Two hairpin DNAs (HP) and a porphyrinic metal-organic framework with peroxidase-mimicking activity are used. The detection limit is 0.62 mU mL^-1 with enzyme assisted signal amplification. This method is selective and can be used to screen for enzyme inhibitors.

Versatile “on–off” biosensing of thrombin and miRNA based on Ag(i) ion-enhanced or Ag nanocluster-quenched electrochemiluminescence coupled with hybridization chain reaction amplification

A novel biosensing platform based on Ag(i) ion-enhanced or Ag nanoclusters (NCs)-quenched electrochemiluminescence (ECL) of CdSe quantum dots (QDs) was designed for versatile “on–off” assays of thrombin (TB) and miRNA.

A novel fluorescence method for activity assay and drug screening of T4 PNK by coupling rGO with ligase reaction

T4 polynucleotide kinase (PNK) is the primary member of the 5′-kinase family that can transfer the γ-phosphate residue of ATP to the 5′-hydroxyl group of oligonucleotides.

A DNA walker powered by endogenous enzymes for imaging uracil-DNA glycosylase activity in living cells

A DNA walker powered by endogenous enzymes detects uracil-DNA glycosylase activity in living cells.