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

Nanomaterials in electrochemical nanobiosensors of miRNAs

Nanomaterial-based biosensors have received significant attention owing to their unique properties, especially enhanced sensitivity. Recent advancements in biomedical diagnosis have highlighted the role of microRNAs (miRNAs) as sensitive prognostic and diagnostic biomarkers for various diseases. Current diagnostics methods, however, need further improvements with regards to their sensitivity, mainly due to the low concentration levels of miRNAs in the body. The low limit of detection of nanomaterial-based biosensors has turned them into powerful tools for detecting and quantifying these biomarkers. Herein, we assemble an overview of recent developments in the application of different nanomaterials and nanostructures as miRNA electrochemical biosensing platforms, along with their pros and cons. The techniques are categorized based on the nanomaterial used.

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.

Exploring the diverse biomedical applications of programmable and multifunctional DNA nanomaterials

DNA nanoparticles hold great promise for a range of biological applications, including the development of cutting-edge treatments and diagnostic tests. Their subnanometer-level addressability enables precise, specific modifications with a variety of chemical and biological entities, making them ideal as diagnostic instruments and carriers for targeted delivery. This paper focuses on the potential of DNA nanomaterials, which offer scalability, programmability, and functionality. For example, they can be engineered to provide highly specific biosensing and bioimaging capabilities and show promise as a platform for disease diagnosis and treatment. Successful operation of various biomedical nanomaterials has been demonstrated both in vitro and in vivo. However, there are still significant challenges to overcome, including the need to improve the scalability and reliability of the technology, and to ensure safety in clinical applications. We discuss these challenges and opportunities in detail and highlight the progress and prospects of DNA nanotechnology for biomedical applications.

Wheel drive-based DNA sensing system for highly specific and rapid one-step detection of MiRNAs at the attomolar level

With the use of DNA as building blocks, a variety of microRNA amplification-based sensing systems have been developed. Nevertheless, ultrasensitive, selective and rapid detection of microRNAs with a high signal-to-background ratio and point mutation discrimination ability remains a challenge. Herein, we propose a novel wheel drive-based DNA sensing system (NWDS) based on a self-assembled, self-quenched nanoprobe (SQP) to conduct highly specific and ultrasensitive one-step measurement of microRNAs. In this work, a signalling recognition DNA hairpin (DH) sequence with a self-complementary stem domain of 14 base pairs was used, which contained three functional regions, namely a recognition region for the target miRNA-21, a sticky region with 9 complementary nucleotides to the 3'terminus of a DNA wheel (DW) and a region for the hybridization with a quenching DNA primer (DP). The SQP was ingeniously self-assembled at room temperature by the DH and DP, which was capable of eliminating unwanted background signals. MiRNA-21 was employed as a target model to specifically activate the SQP, leading to specific hybridization between the HP and DW. With the assistance of a polymerase, an SQP-based wheel driving took place to induce hybridization/polymerization displacement cycles, initiating target recycling and DP displacement. As a result, a large amount of the newly formed hybrid SQP/DW accumulated to generate a substantially enhanced fluorescence signal. In this way, the newly proposed NWDS exhibits ultrasensitivity with a detection limit of 5.62 aM across a wide linear dynamic response range up to 200 nM, excellent selectivity with the capability to discriminate homologous miRNAs and one-base, two-base and three-base mismatched sequences, and an outstanding analytical performance in complex systems. In addition, the significant simultaneous advantages of one-step operation, rapid detection within 15 min and a high signal-to-background ratio of 26 offer a unique opportunity to promote the early diagnosis of cancer-related diseases and molecular biological analysis.

Irregular DNA Triangular Prism/Triplex Assembly for Duplicate MiRNA Analysis with Nicking Endonuclease-Mediated Amplification

Highly sensitive and selective detection of microRNA (miRNA) is becoming more and more important in the discovery, diagnosis, and prognosis of various diseases. Herein, we develop a three-dimensional DNA nanostructure based electrochemical platform for duplicate detection of miRNA amplified by nicking endonuclease. Target miRNA first helps construction of three-way junction structures on the surfaces of gold nanoparticles. After nicking endonuclease-powered cleavage reactions, single-stranded DNAs labeled with electrochemical species are released. These strands can be facilely immobilized at four edges of the irregular triangular prism DNA (iTPDNA) nanostructure via triplex assembly. By evaluating the electrochemical response, target miRNA levels can be determined. In addition, the triplexes can be disassociated by simply changing pH conditions, and the iTPDNA biointerface can be regenerated for duplicate analyses. The developed electrochemical method not only exhibits an excellent prospect in the detection of miRNA but also may inspire the engineering of recyclable biointerfaces for biosensing platforms.

Gold Nanoparticles as a Biosensor for Cancer Biomarker Determination

Molecular biology applications based on gold nanotechnology have revolutionary impacts, especially in diagnosing and treating molecular and cellular levels. The combination of plasmonic resonance, biochemistry, and optoelectronic engineering has increased the detection of molecules and the possibility of atoms. These advantages have brought medical research to the cellular level for application potential. Many research groups are working towards this. The superior analytical properties of gold nanoparticles can not only be used as an effective drug screening instrument for gene sequencing in new drug development but also as an essential tool for detecting physiological functions, such as blood glucose, antigen-antibody analysis, etc. The review introduces the principles of biomedical sensing systems, the principles of nanomaterial analysis applied to biomedicine at home and abroad, and the chemical surface modification of various gold nanoparticles.

Biological implications and clinical potential of invasion and migration related miRNAs in glioma

Gliomas are the most common primary malignant brain tumors and are highly aggressive. Invasion and migration are the main causes of poor prognosis and treatment resistance in gliomas. As migration and invasion occur, patient survival and prognosis decline dramatically. MicroRNAs (miRNAs) are small, non-coding 21–23 nucleotides involved in regulating the malignant phenotype of gliomas, including migration and invasion. Numerous studies have demonstrated the mechanism and function of some miRNAs in glioma migration and invasion. However, the biological and clinical significance (including diagnosis, prognosis, and targeted therapy) of glioma migration and invasion-related miRNAs have not been systematically discussed. This paper reviews the progress of miRNAs-mediated migration and invasion studies in glioma and discusses the clinical value of migration and invasion-related miRNAs as potential biomarkers or targeted therapies for glioma. In addition, these findings are expected to translate into future directions and challenges for clinical applications. Although many biomarkers and their biological roles in glioma invasion and migration have been identified, none have been specific so far, and further exploration of clinical treatment is still in progress; therefore, we aimed to further identify specific markers that may guide clinical treatment and improve the quality of patient survival.

Overview on the Design of Magnetically Assisted Electrochemical Biosensors

Electrochemical biosensors generally require the immobilization of recognition elements or capture probes on the electrode surface. This may limit their practical applications due to the complex operation procedure and low repeatability and stability. Magnetically assisted biosensors show remarkable advantages in separation and pre-concentration of targets from complex biological samples. More importantly, magnetically assisted sensing systems show high throughput since the magnetic materials can be produced and preserved on a large scale. In this work, we summarized the design of electrochemical biosensors involving magnetic materials as the platforms for recognition reaction and target conversion. The recognition reactions usually include antigen-antibody, DNA hybridization, and aptamer-target interactions. By conjugating an electroactive probe to biomolecules attached to magnetic materials, the complexes can be accumulated near to an electrode surface with the aid of external magnet field, producing an easily measurable redox current. The redox current can be further enhanced by enzymes, nanomaterials, DNA assemblies, and thermal-cycle or isothermal amplification. In magnetically assisted assays, the magnetic substrates are removed by a magnet after the target conversion, and the signal can be monitored through stimuli-response release of signal reporters, enzymatic production of electroactive species, or target-induced generation of messenger DNA.

DNA walking system integrated with enzymatic cleavage reaction for sensitive surface plasmon resonance detection of miRNA

Abnormal expression levels of miRNA are associated with various tumor diseases, for example, glioma tumors are characterized by the up-regulation of miRNA-182. Surface plasmon resonance (SPR) assay for miRNA-182 from glioma patients was performed via DNA walking amplification strategy. The duplex between aminated swing arm DNA (swDNA) and block DNA (blDNA), and aminated track DNA (trDNA) with a biotin tag were tethered on the poly(ethylene glycol) (PEG)-modified chips. Upon formation of miRNA/blDNA duplex, the SPR signal decreased with the walking process of swDNA, as the biotinylated fragment of trDNA (biotin-TTGGAGT) was detached from the sensor surface caused by the nicking endonuclease Nb.BbvCI. Such a repeated hybridization and cleavage cycle occurred continuously and the detachment of more biotinylated fragments of trDNA from the chips led to the attachment of fewer streptavidin (SA) molecules and then smaller SPR signals. MiRNA-182 with concentrations ranging from 5.0 fM to 1.0 pM could be readily determined and a detection limit of 0.62 fM was achieved. The proposed method was highly selective and possessed remarkable capability for evaluating the expression levels of miRNA-182 in serum samples from healthy donors and glioma patients. The sensing protocol holds great promise for early diagnosis of cancer patients.

Exploring the Role of 2D-Graphdiyne as a Charge Carrier Layer in Field-Effect Transistors for Non-Covalent Biological Immobilization against Human Diseases

Graphdiyne's (GDY's) outstanding features have made it a novel 2D nanomaterial and a great candidate for electronic gadgets and optoelectronic devices, and it has opened new opportunities for the development of highly sensitive electronic and optical detection methods as well. Here, we testified a non-covalent grafting strategy in which GDY serves as a charge carrier layer and a bioaffinity substrate to immobilize biological receptors on GDY-based field-effect transistor (FET) devices. Firm non-covalent anchoring of biological molecules via pyrene groups and electrostatic interactions in addition to preserved electrical properties of GDY endows it with features of an ultrasensitive and stable detection mechanism. With emerging new forms and extending the subtypes of the already existing fatal diseases, genetic and biological knowledge demands more details. In this regard, we constructed simple yet efficient platforms using GDY-based FET devices in order to detect different kinds of biological molecules that threaten human health. The resulted data showed that the proposed non-covalent bioaffinity assays in GDY-based FET devices could be considered reliable strategies for novel label-free biosensing platforms, which still reach a high on/off ratio of over 10⁴. The limits of detection of the FET devices to detect DNA strands, the CA19-9 antigen, microRNA-155, the CA15-3 antigen, and the COVID-19 antigen were 0.2 aM, 0.04 pU mL^-1, 0.11 aM, 0.043 pU mL^-1, and 0.003 fg mL^-1, respectively, in the linear ranges of 1 aM to 1 pM, 1 pU mL^-1 to 0.1 μU mL^-1, 1 aM to 1 pM, 1 pU mL^-1 to 10 μU mL^-1, and 1 fg mL^-1 to 10 ng mL^-1, respectively. Finally, the extraordinary performance of these label-free FET biosensors with low detection limits, high sensitivity and selectivity, capable of being miniaturized, and implantability for in vivo analysis makes them a great candidate in disease diagnostics and point-of-care testing.

Metal-Based Nanostructured Therapeutic Strategies for Glioblastoma Treatment-An Update

Glioblastoma (GBM) is the most commonly diagnosed and most lethal primary malignant brain tumor in adults. Standard treatments are ineffective, and despite promising results obtained in early phases of experimental clinical trials, the prognosis of GBM remains unfavorable. Therefore, there is need for exploration and development of innovative methods that aim to establish new therapies or increase the effectiveness of existing therapies. One of the most exciting new strategies enabling combinatory treatment is the usage of nanocarriers loaded with chemotherapeutics and/or other anticancer compounds. Nanocarriers exhibit unique properties in antitumor therapy, as they allow highly efficient drug transport into cells and sustained intracellular accumulation of the delivered cargo. They can be infused into and are retained by GBM tumors, and potentially can bypass the blood-brain barrier. One of the most promising and extensively studied groups of nanostructured therapeutics are metal-based nanoparticles. These theranostic nanocarriers demonstrate relatively low toxicity, thus they might be applied for both diagnosis and therapy. In this article, we provide an update on metal-based nanostructured constructs in the treatment of GBM. We focus on the interaction of metal nanoparticles with various forms of electromagnetic radiation for use in photothermal, photodynamic, magnetic hyperthermia and ionizing radiation sensitization applications.

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.

Ratiometric electrochemical detection of miRNA based on DNA nanomachines and strand displacement reaction

MicroRNAs (miRNAs) play an important role in regulating gene expression in cells. Abnormal expression of miRNAs has been associated with a variety of diseases. A ratiometric electrochemical method for miRNA detection based on DNA nanomachines and strand displacement reaction was developed. Signal probe with ferrocene label and reference probe with methylene blue label were immobilized on gold nanoparticle (AuNP)-coated magnetic microbeads (AuNP-MMBs). The miRNA triggers the strand displacement reaction and forms a duplex with the protect probe, releasing one end of the DNA walker (DW); the released DW hybridizes with the ferrocene (Fc)-labeled signal probe. The signal probe detached from AuNP-MMBs upon cleavage of the Nb.BbvCI enzyme. The oxidation peak of MB moieties on the reference probe remains unchanged and the signals of Fc moieties on the signal probe are inversely proportional to the concentrations of miRNA. The ratio between Fc moieties at 0.35 V and MB moieties at -0.22 V (vs. Ag/AgCl) was used to quantify the expression level of miRNA with a detection limit down to 0.12 fM. The ratiometric assay possesses a strong ability to eliminate interference from environmental changes, thus offering the high selectivity of miRNA from the complexed biosystems, holding great significance for miRNA sensing. A ratiometric assay with high selectivity of miRNA has been developed based on DNA nanomachines and strand displacement reaction.

Two-Step Competitive Hybridization Assay: A Method for Analyzing Cancer-Related microRNA Embedded in Extracellular Vesicles

With an increased understanding of the role of microRNAs (miRNAs) in cancer evolution, there is a growing interest in the use of these non-coding nucleic acids in cancer diagnosis, prognosis, and treatment monitoring. miRNAs embedded in extracellular vesicles (EVs) are of particular interest given that circulating EVs carry cargo that are strongly correlated to their cells of origin such as tumor cells while protecting them from degradation. As such, there is a tremendous interest in new simple-to-operate vesicular microRNA analysis tools for widespread use in performing liquid biopsies. Herein, we present a two-step competitive hybridization assay that is rationally designed to translate low microRNA concentrations to large electrochemical signals as the measured signal is inversely proportional to the microRNA concentration. Using this assay, with a limit-of-detection of 122 aM, we successfully analyzed vesicular miRNA 200b from prostate cancer cell lines and human urine samples, demonstrating the expected lower expression levels of miRNA 200b in the EVs from prostate cancer cells and in the prostate cancer patient's urine samples compared to healthy patients and non-tumorigenic cell lines, validating the suitability of our approach for clinical analysis.

Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing

With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.

An "off-on" electrochemiluminescence biosensor coupled with strand displacement-powered 3D micromolecule walking nanomachine for ultrasensitive detection of adenosine triphosphate

A three-dimensional (3D) micromolecule walking nanomachine propelled by strand displacement was developed to establish a novel switching electrochemiluminescence (ECL) biosensor for ultrasensitive detection of adenosine triphosphate (ATP). Generally, walking nanomachines reported previously were limited to DNA walkers, while the proposed 3D walking nanomachine focused on the micromolecule walker. Firstly, TiO₂ and silver nanoparticles (Ag NPs) functionalized N-(4-aminobutyl)-N-(ethylisoluminol) (Ag-ABEI) were deposited onto the electrode surface to offer an enhanced ECL signal, resulting from the double catalytic effect of TiO₂ and Ag NPs for H₂O₂. Following, dopamine (DA)-labeled DNA duplex probes (S1/S2-DA) immobilized onto the modified electrode cut down the original ECL signal due to the quenching of DA toward ABEI (signal-off). Target ATP walker moved along the 3D DNA track, simultaneously releasing numerous DNA3, which was applied to displace S2-DA, resulting in the quenched ECL intensity recovery (signal-on). As a result, the biosensor showed a low limit of detection down to 0.5 nM (S/N = 3) and was successfully employed to determine ATP in human serum samples. Thus, the established biosensing strategy holds great potential for biochemical studies and clinical diagnosis.

Novel preparation method of bipedal DNA walker based on hybridization chain reaction for ultrasensitive DNA biosensing

In this work, a novel strategy for preparation of bipedal DNA walker (BDW) based on hybridization chain reaction (HCR) with the assistance of Exonuclease III (Exo III) was proposed. Based on this strategy, an electrochemical biosensor was constructed to achieve sensitive detection of CYFRA 21-1 DNA. Firstly, target recognition and circulation were achieved through a one-step catalytic hairpin assembly (CHA) reaction. For further amplification, hybridization chain reaction (HCR) was employed to form duplex-stranded DNA (dsDNA) nanostructure in homogeneous solution. In particular, the elongated single strand of the hairpin DNA for HCR was designed as the Mg²⁺ DNAzyme sequence. With the assistance of Exo III, dsDNA nanostructure can be digested and transformed into large amounts of BDW. These BDW can cleave the signal probe driven by Mg²⁺, which was modified on the electrode surface and thus achieved "signal-off" detection of target. This BDW preparation method based on HCR with the digestion of Exo III converted one target input into large amount of BDW. Coupled with the walking cleavage of BDW, a series of cascade amplification endowed high sensitivity with this biosensor and realized ultrasensitive detection of target DNA with the detection limit as low as 3.01 aM.

Algorithm-Assisted Detection and Imaging of microRNAs in Living Cancer Cells via the Disassembly of Plasmonic Core-Satellite Probes Coupled with Strand Displacement Amplification

Acute detection and high-resolution imaging of microRNAs (miRNAs) in living cancer cells have attracted great attention in clinical diagnosis and therapy. However, current methods suffer from low detection sensitivity or heavy dependence on expensive and sophisticated spectrometers. Herein, a novel algorithm-assisted system of detecting and imaging miRNAs in living cancer cells was developed via the disassembly of plasmonic core-satellite probes coupled with strand displacement amplification (SDA). The target miRNAs in the system could trigger the disassembly of plasmonic core-satellite probes, leading to the color change in the scattering light of the probes, which could be captured by dark-field microscopy (DFM). The concentration of the target miRNAs was obtained by analyzing the dark-field image based on the proposed algorithm with a detection limit of 2 pM for miRNA-21. Thus, the performance in terms of simplicity and sensitivity of the system compared with one of the conventional spectrophotometers was well presented, which could inspire more clinical applications of inexpensive, intelligent, and rapid screening of cancer cells. The application software based on the proposed algorithm running on the Android platform was also developed, demonstrating the potential of remote diagnosis.