Entropy-Driven Three-Dimensional DNA Nanofireworks for Simultaneous Real-Time Imaging of Telomerase and MicroRNA in Living Cells

Advancements in functional tetrahedral DNA nanostructures for multi-biomarker biosensing: Applications in disease diagnosis, food safety, and environmental monitoring

Deoxyribonucleic acid (DNA) offers the fundamental building blocks for the precisely controlled assemblies due to its inherent self-assembly and programmability. The tetrahedral DNA nanostructure (TDN) stands out as a widely utilized nanostructure, attracting attention for its high biostability, excellent biocompatibility, and versatile modification sites. The capability of DNA tetrahedron to interact with various signal outputs makes it ideal for developing functional DNA nanostructures in biosensing platforms. This review highlights recent advancements in functional tetrahedral DNA nanostructures (FTDN) for various biomarkers monitoring, including nucleic acid, protein, mycotoxin, agent, and metal ion. Additionally, it discusses the potential of FTDN in the fields of disease diagnosis, food safety, and environmental monitoring. The review also introduces the application of FTDN-based biosensors for simultaneous identification of multiple biomarkers. Finally, challenges and prospects are addressed to provide guidance for the continued development of FTDN-based biosensing platforms.

Entropy driven-based catalytic biosensors for bioanalysis: From construction to application-A review

The rapid advancement of precision medicine and the continuous emergence of novel pathogens have presented new challenges for biosensors, necessitating higher requirements. Target amplification technology serves as the core component in biosensor construction. Enzyme-based amplification methods are often sensitive and selective but involve relatively complex operational steps, whereas enzyme-free amplification methods offer simplicity but frequently fail to meet both sensitivity and selectivity simultaneously. Existing research has confirmed that entropy-driven catalyst (EDC) biosensors not only fulfills the demands for sensitivity and selectivity concurrently but also offers ease of operation and flexibility in construction. In this review, we summarize the key advantages of EDC, explore how to construct DNA nanomachines based on these advantages to achieve intracellular detection and simultaneous detection of multiple targets, as well as point-of-care testing (POCT) to address practical issues in clinical diagnosis and treatment. We also anticipate potential challenges, propose corresponding solutions, and outline future development directions for EDC-based biosensors in practical clinical applications. We firmly believe that EDC sensors will emerge as a crucial branch within the realm of biosensor development.

Supramolecular DNA Nanodevice Assembled via RCA and HCR Cascade Reaction on Tetrahedral DNA Nanostructure for Sensitive Detection and Intracellular Imaging of Dual-miRNAs Associated with Liver Cancer

Herein, a supramolecular DNA nanodevice was formed via the rolling circle amplification (RCA) and hybridization chain reaction (HCR) cascade reaction on a tetrahedral DNA nanostructure (TDN) to achieve simultaneous sensitive detection and intracellular imaging of dual-miRNAs related to liver cancer. The supramolecular DNA nanodevice effectively addressed the limitations of low probe loading capacity in traditional TDN nanodevices by enriching plenty of signal probes around a single TDN, significantly enhancing the fluorescence signal. Impressively, the supramolecular DNA nanodevice with a TDN fulcrum and dense DNA structure imparted the nanodevice with strong rigidity, ensuring the stability of the signal probes to decrease aggregation quenching for further increasing the fluorescence response. Consequently, the biosensor based on supramolecular DNA nanodevice enabled simultaneous and sensitive detection of miRNA221 and miRNA222, and further achieved accurate in situ intracellular imaging of miRNA221 and miRNA222, displaying significantly improved imaging capabilities compared to traditional TDN-based nanodevices. More importantly, simultaneous and precise intracellular imaging of miRNA221 and miRNA222 could effectively distinguish hepatocellular carcinoma cells with different degrees of metastasis from human normal liver cells, providing more precise information for the diagnosis and development of hepatocellular carcinoma.

Recent Progress in DNA Biosensors for Detecting Biomarkers in Living Cells

Analysis of biomarkers in living cells is crucial for deciphering the dynamics of cells as well as for precise diagnosis of diseases. DNA biosensors employ DNA sequences as probes to offer insights into living cells, and drive progress in disease diagnosis and drug development. In this review, we present recent advances in DNA biosensors for detecting biomarkers in living cells. The basic structural components of DNA biosensors and the signal output method are presented. The strategies of DNA biosensors crossing the cell membrane are also described, including coincubation, nanocarriers, and nanoelectroporation techniques. Based on biomarker categorization, we detail recent applications of DNA biosensors for detecting small molecules, RNAs, proteins, and integrated targets in living cells. Furthermore, the future development directions of DNA biosensors are summarized to encourage further research in this growing field.

Intelligent near-infrared light-activatable DNA machine with DNA wire nano-scaffold-integrated fast domino-like driving amplification for high-performance imaging in live biological samples

While there is significant potential for DNA machine-built enzyme-free fluorescence biosensors in the imaging analysis of live biological samples, they persist certain shortcomings. These encompass a deficiency of signal enrichment within a singular interface, uncontrolled premature activation during bio-delivery, and a slow reaction rate due to free nucleic acid collisions. In this contribution, we are committed to resolving the above challenges. Firstly, a single-interface-integrated domino-like driving amplification is constructed. In this conception, a specific target acts as the domino promotor (namely the energy source), initiating a cascading chain reaction that grafts onto a singular interface. Next, an 808 nm near-infrared (NIR) light-excited up-converting luminescence-induced light-activatable biosensing technique is introduced. By locking the target-specific identification segment with a photo-cleavage connector, the up-converted ultraviolet emission can activate target binding in a completely controlled manner. Moreover, a fast reaction rate is achieved by confining nucleic acid collisions within the surface of a DNA wire nano-scaffold, leading to a substantial enhancement in local contact concentration (30.8-fold increase, alongside a 15 times elevation in rate). When a non-coding microRNA (miRNA-221) is positioned as the model low-abundance target for proof-of-concept validation, our intelligent DNA machine demonstrates ultra-high sensitivity (with a limit of detection down to 62.65 fM) and good specificity for this hepatic malignant tumor-associated biomarker in solution detection. Going further, it is worth highlighting that the biosensing system can be employed to carry out high-performance imaging analysis in live bio-samples (ranging from the cellular level to the nude mouse body), thereby propelling the field of DNA machines in disease diagnosis.

A Fluorescence Light-Up 3D DNA Walker Driven and Accelerated by Endogenous Adenosine-5'-triphosphate for Sensitive and Rapid Label-Free MicroRNA Detection and Imaging in Living Cells

Herein, a fluorescence light-up 3D DNA walker (FLDW) was powered and accelerated by endogenous adenosine-5'-triphosphate (ATP) molecules to construct a biosensor for sensitive and rapid label-free detection and imaging of microRNA-221 (miRNA-221) in malignant tumor cells. Impressively, ATP as the driving force and accelerator for FLDW could significantly accelerate the operation rate of FLDW, reduce the likelihood of errors in signaling, and improve the sensitivity of detection and imaging. When FLDW was initiated by output DNA H1-op transformed by target miRNA-221, G-rich sequences in the S strand, anchored to AuNP, were exposed to form G-quadruplexes (G4s), and thioflavin T (ThT) embedded in the G4s emitted intense fluorescence to realize sensitive and rapid detection of target miRNA-221. Meanwhile, the specific binding of ThT to G4 with a weak background fluorescence response was utilized to enhance the signal-to-noise ratio of the label-free assay straightforwardly and cost-effectively. The proposed FLDW system could realize sensitive detection of the target miRNA-221 in the range of 1 pM to 10 nM with a detection limit of 0.19 pM by employing catalytic hairpin assembly (CHA) to improve the conversion of the target. Furthermore, by harnessing the abundant ATP present in the tumor microenvironment, FLDW achieved rapid and accurate imaging of miRNA-221 in cancer cells. This strategy provides an innovative and high-speed label-free approach for the detection and imaging of biomarkers in cancer cells and is expected to be a powerful tool for bioanalysis, diagnosis, and prognosis of human diseases.

A dual-signal aptasensor based on cascade amplification for ultrasensitive detection of aflatoxin B1

Aflatoxin B1 (AFB1) is considered as a serious carcinogenic mycotoxin that was widely detected in grains and foods, and its sensitive analysis is of key importance to avoid the health threats for consumers. In this study, a dual-signal aptasensor based on cascade of entropy-driven strand displacement reaction (ESDR) and linear rolling circle amplification (LRCA) was fabricated for ultrasensitive determination of AFB1. At the sensing system, the complementary strand would be released after the aptamer combined with AFB1, which will bring about the functional domains exposed, triggering the subsequent ESDR. Meanwhile, the two strands that were outputted by ESDR would incur the downstream LRCA reaction to produce a pair of long strands to assist in the generation of fluorescence and absorbance signals. Under the optimized conditions, the proposed aptasensor could achieve excellent sensitivity (limit of detection, 0.427 pg/mL) with satisfactory accuracy (recoveries, 92.8-107.9 %; RSD, 2.4-5.0 %), mainly ascribed to the cascade amplification. Importantly, owing to the flexibility design of nucleic acid primer, this analytical method can be applied in monitoring various hazardous substances according to the specific requirements. Our strategy provides some novel insights at signal amplification for rapid detection of AFB1 and other targets.

Genetically engineered virus-like particle-armoured and multibranched DNA scaffold-corbelled ultra-sensitive hierarchical hybridization chain reaction for targeting-enhanced imaging in living biosystems under spatiotemporal light powering

Although nucleic acids-based fluorescent biosensors, exemplified by the hybridization chain reaction (HCR), have exhibited promise as an imaging tool for detecting disease-related biomolecular makers in living biosystems, they still face certain challenges. These include the need for improved sensitivity, poor bio-targeting capability, the absence of signal enrichment interface and the uncontrollable biosensing initiation. Herein, we present a range of effective solutions. First, a stacking design resembling building blocks is used to construct a special hierarchical HCR (termed H-HCR), for which a hierarchical bridge is employed to graft multiunit HCR products. Furthermore, the H-HCR components are encapsulated into a virus-like particle (VLP) endowed with a naturally peptide-mediated targeting unit through genetic engineering of plasmids, after which the biosensor can specifically identify cancer cytomembranes. By further creating a multibranched DNA scaffold to enrich the H-HCR produced detection signals, the biosensor's analyte recognition module is inserted with a photocleavage-linker, allowing that the biosensing process can be spatiotemporally initiated via a light-powered behavior. Following these innovations, this genetically engineered VLP-armoured and multibranched DNA-scaffold-corbelled H-HCR demonstrates an ultra-sensitive and specific biosensing performance to a cancer-associated microRNA marker (miRNA-155). Beyond the worthy in vitro analysis, our method is also effective in performing imaging assays for such low-abundance analyte in living cells and even bodies, thus providing a roust platform for disease diagnosis.

DNA nanotechnology-based nucleic acid delivery systems for bioimaging and disease treatment

Nucleic acids, including DNA and RNA, have been considered as powerful and functional biomaterials owing to their programmable structure, good biocompatibility, and ease of synthesis. However, traditional nucleic acid-based probes have always suffered from inherent limitations, including restricted cell internalization efficiency and structural instability. In recent years, DNA nanotechnology has shown great promise for the applications of bioimaging and drug delivery. The attractive superiorities of DNA nanostructures, such as precise geometries, spatial addressability, and improved biostability, have enabled them to be a novel category of nucleic acid delivery systems for biomedical applications. In this review, we introduce the development of DNA nanotechnology, and highlight recent advances of DNA nanostructure-based delivery systems for cellular imaging and therapeutic applications. Finally, we propose the challenges as well as opportunities for the future development of DNA nanotechnology in biomedical research.

Cell Membrane-Anchored DNA Nanoinhibitor for Inhibition of Receptor Tyrosine Kinase Signaling Pathways via Steric Hindrance and Lysosome-Induced Protein Degradation

Receptor tyrosine kinase (RTK) plays a crucial role in cancer progression, and it has been identified as a key drug target for cancer targeted therapy. Although traditional RTK-targeting drugs are effective, there are some limitations that potentially hinder the further development of RTK-targeting drugs. Therefore, it is urgently needed to develop novel, simple, and general RTK-targeting inhibitors with a new mechanism of action for cancer targeted therapy. Here, a cell membrane-anchored RTK-targeting DNA nanoinhibitor is developed to inhibit RTK function. By using a DNA tetrahedron as a framework, RTK-specific aptamers as the recognition elements, and cholesterol as anchoring molecules, this DNA nanoinhibitor could rapidly anchor on the cell membrane and specifically bind to RTK. Compared with traditional RTK-targeting inhibitors, this DNA nanoinhibitor does not need to bind at a limited domain on RTK, which increases the possibilities of developing RTK inhibitors. With the cellular-mesenchymal to epithelial transition factor (c-Met) as a target RTK, the DNA nanoinhibitor can not only induce steric hindrance effects to inhibit c-Met activation but also reduce the c-Met level via lysosome-mediated protein degradation and thus inhibition of c-Met signaling pathways and related cell behaviors. Moreover, the DNA nanoinhibitor is feasible for other RTKs by just replacing aptamers. This work may provide a novel, simple, and general RTK-targeting nanoinhibitor and possess great value in RTK-targeted cancer therapy.

Poly-adenine-mediated tetrahedral DNA nanostructure with multiple target-recognition sites for ultrasensitive and rapid electrochemical detection of Aflatoxin B1

Tetrahedral DNA nanostructures (TDNs) are widely used in the development of electrochemical biosensors due to their structural stability, programmability, and strong interfacial orderliness. However, the complex modifications on the electrode and the single vertex target recognition of the TDNs limit their applications in electrochemical biosensing. Herein, we developed a universal detection system based on a novel polyadenine-based tetrahedral DNA nanostructure (ATDN) using Aflatoxin B1 (AFB1) as the model target for analysis. In the absence of target AFB1, the signal probes (SP) modified with ferrocene would be anchored by five aptamers on ATDN. The target capture by aptamers led to a release of SP from the electrode surface, resulting in a significant reduction of the electrochemical signal. This new nanostructure was not only dispensed with multi-step electrode modifications and strong mechanical rigidity but also had five modification sites which enhanced the detection sensitivity for the target. As a result, this biosensor shows good analytical performance in the linear range of 1 fg mL-1 to 1 ng mL-1, exhibiting a low detection limit of 0.33 fg mL-1. Satisfactory accuracy has also been demonstrated through good recoveries (95.2%-98.9%). The proposed new tetrahedral DNA nanostructure can provide a more rapid and sensitive alternative to previous electrochemical sensors based on the conventional TDN. Since DNA sequences can be designed flexibly, the sensing platform in this strategy can be extended to detect various targets in different fields.

Current research status of tumor cell biomarker detection

With the annual increases in the morbidity and mortality rates of tumors, the use of biomarkers for early diagnosis and real-time monitoring of tumor cells is of great importance. Biomarkers used for tumor cell detection in body fluids include circulating tumor cells, nucleic acids, protein markers, and extracellular vesicles. Among them, circulating tumor cells, circulating tumor DNA, and exosomes have high potential for the prediction, diagnosis, and prognosis of tumor diseases due to the large amount of valuable information on tumor characteristics and evolution; in addition, in situ monitoring of telomerase and miRNA in living cells has been the topic of extensive research to understand tumor development in real time. Various techniques, such as enzyme-linked immunosorbent assays, immunoblotting, and mass spectrometry, have been widely used for the detection of these markers. Among them, the detection of tumor cell markers in body fluids based on electrochemical biosensors and fluorescence signal analysis is highly preferred because of its high sensitivity, rapid detection and portable operation. Herein, we summarize recent research progress in the detection of tumor cell biomarkers in body fluids using electrochemical and fluorescence biosensors, outline the current research status of in situ fluorescence monitoring and the analysis of tumor markers in living cells, and discuss the technical challenges for their practical clinical application to provide a reference for the development of new tumor marker detection methods.

Integration of Isothermal Enzyme-Free Nucleic Acid Circuits for High-Performance Biosensing Applications

The isothermal enzyme-free nucleic acid amplification method plays an indispensable role in biosensing by virtue of its simple, robust, and highly efficient properties without the assistance of temperature cycling or/and enzymatic biocatalysis. Up to now, enzyme-free nucleic acid amplification has been extensively utilized for biological assays and has achieved the highly sensitive detection of various biological targets, including DNAs, RNAs, small molecules, proteins, and even cells. In this Review, the mechanisms of entropy-driven reaction, hybridization chain reaction, catalytic hairpin assembly and DNAzyme are concisely described and their recent application as biosensors is comprehensively summarized. Furthermore, the current problems and the developments of these DNA circuits are also discussed.

Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1

Traditional hybridization chain reaction (HCR) as a popular isothermal amplification technique shows some inevitable disadvantages in bioanalysis due to its relatively slow kinetics, which could be markedly promoted when the HCR initiator occurs under tension. Herein, a poly DNA tetrahedrons (pTDNs)-mediated HCR was successfully constructed to make its initiator in a stretched state by long-range electrostatic forces owing to the superimposed electrostatic interactions derived from the synthesized pTDNs, and it was hypothesized that it could remarkably enhance HCR performance, which was testified by theoretical simulations and experimental studies. Consequently, pTDNs-mediated HCR was applied to develop a novel immunoassay for rapid and sensitive detection of aflatoxin B1 as a proof-of-concept, and its signal amplification was attributed to the increased G4 DNAzyme that loaded on the second antibody. Our work paves a promising way using simple DNA frameworks alone to heighten HCR kinetics for reaction speed improvement and signal amplification in bioanalysis.

Efficient Three-Dimensional DNA Nanomachine Guided by a Robust Tetrahedral DNA Nanoarray Structure for the Rapid and Ultrasensitive Electrochemical Detection of Matrix Metalloproteinase 2

Herein, a giant-sized DNA nanoarray was subtly assembled by two kinds of independent tetrahedral DNA structures as the DNA track for a multi-armed three-dimensional (3D) DNA nanomachine to perform signal transduction and amplification efficiently, which was developed as an electrochemical biosensor for the rapid and ultrasensitive detection of matrix metalloproteinase 2 (MMP-2). Impressively, in contrast to conventional DNA walkers with inefficiency, which walked on random DNA tracks composed of a two-dimensional (2D) probe or a one-dimensional (1D) single-stranded (ss)DNA probe, the multi-armed 3D DNA nanomachine from exonuclease III (Exo III) enzyme-assisted target recycling amplification would be endowed with faster reaction speed and better walking efficiency because of the excellent rigidity and orderliness of the tetrahedral DNA nanoarray structure. Once the hairpin H3-label with the signal substance ferrocene (Fc) was added to the modified electrode surface, the multi-armed 3D DNA nanomachine would be driven to move along the well-designed nanoarray tracks by toehold-mediated DNA strand displacement, resulting in most of the ferrocene (Fc) binding to the electrode surface and a remarkable increase in electrochemical signals within 60 min. As a proof of concept, the prepared biosensor attained a low detection limit of 11.4 fg/mL for the sensitive detection of the target MMP-2 and was applied in Hela and MCF-7 cancer cell lysates. As a result, this strategy provided a high-performance sensing platform for protein detection in tumor diagnosis.

Multicolor-Encoded DNA Framework Enables Specific and Amplified In Situ Detection of the Mitochondrial Apoptotic Signaling Pathway

Monitoring the molecular activation networks of cellular processes through fluorescence imaging to accurately elucidate the signaling pathways of mitochondrial apoptosis and the regulation of upstream and downstream molecules remains a current major challenge. In this work, a multicolor-encoded tetrahedral DNA framework (meTDF) carrying two pairs of catalytic hairpins is synthesized to monitor the intracellular upstream manganese superoxide dismutase (MnSOD) mRNA and the downstream cytochrome c (Cyt c) molecules for specific and sensitive detection of the mitochondrial apoptotic signaling pathway. These two types of molecules can trigger catalytic hairpin assembly (CHA) reactions with accelerated reaction kinetics for the hairpin pairs confined on meTDF to show highly amplified fluorescence for sensitive and simultaneous detection of MnSOD mRNA and Cyt c with detection limits of 3.7 pM and 0.23 nM in vitro, respectively. Moreover, the high stability and biocompatibility of the designed meTDF can facilitate efficient delivery of the probes into cells to monitor intracellular MnSOD mRNA and Cyt c for specific detection of the mitochondrial apoptosis pathway regulated by different drugs. With the successful demonstration of their robust capability, the meTDF nanoprobes can thus open new opportunities for detecting cell apoptotic mechanisms for studying the corresponding apoptotic signaling pathways and for screening potential therapeutic drugs.