Binding‐Induced DNA Nanomachines Triggered by Proteins and Nucleic Acids

Target-induced DNA nanomachine operation for the detection of proteins

Accurate and sensitive detection of disease-associated proteins in early stage of patients plays an important role in timely treatment and successfully extending patients' lives. To meet this demand, we herein rationally designed a flexible target-induced DNA nanomachine operation (TIDNMO) sensor for the detection of proteins. The TIDNMO system was composed of DNA nanoswitch and DNA walker. Triplex DNA nanoswitch was triggered by specific target, followed by the release of the walking strand, which initiated the DNA walker amplification as signal output. In addition, the Exo III could drive walking strand autonomously move on gold nanoparticle surface to realize 2 orders of magnitude signal amplification. What's more, this sensor could transform its suitable functional recognition element of DNA nanoswitch to recognize other specific molecule and realize different targets sensing based on identical walking tracks. Considering the facile reporter elements and efficient amplification performance, the present DNA nanomachine as a sensor could achieve a detection limit of 68 pM for anti-Dig antibody, 0.95 pM for mucin-1 respectively, along with a superb specificity. Furthermore, the method reported here opened a new chapter in disease-related protein sensing for the development of clinical early diagnosis.

Pt-Decorated Gold Nanoflares for High-Fidelity Phototheranostics: Reducing Side-Effects and Enhancing Cytotoxicity toward Target Cells

Functionalized with the Au-S bond, gold nanoflares have emerged as promising candidates for theranostics. However, the presence of intracellular abundantly biothiols compromises the conventional Au-S bond, leading to the unintended release of cargoes and associated side-effects on non-target cells. Additionally, the hypoxic microenvironment in diseased regions limits treatment efficacy, especially in photodynamic therapy. To address these challenges, high-fidelity photodynamic nanoflares constructed on Pt-coated gold nanoparticles (Au@Pt PDNF) were communicated to avoid false-positive therapeutic signals and side-effects caused by biothiol perturbation. Compared with conventional photodynamic gold nanoflares (AuNP PDNF), the Au@Pt PDNF were selectively activated by cancer biomarkers and exhibited high-fidelity phototheranostics while reducing side-effects. Furthermore, the ultrathin Pt-shell catalysis was confirmed to generate oxygen which alleviated hypoxia-related photodynamic resistance and enhanced the antitumor effect. This design might open a new venue to advance theranostics performance and is adaptable to other theranostic nanomaterials by simply adding a Pt shell.

DNA-Based Molecular Machines: Controlling Mechanisms and Biosensing Applications

The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed.

Label-free detection of biomolecules using inductively coupled plasma mass spectrometry (ICP-MS)

Bioassays using inductively coupled plasma mass spectrometry (ICP-MS) have gained increasing attention because of the high sensitivity of ICP-MS and the various strategies of labeling biomolecules with detectable metal tags. The classic strategy to tag the target biomolecules is through direct antibody-antigen interaction and DNA hybridization, and requires the separation of the bound from the unbound tags. Label-free ICP-MS techniques for biomolecular assays do not require direct labeling: they generate detectable metal ions indirectly from specific biomolecular reactions, such as enzymatic cleavage. Here, we highlight the development of three main strategies of label-free ICP-MS assays for biomolecules: (1) enzymatic cleavage of metal-labeled substrates, (2) release of immobilized metal ions from the DNA backbone, and (3) nucleic acid amplification-assisted aggregation and release of metal tags to achieve amplified detection. We briefly describe the fundamental basis of these label-free ICP-MS assays and discuss the benefits and drawbacks of various designs. Future research is needed to reduce non-specific adsorption and minimize background and interference. Analytical innovations are also required to confront challenges faced by in vivo applications.

Antibody-Bridged DNAzyme Walker for Sensitive Detection of Small Molecules

Sensitive detection of small molecules with biological and environmental interests is important for many applications, such as food safety, disease diagnosis, and environmental monitoring. Herein, we propose a highly selective antibody-bridged DNAzyme walker to sensitively detect small molecules. The antibody-bridged DNAzyme walker consists of a track, small-molecule-labeled DNAzyme walking strand, and antibody against small molecules. The track is built by co-modifying fluorophore-labeled substrates and small-molecule-labeled DNA linkers onto a gold nanoparticle (AuNP). In the absence of the target molecule, the antibody binds small molecule labels at the DNAzyme walking strand and the DNA linker, driving the DNAzyme walking strand on the surface of the AuNP. The attached DNAzyme walking strand moves along the track and cleaves substrates to generate high fluorescence signals to achieve signal amplification. As target molecules exist, they competitively bind with antibody to displace the small-molecule-labeled linker and DNAzyme walking strand, rendering the DNAzyme walker inactive in substrate cleavage and causing weak fluorescence. By using this antibody-bridged DNAzyme walker, we achieved sensitive detection of two biologically important small molecules, digoxin and folic acid. This work provides a new paradigm by combining the signal amplification strategy of a DNA walker and immunorecognition for sensitive and selective detection of small molecules.

Self-Feedback DNAzyme Motor for Cascade-Amplified Imaging of mRNA in Live Cells and In Vivo

DNA motors have attracted extensive interest in biosensing and bioimaging. However, the amplification capacity of the existing DNA motor systems is limited since the products from the walking process are unable to feedback into the original DNA motor systems. As a result, the sensitivities of such systems are limited in the contexts of biosensing and bioimaging. In this study, we report a novel self-feedback DNAzyme motor for the sensitive imaging of tumor-related mRNA in live cells and in vivo with cascade signal amplification capacity. Gold nanoparticles (AuNPs) are modified with hairpin-locked DNAzyme walker and track strands formed by hybridizing Cy5-labeled DNA trigger-incorporated substrate strands with assistant strands. Hybridization of the target mRNA with the hairpin strands activates DNAzyme and promotes the autonomous walking of DNAzyme on AuNPs through DNAzyme-catalyzed substrate cleavage, resulting in the release of many Cy5-labeled substrate segments containing DNA triggers and the generation of an amplified fluorescence signal. Moreover, each released DNA trigger can also bind with the hairpin strand to activate and operate the original motor system, which induces further signal amplification via a feedback mechanism. This motor exhibits a 102-fold improvement in detection sensitivity over conventional DNAzyme motors and high selectivity for target mRNA. It has been successfully applied to distinguish cancer cells from normal cells and diagnose tumors in vivo based on mRNA imaging. The proposed DNAzyme motor provides a promising paradigm for the amplified detection and sensitive imaging of low-abundance biomolecules in vivo.

Enhancing 3D DNA Walker-Induced CRISPR/Cas12a Technology for Highly Sensitive Detection of ExomicroRNA Associated with Osteoporosis

Exosomal microRNAs (exomiRNAs) have emerged as promising biomarkers for the early clinical diagnosis of osteoporosis. However, their limited abundance and short length in peripheral blood present significant challenges for the accurate detection of exomiRNAs. Herein, we have designed and implemented an efficacious fluorescence-based biosensor for the highly sensitive detection of exomiRNA associated with osteoporosis, leveraging the enhancing 3D DNA walker-induced CRISPR/Cas12a technology. The engineered DNA walker is capable of efficiently transforming target exomiRNA into amplifying DNA strands, thereby enhancing the sensitivity of the developed biosensor. Concurrently, the liberated DNA strands serve as activators to trigger Cas12a trans-cleavage activity, culminating in a significantly amplified fluorescent signal for the highly sensitive detection of exomiRNA-214. Under optimal conditions, the devised technology demonstrated the capacity to detect target exomiRNA-214 at concentrations as low as 20.42 fM, encompassing a wide linear range extending from 50.0 fM to 10.0 nM. Moreover, the fluorescence-based biosensor could accurately differentiate between healthy individuals and osteoporosis patients via the detection of exomiRNA-214, which was in agreement with RT-qPCR results. As such, this biosensing technology offers promise as a valuable tool for the early diagnosis of osteoporosis.

Single Multifunctional Nanocabinets-Based Target-Activated Feedback for Simultaneously Precise Monitoring and Therapy

Stimulus-responsive mode is highly desirable for improving the precise monitoring and physiological efficacy of endogenous biomarkers (EB). However, its integrated application for visual detection and therapy is limited by inappropriate use of responsive triggers and poor delivery of EB signal-transducing agents, which remain challenging in simultaneous monitoring and noninvasive therapy of EB and EB-mediated pathological events. Target microRNA (miRNA) as controllable reaction triggers and DNAzyme as signal-transducing agent are proposed to develop target-stimulated multifunctional nanocabinets (MFNCs) for the visual tracking of both miRNA and miRNA-mediated anticancer events. The MFNCs, equipped with a target-discriminating sequence-incorporated DNAzyme motif, can specifically release therapeutic molecules through target-triggered conformational switches, accompanied by transduction signal output. Target detection and molecule release performance are recorded in parallel via reverse dual-signal feedback at the single-molecule level. In addition, the intrinsic thermal-replenishing of the MFNCs leads to tumor ablation without invasive exogenous aids. The system achieves visual target quantification, anticancer molecule real-time tracking, and tumor suppression in vivo and in vitro. This work proposes a new paradigm for precise visual exploration of EB or EB-mediated bio-events and provides a demonstration of efficacious all-in-one detection and therapy based on the target-triggered multifunctional nanosystem.

Construction of a Near-Infrared Photoswitched Nanomachine Powered by an Endogenous Trigger for Activatable Imaging of Intracellular MicroRNA and Amplified Photodynamic Therapy for Cancer Cells

DNA nanomachines could initiate the cascade reaction in an autonomous mode under the drive of triggers, which achieve the signal amplification for the bioimaging of intracellular biomarkers. Compared with the "always-on" nanomachine that possibly produces false-positive signals, a controllable nanomachine with the on-site activation could be better for accurate tumor imaging and precise tumor therapy. Till now, the endogenous and exogenous triggers have been developed to design the controllable nanosensors. However, their combinations to develop feasible DNA nanomachines have been rarely studied. Herein, we constructed a near-infrared (NIR)-light-controlled DNA nanomachine that was first activated by the NIR light and then induced a target-triggered amplification process under the drive of an endogenous stimulus. Owing to adenosine-5'-triphosphate (ATP) having much higher concentration in cancer cells than that in healthy cells and the extracellular fluid, the obtained DNA nanomachine was selectively activated in cancer cells with inhibited interference signals from the surrounding healthy tissues. With obvious advantages including the exogenous NIR light initiation, the selective activation by the target microRNA, and the sensitive acceleration by the ATP-induced strand recycling reaction, the constructed nanomachine could be used to image the intracellular microRNA with increased sensitivity. Besides, after modifying the DNA sequence with the photosensitizer molecules, the obtained nanomachine could perform the selective photodynamic therapy on the tumor sections with the outstandingly decreased side effects. Thus, we hope the designed nanomachine could provide some important hints to design feasible nanomachines for accurate tumor diagnosis and precise tumor therapy.

Development of a DNAzyme Walker for the Detection of APE1 in Living Cancer Cells

DNAzyme walker technology is a compelling option for bioanalytical and drug delivery applications. While nucleic acid and protein targets have been used to activate DNAzyme walkers, investigations into enzyme-triggered DNAzyme walkers in living cells are still in their early stages. The base excision repair (BER) pathway presents an array of enzymes that are overexpressed in cancer cells. Here, we introduce a DNAzyme walker system that sensitively and specifically detects the BER enzyme apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1). We constructed the DNAzyme walker on the surface of 20 nm-diameter gold nanoparticles. We achieved a detection limit of 160 fM of APE1 in a buffer and in whole cell lysate equivalent to the amount of APE1 in a single HeLa cell in a sample volume of 100 μL. Confocal imaging of the DNAzyme walking reveals a cytoplasmic distribution of APE1 in HeLa cells. Walking activity is tunable to exogenous Mn2+ concentrations and the uptake of the DNAzyme walker system does not require transfection assistance. We demonstrate the investigative potential of the DNAzyme walker for up-regulated or overactive enzyme biomarkers of the BER pathway in cancer cells.

The rate-limiting procedure of 3D DNA walkers and their applications in tandem technology

DNA walkers, artificial dynamic DNA nanomachines, can mimic actin to move rapidly along a predefined nucleic acid track. They can generally be classified as one- (1D), two- (2D), and three-dimensional (3D) DNA walkers. In particular, 3D DNA walkers demonstrate amazing sustainable walking ability, strong enrichment ability, and fantastic signal amplification ability. In light of these, 3D DNA walkers have been widely used in fields such as biosensors, bioanalysis and cell imaging. Most notably, the strong compatibility of 3D DNA walkers allows their integration with a range of amplification strategies, effectively enhancing signal transduction and amplifying biosensor sensing signals. Herein, we first systematically expound the walking principle of the 3D walkers in this review. Then, by presenting representative examples, the research direction of 3D walkers in recent years is discussed. Furthermore, we also categorize and evaluate diverse tandem signal amplification strategies in 3D walkers. Finally, the challenges and development trends of 3D DNA walkers in the emerging field of analysis are carefully discussed. It is believed that this work can provide new ideas for researchers to quickly understand 3D DNA walkers and their applications in diverse biosensors.

Thermofluorimetric Analysis (TFA) using Probes with Flexible Spacers: Application to Direct Antibody Sensing and to Antibody-Oligonucleotide (AbO) Conjugate Valency Monitoring

Antibodies have long been recognized as clinically relevant biomarkers of disease. The onset of a disease often stimulates antibody production in low quantities, making it crucial to develop sensitive, specific, and easy-to-use antibody assay platforms. Antibodies are also extensively used as probes in bioassays, and there is a need for simpler methods to evaluate specialized probes, such as antibody-oligonucleotide (AbO) conjugates. Previously, we demonstrated that thermofluorimetric analysis (TFA) of analyte-driven DNA assembly can be leveraged to detect protein biomarkers using AbO probes. A key advantage of this technique is its ability to circumvent autofluorescence arising from biological samples, which otherwise hampers homogeneous assays. The analysis of differential DNA melt curves (dF/dT) successfully distinguishes the signal from the background and interferences. Expanding the applicability of TFA further, herein we demonstrate a unique proximity based TFA assay for antibody quantification that is functional in 90% human plasma. We show that the conformational flexibility of the DNA-based proximity probes is critically important for optimal performance in these assays. To promote stable, proximity-induced hybridization of the short DNA strands, substitution of poly(ethylene glycol) (PEG) spacers in place of ssDNA segments led to improved conformational flexibility and sensor performance. Finally, by applying these flexible spacers to study AbO conjugates directly, we validate this modified TFA approach as a novel tool to elucidate the probe valency, clearly distinguishing between monovalent and multivalent AbOs and reducing the reagent amounts by 12-fold.

DNAzyme-Based Microscale Thermophoresis Sensor

Microscale thermophoresis (MST) technology has emerged as a powerful growing method in a molecular interaction study by measuring fluorescence responses of molecules inside a capillary to infrared (IR) laser heating with the benefits of rapid ratiometric measurement, separation-free, no immobilization, and low sample consumption. Combining the advantages of RNA-cleaving DNAzymes in target recognition and enzymatic catalysis and the strength of MST technology for fluorescence signaling, here, we reported a DNAzyme-based MST method for sensitive target detection. We introduced a fluorescein terminal label at the RNA-cleaving DNAzyme, and the substrate was linked to DNAzyme together with a poly-T sequence in a unimolecular design or not conjugated with DNAzyme in a bimolecular design. The presence of the cofactor activated DNAzyme to catalytically cleave the substrate, causing molecular structure alteration and significant changes in MST signals. This DNAzyme MST sensor enabled sensitively detecting activator targets Pb²⁺ and l-histidine, with a detection limit of 49 pM Pb²⁺ and 3.9 μM l-histidine. This biosensing strategy is universal and promising for wide applications.

Homogeneous protein assays mediated by dynamic DNA nanotechnology

Driven by recent advances in DNA nanotechnology, analytical methods have been greatly improved for designing simple and homogeneous assays for proteins. The translation from target proteins to DNA outputs dramatically enhances the sensitivity of protein assays. More importantly, the protein-responsive DNA nanotechnology has offered diverse assay mechanisms, allowing flexible assay designs and high sensitivity without the need for sophisticated operational procedures. This review will focus on the design principles and mechanistic insight of analytical assays mediated by protein-responsive DNA nanotechnology, which will serve a general guide for assay design and applications.

Applications of Functional DNA Materials in Immunomodulatory Therapy

In recent years, nanoscale or microscale functional materials derived from DNA have shown great potential for immunotherapy as superior delivery carriers. DNA nanostructures with excellent programmability and addressability enable the precise assembly of molecules or nanoparticles. DNA hydrogels have predictable structures and adjustable mechanical strength, thus being advantageous in controllable release of cargos. In addition, utilizing systematic evolution of ligands by exponential enrichment technology, a variety of DNA aptamers have been screened for specific recognition of ions, molecules, and even cells. Moreover, a wide variety of chemical modifications can further enrich the function of DNA. The unique advantages of functional DNA materials make them extremely attractive in immunomodulation. Recently, functional DNA materials-based immunotherapy has shown great potential in fighting against many diseases like cancer, viral infection, and inflammation. Therefore, in this review, we focus on discussing the progress of the applications of functional DNA materials in immunotherapy; before that, we also summarize the characteristics of the functional DNA materials descried above. Finally, we discuss the challenges and future opportunities of functional DNA materials in immunomodulatory therapy.

DNAzyme motor systems and logic gates facilitated by toehold exchange translators

DNAzyme motor systems using gold nanoparticles (AuNPs) as scaffolds are useful for biosensing and in situ amplification because these systems are free of protein enzymes, isothermal, homogeneous, and sensitive. However, detecting different targets using the available DNAzyme motor techniques requires redesigns of the DNAzyme motor. We report here a toehold-exchange translator and the translator-mediated DNAzyme motor systems, which enable sensitive responses to various nucleic acid targets using the same DNAzyme motor without requiring redesign. The translator is able to efficiently convert different nucleic acid targets into a specific output DNA that further activates the pre-silenced DNAzyme motor and consequently initiates the autonomous walking of the DNAzyme motor. Simply adjusting the target-binding region of the translator enables the same DNAzyme motor system to respond to various nucleic acid targets. The translator-mediated DNAzyme motor system is able to detect as low as 2.5 pM microRNA-10b and microRNA-21 under room temperature without the need of separation or washing. We further demonstrate the versatility of the translator and the DNAzyme motor by successful construction and operation of four logic gates, including OR, AND, NOR, and NAND logic gates. These logic gates use two microRNA targets as inputs and generate amplified fluorescence signals from the operation of the same DNAzyme motor. Incorporation of the toehold-exchange translator into the DNAzyme motor technology improves the biosensing applications of DNA motors to diverse nucleic acid targets.

Recent advancements in coralyne (COR)-based biosensors: Basic principles, various strategies and future perspectives

As a kind of protoberberine alkaloid heterocyclic analogues, coralyne (COR) has been reported to exhibit superior antileukemic ability and used as anticancer drug agent. While, the severe hazards and side effects caused by unreasonable use have made its accurate detection more and more important. Although scientists have explored various methods to sense COR and other related targets, a systematical review which could not only elaborate recent developments and analyze current challenges of COR-based biosensors, but also present future perspective has not been reported and is urgently needed. In this review, we attempt to summarize latest advancements in COR-based biosensors in recent decade. Firstly, the operating principles, advantages and disadvantages of various strategies for COR detection (colorimetric, fluorescent, electrochemical and other ones) are comprehensively demonstrated and reviewed. Secondly, COR-assisted biosensors for detection of different non-COR targets (heparin, toxins, nucleic acids and other small molecules) are further discussed. Finally, we analyze current challenges and also suggest potential perspectives for this area.

DNA Walkers for Biosensing Development

The ability to design nanostructures with arbitrary shapes and controllable motions has made DNA nanomaterials used widely to construct diverse nanomachines with various structures and functions. The DNA nanostructures exhibit excellent properties, including programmability, stability, biocompatibility, and can be modified with different functional groups. Among these nanoscale architectures, DNA walker is one of the most popular nanodevices with ingenious design and flexible function. In the past several years, DNA walkers have made amazing progress ranging from structural design to biological applications including constructing biosensors for the detection of cancer-associated biomarkers. In this review, the key driving forces of DNA walkers are first summarized. Then, the DNA walkers with different numbers of legs are introduced. Furthermore, the biosensing applications of DNA walkers including the detection- of nucleic acids, proteins, ions, and bacteria are summarized. Finally, the new frontiers and opportunities for developing DNA walker-based biosensors are discussed.

Engineering DNA walkers for bioanalysis: A review

Considerable advances have been made in the design, modularization, functionalization, and regulation of DNA nanostructures over the past 40 years. These advances have accelerated the development of DNA nanomachines such as DNA walkers, dynamic nanomachines with walking feet, tracks, and driven forces, which have highly sensitive detection and signal amplification abilities that can be applied to various bioanalytical contexts and therapeutic strategies. Here, we describe a rational design of the nano-bio interface, the kinetics of DNA walkers and the strategies for improving their efficiency and sensitivity. We also outline the various bioanalytic and imaging applications to which DNA walkers have been applied, such as electrochemical and optical measurements, when integrated with other simulation and activation tools. Finally, we compare the performances of novel DNA walker-based strategies for bioanalysis and propose a method to improve DNA walker design.

Development of the DNA-based biosensors for high performance in detection of molecular biomarkers: More rapid, sensitive, and universal

The molecular biomarkers are molecules that are closely related to specific physiological states. Numerous molecular biomarkers have been identified as targets for disease diagnosis and biological research. To date, developing highly efficient probes for the precise detection of biomarkers has become an attractive research field which is very important for biological and biochemical studies. During the past decades, not only the small chemical probe molecules but also the biomacromolecules such as enzymes, antibodies, and nucleic acids have been introduced to construct of biosensor platform to achieve the detection of biomarkers in a highly specific and highly efficient way. Nevertheless, improving the performance of the biosensors, especially in clinical applications, is still in urgent demand in this field. A noteworthy example is the Corona Virus Disease 2019 (COVID-19) that breaks out globally in a short time in 2020. The COVID-19 was caused by the virus called SARS-CoV-2. Early diagnosis is very important to block the infection of the virus. Therefore, during these months scientists have developed dozens of methods to achieve rapid and sensitive detection of the virus. Nowadays some of these new methods have been applied for producing the commercial detection kit and help people against the disease worldwide. DNA-based biosensors are useful tools that have been widely applied in the detection of molecular biomarkers. The good stability, high specificity, and excellent biocompatibility make the DNA-based biosensors versatile in application both in vitro and in vivo. In this paper, we will review the major methods that emerged in recent years on the design of DNA-based biosensors and their applications. Moreover, we will also briefly discuss the possible future direction of DNA-based biosensors design. We believe this is helpful for people interested in not only the biosensor field but also in the field of analytical chemistry, DNA nanotechnology, biology, and disease diagnosis.

Multiplex DNA Walking Machines for Lung Cancer-Associated miRNAs

Biomimetic DNA walking machines have gained great success in scrutinizing the microscopic world and sensitive biosensing of disease biomarkers. Despite superb achievements, the research on DNA walking machines for simultaneous detection of multiple analytes is still rare, while the design and realization of multiplexing are considered as an important bottleneck. The multiplex detection of biomarkers can not only improve the specificity of bioassays but also avoid the squander of valuable biological specimens. Herein, we reported multiplex three-dimensional (3D) DNA walking machines based on high-resolution inductively coupled plasma mass spectrometry (HR-ICPMS) for lung cancer-associated miRNA detection. In the presence of lung cancer-associated target miRNAs (miR-21, miR-141, and miR-125b), DNA walking machines were stimulated and operated to liberate a large number of lanthanide elements (Tb, Ho, and Tm), and then the signals were collected simultaneously by HR-ICPMS. The recovery test of target miRNAs in human serum and the simultaneous monitoring experiment of three miRNAs in human lung cancer cell line (A549) and normal cell line (HBE) specimens display satisfactory analysis capabilities for complex biological samples. Thanks to the vast potential of lanthanide tags and the modular design, the proposed bioassay might flexibly detect different miRNA combinations with corresponding sets of DNA walking machines to meet the requirements of various tasks.

Protein recognition-initiated exponential amplification reaction (PRIEAR) and its application in clinical diagnosis

The isothermal exponential amplification technology have rarely been fabricated as the universal sensing platform for the detection of various proteins. To broaden its application, we here developed a strategy named protein recognition-initiated exponential amplification reaction (PRIEAR) using protein recognition to induce the DNA assembly which converts protein recognition events into ssDNA amplicons and combining two-stage amplification to achieve exponential amplification technology. Taking advantage of this principle, diverse biomarkers can be quantified at sub-picomolar concentrations in the homogenous manner, making the PRIEAR suitable for clinical practice. Therefore, this strategy can expand the powerful isothermal exponential amplification technology to protein targets and thus provide a new toolbox into the clinical and biomedical applications.

Copper nanocluster-Ru(dcbpy)32+ as a cathodic ECL-RET probe combined with 3D bipedal DNA walker amplification for bioanalysis

In this study, an intra-molecular ECL-RET probe combining the 3D bipedal DNA walker amplification strategy was exquisitely designed to monitor platelet-derived growth factor BB (PDGF-BB).

Three-dimensional self-powered DNA walking machine based on catalyzed hairpin assembly energy transfer strategy

Herein, catalyzed hairpin assembly is implemented as an automated strategy, which can respond in living cells to detect specific target DNA. Using the principle of catalyzed hairpin assembly (CHA), the auxiliary chain connects the fuel and starting chain to form a triple-stranded DNA to complete such a single system. Hundreds of single systems are modified on gold nanoparticles as DNA orbitals. Through the specific recognition of base complementation, the target DNA can realize the automatic walking of the three-dimensional fluorescence machine. This is a novel walking nanomachine that has a simple structure and can independently exist in cells to achieve automatic operation.

Integration of exonuclease III-powered three-dimensional DNA walker with single-molecule detection for multiple initiator caspases assay

Initiator caspases are important components of cellular apoptotic signaling and they can activate effector caspases in extrinsic and intrinsic apoptotic pathways. The simultaneous detection of multiple initiator caspases is essential for apoptosis mechanism studies and disease therapy. Herein, we develop a sensitive nanosensor based on the integration of exonuclease III (Exo III)-powered three-dimensional (3D) DNA walker with single-molecule detection for the simultaneous measurement of initiator caspase-8 and caspase-9. This assay involves two peptide-DNA detection probe-conjugated magnetic beads and two signal probe-conjugated gold nanoparticles (signal probes@AuNPs). The presence of caspase-8 and caspase-9 can induce the cleavage of peptides in two peptide-DNA detection probes, releasing two trigger DNAs from the magnetic beads, respectively. The two trigger DNAs can serve as the walker DNA to walk on the surface of the signal probes@AuNPs powered by Exo III digestion, liberating numerous Cy5 and Texas Red fluorophores which can be quantified by single-molecule detection, with Cy5 indicating caspase-8 and Texas Red indicating caspase-9. Notably, the introduction of the AuNP-based 3D DNA walker greatly reduces the background signal and amplifies the output signals, and the introduction of single-molecule detection further improves the detection sensitivity. This nanosensor is very sensitive with a detection limit of 2.08 × 10-6 U μL-1 for caspase-8 and 1.71 × 10-6 U μL-1 for caspase-9, and it can be used for the simultaneous screening of caspase inhibitors and the measurement of endogenous caspase activity in various cell lines at the single-cell level. Moreover, this nanosensor can be extended to detect various proteases by simply changing the peptide sequences of the detection probes.

A mismatch-suppressed, duplex-specific nuclease powered nanowalker for multiplexed sensing of microRNA

DNA molecular machines have attracted immense interest for their potential in biosensing, drug delivery, and cellular imaging. Herein, we report a duplex-specific nuclease (DSN) powered nanowalker that can autonomously and progressively move on a spherical three-dimensional track, which is constructed by functionalizing a 13 nm diameter gold nanoparticle (AuNP) with densely mismatched DNA duplexes. The motion is initiated by an RNA walking strand, and in its absence, the walker is suppressed because the DSN is inactive toward the mismatched DNA duplexes. Once the walking strand is added, perfectly matched DNA-RNA hybrid is formed via a toehold-mediated displacement reaction between the walking strand and mismatched duplex. Thereafter, the DNA-RNA hybrid is simultaneously cleaved by DSN, by releasing the walking strand, which autonomously moves on the track with the aid of DSN. The present study provides a novel energy input and power mechanism for the operation of 3-D nanowalker with high efficiency. Moreover, the proposed nanowalker can be designed in a target microRNA (miRNA)-specific manner by altering the mismatched duplexes, and it exhibits femtomole level sensitivity in both singleplexed and multiplexed sensing of three miRNA targets. In addition, multiplexed quantification of the three miRNAs in biological samples is achieved, further suggesting that the proposed nanowalker has immense potential in biomedical research and early diagnosis of clinical disorders.

Fabrication and microfluidic analysis of graphene-based molecular communication receiver for Internet of Nano Things (IoNT)

Bio-inspired molecular communications (MC), where molecules are used to transfer information, is the most promising technique to realise the Internet of Nano Things (IoNT), thanks to its inherent biocompatibility, energy-efficiency, and reliability in physiologically-relevant environments. Despite a substantial body of theoretical work concerning MC, the lack of practical micro/nanoscale MC devices and MC testbeds has led researchers to make overly simplifying assumptions about the implications of the channel conditions and the physical architectures of the practical transceivers in developing theoretical models and devising communication methods for MC. On the other hand, MC imposes unique challenges resulting from the highly complex, nonlinear, time-varying channel properties that cannot be always tackled by conventional information and communication tools and technologies (ICT). As a result, the reliability of the existing MC methods, which are mostly adopted from electromagnetic communications and not validated with practical testbeds, is highly questionable. As the first step to remove this discrepancy, in this study, we report on the fabrication of a nanoscale MC receiver based on graphene field-effect transistor biosensors. We perform its ICT characterisation in a custom-designed microfluidic MC system with the information encoded into the concentration of single-stranded DNA molecules. This experimental platform is the first practical implementation of a micro/nanoscale MC system with nanoscale MC receivers, and can serve as a testbed for developing realistic MC methods and IoNT applications.

Activating a DNA Nanomachine via Computation across Cancer Cell Membranes for Precise Therapy of Solid Tumors

Taking advantage of cancer cells' endogenous characters, the responsive activation of DNA nanomachines has achieved great success in tumor therapy. Combining with extra stimuli such as external light irradiation provided spatiotemporal control of DNA nanomachine activation. However, specific activation at the cellular level is still challenging considering the macroscopic-scale exposure area of usual light sources. DNA logic gates located at the cell membrane contributed to cellular specificity, but the free diffusion of input DNA strands during the operation process would impair efficiency and result in side effects to circumjacent normal cells in solid tumors. Here we design a transmembrane DNA logical computation strategy to activate a DNA nanomachine only in cancer cells from a complex solid tumor microenvironment. The DNA nanomachine multishell UCNPs-DNA is prepared by modifying DNA strands on upconversion nanoparticles. LA-apt, a DNA strand anchoring to a cancer cell membrane overexpressed receptor, and intracellular miRNA-21 served as inputs 1 and 2, respectively. Hybridization with input 1 at the cell membrane not only exposes the miRNA-21 recognition region at the DNA nanomachine, but also delivers it into cancer cells. The cascade hybridization with intracellular input 2 completes the "AND" gate operation and releases a DNA strand L2 as output. L2 acts as the trigger to operate the DNA nanomachine and correspondingly activates the photosensitizer Rose Bengal for reactive oxygen species generation. Through the "AND" gate operation of the DNA nanomachine across the cancer cell membrane, highly precise therapy only to cancer cells is achieved in a complex solid tumor microenvironment, which could become a promising modality for precise therapy of solid tumors.

Rapid and sensitive leukemia-derived exosome quantification via nicking endonuclease-assisted target recycling

Exosomes as fluid biomarkers hold great promise for noninvasive cancer diagnosis. However, a method for the rapid and convenient detection of exosomes is still a challenge because current analysis processes involve multiple steps and yield low sensitivity. Here, we developed a wash-free fluorescent biosensor for the rapid and sensitive quantification of exosomes by combining aptamer and nicking endonuclease (Nb·BbvCI). In this system, an aptamer-trigger complex was used as the recognition element; the trigger probe could be released, and it hybridized with gold nanoparticles (GNPs)-DNA-FAM conjugates, thereby resulting in Nb·BbvCI-assisted target recycling. As a result, our method allowed the quantification of exosomes with lower analysis time by using a cocktail containing an aptamer-trigger complex, Nb·BbvCI, and GNPs-DNA-FAM. A high sensitivity with a limit of detection (LOD) of 1.0 × 10⁴ particles per μL could be achieved. Besides, this biosensor exhibited potential application for the quantification of exosomes in human plasma, facilitating the development of exosome-based noninvasive cancer diagnosis.

Recent advances in DNA walker machines and their applications coupled with signal amplification strategies: A critical review

DNA walkers, a type of dynamic nanomachines, have become the subject of burgeoning research in the field of biology. These walkers are powered by driving forces based on strand displacement reactions, protein enzyme/DNAzyme reactions and conformational transitions. With the unique properties of high directionality, flexibility and efficiency, DNA walkers move progressively and autonomously along multiple dimensional tracks, offering abundant and promising applications in biosensing, material assembly and synthesis, and early cancer diagnosis. Notably, DNA walkers identified as signal amplifiers can be combined with various amplification approaches to enhance signal transduction and amplify biosensor sensing signals. Herein, we systematically and comprehensively review the walking principles of various DNA walkers and the recent progress on multiple dimensional tracks by presenting representative examples and an insightful discussion. We also summarized and categorized the diverse signal amplification strategies with which DNA walkers have coupled. Finally, we outline the challenges and future trends of DNA walker machines in emerging analytical fields.

Boolean logic gate based on DNA strand displacement for biosensing: current and emerging strategies

DNA computers are considered one of the most prominent next-generation molecular computers that perform Boolean logic using DNA elements. DNA-based Boolean logic gates, especially DNA strand displacement-based logic gates (SDLGs), have shown tremendous potential in biosensing since they can perform the logic analysis of multi-targets simultaneously. Moreover, SDLG biosensors generate a unique output in the form of YES/NO, which is contrary to the quantitative measurement used in common biosensors. In this review, the recent achievements of SDLG biosensing strategies are summarized. Initially, the development and mechanisms of Boolean logic gates, strand-displacement reaction, and SDLGs are introduced. Afterwards, the diversified input and output of SDLG biosensors are elaborated. Then, the state-of-the-art SDLG biosensors are reviewed in the classification of different signal-amplification methods, such as rolling circle amplification, catalytic hairpin assembly, strand-displacement amplification, DNA molecular machines, and DNAzymes. Most importantly, limitations and future trends are discussed. The technology reviewed here is a promising tool for multi-input analysis and lays a foundation for intelligent diagnostics.

Nanosurface energy transfer indicating Exo III-propelled stochastic 3D DNA walkers for HIV DNA detection

DNA-based nanomachines have aroused tremendous interest because of their potential applications in bioimaging, biocomputing, and diagnostic treatment. Herein, we constructed a novel exonuclease III-propelled and signal-amplified stochastic DNA walker that autonomously walked on a spherical particle-based 3D track through a burnt-bridge mechanism, during which nanosurface energy transfer (NSET) occurred between the fluorescent dye modified on hairpin DNA and the surface of gold nanoparticles (AuNPs). As a proof of concept, this stochastic DNA walker achieves prominent detection performance of HIV DNA in the range of 0.05-1.2 nM with a detection limit of 12.7 pM and satisfactory recovery in blood serum, showing high promise in biosensing applications with complicated media.

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.

Autonomous operation of 3D DNA walkers in living cells for microRNA imaging

Three dimensional (3D) DNA walkers hold great potential in serving as an ideal candidate for signal transduction and amplification in bio-assays. However, the autonomous operation of 3D DNA walkers inside living cells is still few and far between, which could be attributed to the lack of suitable driving forces and moderate efficiency in terms of the cellular uptake of such complex 3D DNA components. Herein, a newly updated autonomously operated and highly integrated 3D DNA walker on Au nanoparticles (Au NPs)/zeolitic imidazolate framework-8 (ZIF-8) was activated in a tumor microenviroment and its signal amplified assay capability in living cells was demonstrated using miRNA as a sensing model biomolecule. Specifically, we assembled a 3D DNA motor, including Zn2+-dependent DNAzyme and substrates on the AuNPs grafted on ZIF-8. After being delivered into a living cell, ZIF-8 was efficiently degraded in the tumor microenvironment (low pH value), locally releasing the Zn2+ and DNA motor. Then, a self-sufficient DNA motor autonomously performed the bio-analytical task of imaging miRNA-10b, with a low detection limit of 34 pM. Also, such self-sufficient 3D walkers allowed real-time imaging of MDA-MB-231 cells by intracellular operation. This method demonstrates the self-sufficient 3D DNA motor's bioanalytical application in living cells which may inspire various other biological applications including gene delivery, therapy, etc.

Target-induced activation of polymerase activity for recycling signal amplification cascades for sensitive aptamer-based detection of biomarkers

It is of great importance to develop biosensing methods for the sensitive and selective analysis of biomarkers at very low levels in biological samples. Using a new target-induced activation of the DNA polymerase activity for recycling amplification cascades, we describe an aptamer-based method for highly sensitive detection of platelet-derived growth factor BB (PDGF-BB) in human serums. The polymerase activity is initially inhibited by the binding of the polymerase to the enzyme aptamer sequence. PDGF-BB associates with and switches a PDGF-BB binding aptamer to trigger the release of an active polymerase, which further initiates the simultaneous recycling of the target PDGF-BB molecules and the enzyme aptamer sequence for the subsequent displacement of the fluorescently quenched probes to recover the fluorescence. Due to two recycling cascades, substantial fluorescence magnification is obtained for the highly sensitive detection of PDGF-BB with a low detection limit of 5.1 pM. Moreover, the potential applicability of this method for real samples was verified by determining PDGF-BB in diluted human serums, relying on the excellent specificity and selectivity of the aptamer. The demonstration of the PDGF-BB assay method here thus can be expanded for the construction of diverse sensing platforms for detecting different trace biomarkers with the integration of an elaborate design of the aptamer probes.

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.

A target-activated plasmon coupling surface-enhanced Raman scattering platform for the highly sensitive and reproducible detection of miRNA-21

We have developed an SERS-based platform for the miRNA-21 assay with nucleic acid and Raman dye-modified AuNPs as capture substrates.

Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications

DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

Simple Tripedal DNA Walker Prepared by Target-Triggered Catalytic Hairpin Assembly for Ultrasensitive Electrochemiluminescence Detection of MicroRNA

In contrast to common DNA walkers, multipedal DNA walkers exhibit larger walking area and faster walking kinetics and provide increased amplification efficiency. Consequently, they have received a considerable amount of attention in biosensing. However, most of them are synthesized by immobilizing multiple DNA walking strands on the surface of Au nanoparticles, which is tedious and time-consuming. Simple preparation of multipedal DNA walkers remains a challenge. Herein, we adopted a simple enzyme-free target-triggered catalytic hairpin assembly (CHA) circuit to synthesize a tripedal DNA walker. By walking on a DNA track-functionalized electrode, a sensitive electrochemiluminescence DNA nanomachine biosensor was constructed for sensing miRNA-21. The DNA walker was powered by toehold-mediated strand displacement; the whole process did not need the assistance of enzymes, thus avoiding tedious procedures and enzyme degradation under unfavorable environmental conditions. Specifically, a superior detection limit of 4 aM and a broad linear range of 10 aM to 1 pM were achieved. This CHA-tripedal DNA walker biosensor was then applied for the detection of miRNA-21 in human serum and showed high selectivity and excellent reproducibility, demonstrating its practical application in bioanalysis. In particular, the Y-shaped tripedal DNA walker comes from the DNA circuit, which makes the approach ideally suited for biosensing of small nucleic acid targets.

Cerium Oxide Nanoparticles: Recent Advances in Tissue Engineering

Submicron biomaterials have recently been found with a wide range of applications for biomedical purposes, mostly due to a considerable decrement in size and an increment in surface area. There have been several attempts to use innovative nanoscale biomaterials for tissue repair and tissue regeneration. One of the most significant metal oxide nanoparticles (NPs), with numerous potential uses in future medicine, is engineered cerium oxide (CeO2) nanoparticles (CeONPs), also known as nanoceria. Although many advancements have been reported so far, nanotoxicological studies suggest that the nanomaterial's characteristics lie behind its potential toxicity. Particularly, physicochemical properties can explain the positive and negative interactions between CeONPs and biosystems at molecular levels. This review represents recent advances of CeONPs in biomedical engineering, with a special focus on tissue engineering and regenerative medicine. In addition, a summary report of the toxicity evidence on CeONPs with a view toward their biomedical applications and physicochemical properties is presented. Considering the critical role of nanoengineering in the manipulation and optimization of CeONPs, it is expected that this class of nanoengineered biomaterials plays a promising role in the future of tissue engineering and regenerative medicine.

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.

A photo zipper locked DNA nanomachine with an internal standard for precise miRNA imaging in living cells

DNA nanomachines are capable of converting tiny triggers into autonomous accelerated cascade hybridization reactions and they have been used as a signal amplification strategy for intracellular imaging. However, the "always active" property of most DNA nanomachines with an "absolute intensity-dependent" signal acquisition mode results in "false positive signal amplification" by extracellular analytes and impairs detection accuracy. Here we design a photo zipper locked miRNA responsive DNA nanomachine (PZ-DNA nanomachine) based on upconversion nanoparticles (UCNPs) with a photo-cleavable DNA strand to block the miRNA recognition region, which provided sufficient protection to the DNA nanomachine against nonspecific extracellular activation and allowed satisfactory signal amplification for sensitive miRNA imaging after intracellular photoactivation. Multiple emissions from the UCNPs were also utilized as an internal standard to self-calibrate the intracellular miRNA responsive fluorescence signal. The presented PZ-DNA nanomachine demonstrated the sensitive imaging of intracellular miRNA from different cell lines, which resulted in good accordance with qRT-PCR measurements, providing a universal platform for precise imaging in living cells with high spatial-temporal specificity.