A DNA nanostructure-based biomolecular probe carrier platform for electrochemical biosensing

Electrochemical pan-variant detection of SARS-CoV-2 through host cell receptor-mimicking molecular recognition

The persistent emergence of new SARS-CoV-2 variants has presented significant challenges to vaccines and antiviral therapeutics, highlighting the need for the development of methods that ensure variant-independent responses. This study introduces a unique sensor capable of electrochemically detecting SARS-CoV-2 across a wide range of variants. The comprehensive detection is achieved by using a peptide-DNA hybrid, R7-02, as the capture probe, mimicking the binding interface between a SARS-CoV-2 spike protein and a host cell receptor, hACE2. Since the first step of viral infection is the binding of the spike protein to hACE2 regardless of variant type, the hACE2-mimicking probe can naturally acquire the pan-variant recognition capability. In constructing the sensor, the R7-02 probes are positioned on electrodes via a tetrahedral DNA nanostructure for enhanced detection efficiency. Since R7-02 directly captures the externally-exposed spike protein, our approach does not require sample pretreatments, such as virus particle lysis, unlike conventional diagnostic methods. The R7-02-embedded sensor demonstrated high sensitivity towards Omicron and its major subvariants-commonly known as 'stealth Omicron' (BA.5, BA.2.75, BQ.1.1, and XBB.1.5)-with a detection limit as low as 811.9 pM, along with robust specificity for SARS-CoV-2 against influenza and other human coronaviruses. The sensor also successfully detected SARS-CoV-2 directly from non-treated saliva samples of COVID-19-positive patients. Given the comprehensive and sensitive detection capability, combined with its simple operation, our receptor-mimicking probe-based electrochemical sensor holds the potential to be a sustainable and effective point-of-care diagnostic tool, offering a promising solution to the constant challenges posed by the endemic presence of SARS-CoV-2.

Single-Molecule DNA Hybridization on Tetrahedral DNA Framework-Modified Surfaces

Tetrahedral DNA frameworks (TDFs) have been extensively utilized in biosensing systems. At the macroscopic level, it has been well established that TDFs, when employed as probe scaffolds, significantly enhance the interfacial DNA hybridization efficiency between target single-stranded DNA (ssDNA) and probe ssDNA at the solid-liquid interface. However, a molecular-level understanding of how TDF scaffolds facilitate this interfacial hybridization remains elusive. In this study, we employed single-molecule total internal reflection fluorescence microscopy (SM-TIRFM) to monitor the hybridization processes between freely diffusing target ssDNA and probe ssDNA with or without TDF scaffolds. Statistical analysis of interfacial hybridization kinetics at single probe sites revealed that TDF scaffolds significantly accelerate the interfacial hybridization kinetics, reducing the target dissociation time by 0.5-fold and increasing the association constant (Ka) by nearly 4-fold. This study offers new insights for the development of DNA nanostructure-based biosensors.

Isothermal assembly of DNA nanostructures

DNA nanostructures are typically assembled using a thermal annealing protocol by heating the DNA mixture to high temperatures and then cooling it down to a lower temperature. Recent efforts have shown the assembly of DNA nanostructures by incubation at constant temperatures in a process called isothermal assembly. DNA motifs, polyhedra, lattices, and other nanostructures based on single-stranded tiles and the DNA origami strategy have all been constructed using the isothermal assembly process. Several additives such as denaturing agents, cationic amino acids, and natural products aid in the isothermal process at room temperature and physiological temperature. This review focusses on the developments in isothermal assembly of DNA nanostructures, key takeaways from recent studies, and the advantages and limitations of isothermal assembly in the broader context of DNA nanotechnology.

A DNA Fishhook Electrochemical Sensor Based on a Potassium Ferricyanide-Mediated Dual-Signal-Correlation Enhanced Electrocatalysis Reaction for a Simultaneous and Correlation Assay of Multiple Biomarkers

Simultaneous detection and correlation analysis of multiple biomarkers in a single run are crucial to improving the detection specificity and indicate disease progression, but they remain a challenge. Herein, we propose a DNA fishhook electrochemical sensor based on the potassium ferricyanide-mediated dual-signal correlation enhanced electrocatalysis reaction (DEER). The designed T-shaped DNA fishhook scaffold has two "hooks" to recruit their respective "fish" (targets) with the help of the "fishing bait" (signal probes, Sp), resulting in the different targets and Sp being specifically captured by the DNA fishhook to the electrode interface, respectively. The proposed DEER not only effectively improves the detection sensitivity without introducing nucleic acid amplification but also can reflect the logical correlation between the targets. As proof of principle, the DNA fishhook sensor was successfully applied in the simultaneous detection of two related gene sequences of SARS-CoV-2 and the active-state assay of the PI3K/AKT signaling pathway. In general, our DNA fishhook sensor provides a meaningful potential tool for the sensitive simultaneous detection and correlation analysis of multiple targets.

Aptamer and Oligonucleotide-Based Biosensors for Health Applications

Aptamers have emerged as powerful molecular recognition elements for biosensing applications, offering high specificity, stability, and adaptability. This review explores key considerations in designing aptamer-based sensors (aptasensors), with a focus on biomarker selection, aptamer design, and detection and immobilization strategies. However, challenges such as biofluid stability and reversibility must be addressed to improve biosensor performance. In this study, the potential of aptamer-based platforms in diagnostics is explored, emphasizing their advantages and future applications. Looking ahead, advances in multifunctional aptamers, integration with nanomaterials, and computational optimization are highlighted as promising directions for enhancing their effectiveness in biosensing.

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.

Advances of functional nucleic acids based on specific recognition:A review

Nucleic acids, which are fundamental to living organisms, play a crucial role in carrying and transmitting genetic information. Advances in molecular biology have led to the exploration of functional nucleic acids (FNAs), including aptamers, DNAzymes, and G-quadruplexes, known for specific recognition or catalysis. FNAs with high specificity, sequence programmability, modification ease and biocompatibility, have extensive applications in biosensing, environmental monitoring, drug delivery and cancer diagnosis. This review focuses on the structure and specific recognition principles of FNAs, followed by an exploration for biosensing and biomedical applications, offering insights into current challenges and future trends in FNAs as recognition elements.

Tetrahedral DNA-Enhanced Interparticle Rolling Machine for High-Efficiency Human Neutrophil Elastase SERS Ratiometric Sensing in Serum and Tissue

The development of DNA rolling machines with high rolling efficiency for ratiometric biosensing is of great significance for the accurate diagnosis and evaluation of diseases. Herein, an interparticle DNA rolling machine constructed by well-oriented and ordered DNA nanorollers guided by tetrahedral DNA was exploited for high-efficiency lung tumor-related human neutrophil elastase (HNE) SERS ratiometric sensing. In this design, tetrahedral DNA with blocked DNAzyme was assembled on AuNPs to engineer well-oriented and ordered walking DNA nanorollers (WDNs) endowed with high collision efficiency and accessibility, significantly improving the reaction kinetics and rolling efficiency. When the DNAzyme "leg DNA" on WDNs were activated through the multivalent DNA converted by target HNE, the activated WDNs with polyoriented walkers rolled efficiently along directional hairpin "track DNA" on magnetic NPs (H1@MNPs) that served as continuously "cleaving-rolling-assembly" specific substrates (CRAS), constructing an interparticle rolling machine and finally converting HNE into a ratiometric SERS signal in a nanogap-rich silver nanoisland substrate. The CRAS increased the reaction direction and local concentration, improving the accessibility and signal. The interparticle relative motion with nonplanar polyoriented walking arms weakens the derailment of rolling "leg DNA", improves the processivity, and amplifies capability. Moreover, nanogap-rich silver nanoisland SERS substrates promote the formation of high-density hot spot domains, further improving the detection sensitivity. Of note, the rolling machine ratiometric biosensor successfully measures the HNE with a detection limit of 0.25 pM and can screen inhibitors and discriminate the HNE levels in serum and tissue of normal and lung tumor patients, suggesting that the biosensor provides an effective tool for early diagnosis, prognostic evaluation, and drug discovery of lung tumor.

Tuning the Stability of DNA Tetrahedra with Base Stacking Interactions

DNA nanotechnology uses the programmable assembly of DNA to create nanoscale objects. Recent work from our laboratory suggested that terminal stacking interactions between adjacent strands could be a design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra with sticky ends containing identical base pairing interactions but different stacking interactions. Testing all 16 stacking combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. We also show that a 4 bp sticky end with weak stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to that of a 6 bp sticky end with weak stacking (49.7 ± 2.9 °C). The results likely apply to other DNA nanostructures and suggest that stacking interactions play a role in the formation and stability of DNA nanostructures.

Tetrahedral DNA nanostructures, graphene and carbon nanodots-based electrochemiluminescent biosensor for BRCA1 gene mutation detection

In this study, we present a novel electrochemiluminescent DNA biosensor designed for detecting breast cancer type 1 (BRCA1) gene mutations. The biosensor integrates graphene nanosheets (Graph-NS), tetrahedral DNA nanostructures (TDNs), and carbon nanodots (CNDs) to enhance sensitivity and specificity. Graph-NS are employed to structure the transducer and serve as a platform for DNA immobilization. TDNs are engineered with a BRCA1 gene-specific capture probe located at the apex (TDN-BRCA1), facilitating efficient biorecognition. Additionally, the basal vertices of TDNs are functionalized with amino groups, enabling their attachment to the CSPE/Graph-NS surface via amino-graphene interaction. This platform effectively identifies single-base mutations in the BRCA1 gene utilizing synthesized CNDs as a coreactant and [Ru(bpy)3]2+ as the luminophore through the coreactant pathway. The developed biosensor demonstrates exceptional sensitivity and can detect a single mutation in the BRCA1 gene. Furthermore, it has been successfully validated in real samples obtained from breast cancer patients, showcasing a remarkable detection limit of 1.41 aM.

Harnessing Nanomaterials for Next-Generation DNA Methylation Biosensors

DNA methylation is an epigenetic mechanism that regulates gene expression and is implicated in diseases such as cancer and atherosclerosis. However, traditional clinical methods for detecting DNA methylation often lack sensitivity and specificity, making early diagnosis challenging. Nanomaterials offer a solution with their unique properties, enabling highly sensitive photochemical and electrochemical detection techniques. These advanced methods enhance the accuracy and efficiency of identifying DNA methylation patterns, providing a powerful tool for early diagnosis and treatment of methylation-related diseases. This review summarizes nanomaterial-based techniques, categorized into electrochemical and photochemical methods for developing next-generation biosensors for DNA methylation. Electrochemical approaches based on nanostructured or nanomaterial-modified electrodes can detect methylation through electrical signals and can directly identify methylation sites via ionic current changes based on nanopore sequencing. Photochemical methods based on nanoparticles allow for optical detection through colorimetry, fluorescence, surface plasmon resonance, and Raman spectroscopy. Nanotechnology-implemented methodologies enable ultrasensitive and selective biosensors as point-of-care platforms for DNA methylation analysis, thereby advancing epigenetic research and clinical diagnostics.

MXene@Ni3(HITP)2@AuNPs combined with NiCo@Fc-MWCNTs-LDH for electrochemical detection of extracellular vesicles

This study proposed an electrochemical sensor combining Mxene@Ni3(HITP)2@AuNPs with NiCo@Fc-MWCNTs-LDH for detecting extracellular vesicles (EVs) derived from MCF-7 cells. Mxene exhibits high conductivity and large surface area. Ni3(HITP)2 is a novel conductive metal-organic framework (MOF) with outstanding conductivity, capable of loading more gold nanoparticles (AuNPs) when combined with polyetherimide (PEI). Tetrahedra DNA (TDN) is anchored on the substrate through gold nanoparticles (AuNPs) for the specific capture of EVs, with CD63 aptamers carried at their vertices. In the signal layer, the NiCo@Fc-MWCNTs-LDH loaded with CD63 aptamers was prepared as the electrochemical sensor signal label for EVs detection. This electrochemical sensor exhibits high sensitivity, evidenced by a low limit of detection (LOD) of 13.79 particles/mL and a linear range from 1.6 × 102 to 1.6 × 106 particles/mL, underscoring its potential for early cancer diagnosis.

Tuning the stability of DNA tetrahedra with base-stacking interactions

DNA nanotechnology relies on programmable anchoring of regions of single-stranded DNA through base pair hybridization to create nanoscale objects such as polyhedra, tubes, sheets, and other desired shapes. Recent work from our lab measured the energetics of base-stacking interactions and suggested that terminal stacking interactions between two adjacent strands could be an additional design parameter for DNA nanotechnology. Here, we explore that idea by creating DNA tetrahedra held together with sticky ends that contain identical base pairing interactions but different terminal stacking interactions. Testing all 16 possible combinations, we found that the melting temperature of DNA tetrahedra varied by up to 10 °C from altering a single base stack in the design. These results can inform stacking design to control DNA tetrahedra stability in a substantial and predictable way. To that end, we show that a 4 bp sticky end with weak terminal stacking does not form stable tetrahedra, while strengthening the stacks confers high stability with a 46.8 ± 1.2 °C melting temperature, comparable to a 6 bp sticky end with weak stacking (49.7 ± 2.9 °C). The results likely apply to other types of DNA nanostructures and suggest that terminal stacking interactions play an integral role in formation and stability of DNA nanostructures.

Exploring Framework Nucleic Acids: A Perspective on Their Cellular Applications

Cells are fundamental units of life. The coordination of cellular functions and behaviors relies on a cascade of molecular networks. Technologies that enable exploration and manipulation of specific molecular events in living cells with high spatiotemporal precision would be critical for pathological study, disease diagnosis, and treatment. Framework nucleic acids (FNAs) represent a novel class of nucleic acid materials characterized by their monodisperse and rigid nanostructure. Leveraging their exceptional programmability, convenient modification property, and predictable atomic-level architecture, FNAs have attracted significant attention in diverse cellular applications such as cell recognition, imaging, manipulation, and therapeutic interventions. In this perspective, we will discuss the utilization of FNAs in living cell systems while critically assessing the opportunities and challenges presented in this burgeoning field.

DNA Tetrahedra as Functional Nanostructures: From Basic Principles to Applications

Self-assembled supramolecular DNA tetrahedra composed of programmed sequence-engineered complementary base-paired strands represent elusive nanostructures having key contributions to the development and diverse applications of DNA nanotechnology. By appropriate engineering of the strands, DNA tetrahedra of tuneable sizes and chemical functionalities were designed. Programmed functionalities for diverse applications were integrated into tetrahedra structures including sequence-specific recognition strands (aptamers), catalytic DNAzymes, nanoparticles, proteins, or fluorophore. The article presents a comprehensive review addressing methods to assemble and characterize the DNA tetrahedra nanostructures, and diverse applications of DNA tetrahedra framework are discussed. Topics being addressed include the application of structurally functionalized DNA tetrahedra nanostructure for the assembly of diverse optical or electrochemical sensing platforms and functionalized intracellular sensing and imaging modules. In addition, the triggered reconfiguration of DNA tetrahedra nanostructures and dynamic networks and circuits emulating biological transformations are introduced. Moreover, the functionalization of DNA tetrahedra frameworks with nanoparticles provides building units for the assembly of optical devices and for the programmed crystallization of nanoparticle superlattices. Finally, diverse applications of DNA tetrahedra in the field of nanomedicine are addressed. These include the DNA tetrahedra-assisted permeation of nanocarriers into cells for imaging, controlled drug release, active chemodynamic/photodynamic treatment of target tissues, and regenerative medicine.

Cyclic Enzymatic Signal Amplification-Driven DNA Logic Nanodevices on Framework Nucleic Acid for Highly Sensitive Electrochemiluminescence Detection of Dual Myocardial miRNAs

MicroRNAs (miRNAs) have emerged as promising biomarkers for acute myocardial infarction (AMI). There is an urgent imperative to develop analytical methodologies capable of intelligently discerning multiple circulating miRNAs. Here, we present a dual miRNA detection platform for AMI using DNA logic gates coupled with an electrochemiluminescence (ECL) response. The platform integrates DNA truncated square pyramids as capture probes on gold-deposited electrodes, enabling precise quantification of miRNA associated with AMI. The cyclic enzymatic signal amplification principle of strand displacement amplification enhances the miRNA detection sensitivity. AND and OR logic gates have been successfully constructed, enabling intelligent identification of miRNAs in AMI. Calibration curves show strong linear correlations between ECL intensity and target miRNA concentration (10 fM to 10 nM), with excellent stability in consecutive measurements. When applied to clinical serum samples, the biosensor exhibits consistent performance, underscoring its reliability for clinical diagnostics. This innovative approach not only demonstrates DNA nanotechnology's potential in biosensing but also offers a promising solution for improving AMI diagnosis and prognosis through precise miRNA biomarker detection.

Laser-Induced Graphene for Advanced Sensing: Comprehensive Review of Applications

Laser-induced graphene (LIG) and Laser-scribed graphene (LSG) are both advanced materials with significant potential in various applications, particularly in the field of sustainable sensors. The practical uses of LIG (LSG), which include gas detection, biological process monitoring, strain assessment, and environmental variable tracking, are thoroughly examined in this review paper. Its tunable characteristics distinguish LIG (LSG), which is developed from accurate laser beam modulation on polymeric substrates, and they are essential in advancing sensing technologies in many applications. The recent advances in LIG (LSG) applications include energy storage, biosensing, and electronics by steadily advancing efficiency and versatility. The remarkable flexibility of LIG (LSG) and its transformative potential in regard to sensor manufacturing and utilization are highlighted in this manuscript. Moreover, it thoroughly examines the various fabrication methods used in LIG (LSG) production, highlighting precision and adaptability. This review navigates the difficulties that are encountered in regard to implementing LIG sensors and looks ahead to future developments that will propel the industry forward. This paper provides a comprehensive summary of the latest research in LIG (LSG) and elucidates this innovative material's advanced and sustainable elements.

Programmable Framework Nucleic Acid-Modified Nanomagnetic Beads for Efficient Isolation of Exosomes and Exosomal Proteomics Analysis

Exosomes are increasingly being regarded as emerging and promising biomarkers for cancer screening, diagnosis, and therapy. The downstream molecular analyses of exosomes were greatly affected by the isolation efficiency from biosamples. Among the current exosome isolation strategies, affinity nanomaterials performed comparably better with selectivity and specificity. However, these techniques did not take the structure and size of exosomes into account, which may lead to a loss of isolation efficiency. In this article, a framework nucleic acid was employed to prepare a well-designed nanosized bead Fe3O4@pGMA@DNA TET@Ti4+ for enrichment of exosomes. The abundant phosphate groups in the framework nucleic acid provide binding sites to immobilize Ti4+, and its rigid three-dimensional skeleton makes them act as roadblocks to barricade exosomes and provide affinity interactions on a three-dimensional scale, resulting in the improvement of isolation efficiency. The model exosomes can be effectively isolated with 92% recovery in 5 min. From 100 μL of HeLa cell culture supernatant, 34 proteins out of the top 100 commonly identified exosomal proteins were identified from the isolated exosomes by the novel beads, which is obviously more than that by TiO2 (19 proteins), indicating higher isolation efficiency and exosome purity by Fe3O4@pGMA@DNA TET@Ti4+ beads. The nanobeads were finally applied for comparing exosomal proteomics analysis from real clinical serum samples. Twenty-five upregulated and 10 downregulated proteins were identified in the lung cancer patients group compared to the health donors group, indicating that the novel nanobeads have great potential in isolation of exosomes for exosomal proteomics analysis in cancer screening and diagnosis.

Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors

DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.

Functionalizing tetrahedral framework nucleic acids-based nanostructures for tumor in situ imaging and treatment

Timely in situ imaging and effective treatment are efficient strategies in improving the therapeutic effect and survival rate of tumor patients. In recent years, there has been rapid progress in the development of DNA nanomaterials for tumor in situ imaging and treatment, due to their unsurpassed structural stability, excellent material editability, excellent biocompatibility and individual endocytic pathway. Tetrahedral framework nucleic acids (tFNAs), are a typical example of DNA nanostructures demonstrating superior stability, biocompatibility, cell-entry performance, and flexible drug-loading ability. tFNAs have been shown to be effective in achieving timely tumor in situ imaging and precise treatment. Therefore, the progress in the fabrication, characterization, modification and cellular internalization pathway of tFNAs-based functional systems and their potential in tumor in situ imaging and treatment applications were systematically reviewed in this article. In addition, challenges and future prospects of tFNAs in tumor in situ imaging and treatment as well as potential clinical applications were discussed.

Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity

A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.

New advances in signal amplification strategies for DNA methylation detection in vitro

5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.

An electrochemical biosensor based on DNA tetrahedron nanoprobe for sensitive and selective detection of doxorubicin

Doxorubicin (DOX) is a clinical chemotherapeutic drug and patients usually suffer from dose-dependent cytotoxic and side effects during chemotherapy process with DOX. Therefore, developing a reliable strategy for DOX analysis in biological samples for dosage guidance during chemotherapy process is of great significance. Herein, a sensitive and selective electrochemical biosensor for DOX detection was designed based on gold nanoparticles (AuNPs) and DNA tetrahedron (TDN) nanoprobe bifunctional glassy carbon electrode that could detect DOX in human serum and cell lysate samples. AuNPs not only could enhance electron transfer efficiency and detection sensitivity, but also could improve the biocompatibility of electrode. TDN nanoprobes were employed as specific DOX bind sites that could bind abundant DOX through intercalative characteristics to contribute to sensitive and selective detection. Under the optimal conditions, the proposed TDN nanoprobes-based DOX biosensor exhibited a wide linear range that ranged from 1.0 nM to 50 μM and a low detection limit that was 0.3 nM. Moreover, the proposed DOX biosensor displayed nice selectivity, reproducibility and stability, and was successfully applied for DOX detection in human serum and cell lysate samples. These promising results maybe pave a way for DOX dosage guidance and therapeutic efficacy optimization in clinic.

Chronoamperometric interrogation of an electrochemical aptamer-based sensor with tetrahedral DNA nanostructure pendulums for continuous biomarker measurements

Tetrahedral DNA nanostructure (TDN) is highly promising in developing electrochemical aptamer-based (E-AB) sensors for biomolecular detection, owing to its inherit programmability, spatial orientation and structural robustness. However, current interrogation strategies applied for TDN-based E-AB sensors, including enzyme-based amperometry, voltammetry, and electrochemical impedance spectroscopy, either require complicated probe design or suffer from limited applicability or selectivity. In this study, a TDN pendulum-empowered E-AB sensor interrogated by chronoamperometry for reagent-free and continuous monitoring of a blood clotting enzyme, thrombin, was developed. TDN pendulums with extended aptamer sequences at three vertices were immobilized on a gold electrode via a thiolated double-stranded DNA (dsDNA) at the fourth vertex, and their motion is modulated by the bonding of target thrombin to aptamers. We observed a significantly amplified signalling output on our sensor based on the TDN pendulum compared to E-AB sensors modified with linear pendulums. Moreover, our sensor achieved highly selective and rapidly responsive measurement of thrombin in both PBS and artificial urine, with a wide dynamic range from 1 pM to 10 nM. This study shows chronoamperometry-enabled continuous biomarker monitoring on a sub-second timescale with a drift-free baseline, demonstrating a novel approach to accurately detect molecular dynamics in real time.

Quantification of ssDNA Scaffold Production by Ion-Pair Reverse Phase Chromatography

DNA origami is an emerging technology that can be used as a nanoscale platform in numerous applications ranging from drug delivery systems to biosensors. The DNA nanostructures are assembled from large single-stranded DNA (ssDNA) scaffolds, ranging from hundreds to thousands of nucleotides and from short staple strands. Scaffolds are usually obtained by asymmetric PCR (aPCR) or Escherichia coli infection/transformation with phages or phagemids. Scaffold quantification is typically based on agarose gel electrophoresis densitometry for molecules obtained by aPCR, or by UV absorbance, in the case of scaffolds obtained by infection or transformation. Although these methods are well-established and easy-to-apply, the results obtained are often inaccurate due to the lack of selectivity and sensitivity in the presence of impurities. Herein, we present an HPLC method based on ion-pair reversed-phase (IP-RP) chromatography to quantify DNA scaffolds. Using IP-RP chromatography, ssDNA products (449 and 1000 nt) prepared by aPCR were separated from impurities and from the double stranded (ds) DNA byproduct. Additionally, both ss and dsDNA were quantified with high accuracy. The method was used to guide the optimization of the production of ssDNA by aPCR, which targeted the maximization of the ratio of ssDNA to dsDNA obtained. Moreover, ssDNA produced from phage infection of E. coli cells was also quantified by IP-RP using commercial ssDNA from the M13mp18 phage as a standard.

A trivalent aptasensor by using DNA tetrahedron as scaffold for label-free determination of antibiotics

Owing to advantage in high sensitivity and fast response, aptamer based electrochemical biosensors have attracted much more attention. However, inappropriate interfacial engineering strategy leads to poor recognition performance, which ascribe to the following factors of immobilized oligonucleotide strand including steric hindrance, interchain entanglement, and unfavorable conformation. In this work, we proposed a DNA tetrahedron based diblock aptamer immobilized strategy for the construction of label-free electrochemical biosensor. The diblock aptamer sequence is composite of T-rich anchor domain and recognition domain, where T-rich domain enabling anchored on the edge of DNA tetrahedron via Hoogsteen hydrogen bond at neutral condition. The DNA tetrahedron scaffold offers an appropriate lateral space for target recognition of diblock aptamer. More importantly, this trivalent aptamer recognition interface can be regenerated by simply adjusting the pH environment to alkaline, resulting in the dissociation of diblock aptamer. Under the optimum condition, proposed electrochemical aptasensor manifested a satisfied sensitivity for aminoglycosides antibiotic, kanamycin with a limit of detection of 0.69 nM, which is 45-fold lower than traditional Au-S immobilization strategy. Moreover, the proposed aptasensor had also successfully been extended to ampicillin detection by changing the sequence of recognition domain in diblock aptamer. This work paves a new way for the rational design of aptamer-based electrochemical sensor.

A "signal off-on" fluorescence bioassay based on 2D-MoS2-tetrahedral DNA bioconjugate for rapid virus detection

In this work we present the preparation of a 2D molybdenum disulphide nanosheets (2D-MoS2) and tetrahedral DNA nanostructures (TDNs) bioconjugate, and its application to the development of a bioassay for rapid and easy virus detection. The bioconjugate has been prepared by using TDNs carrying the capture probe labelled with 6-carboxyfluoresceine (6-FAM). As case of study to assess the utility of the assay developed, we have chosen the SARS-CoV-2 virus. Hence, as probe we have used a DNA sequence complementary to a region of the SARS-CoV-2 ORF1ab gene (TDN-ORF-FAM). This 6-FAM labelled capture probe is located on the top vertex of the tetrahedral DNA nanostructure, the three left vertices of TDNs have a thiol group. These TDNs are bounded to 2D-MoS2 surface through the three thiol groups, allowing the capture probe to be oriented to favour the biorecognition reaction with the analyte. This biorecognition resulting platform has finally been challenged to the detection of the SARS-CoV-2 ORF1ab gene sequence as the target model by measuring fluorescence before and after the hybridization event with a detection limit of 19.7fM. Furthermore, due to high sensitivity of the proposed methodology, it has been applied to directly detect the virus in nasopharyngeal samples of infected patients without the need of any amplification step. The developed bioassay has a wide range of applicability since it can be applied to the detection of any pathogen by changing the probe corresponding to the target sequence. Thus, a novel, hands-on strategy for rapid pathogen detection has proposed and has a high potential application value in the early diagnosis of infections causes by virus or bacteria.

Multifunctional DNA scaffold mediated gap plasmon resonance: Application to sensitive PD-L1 sensor

The introduction of noble metal nanoparticles with good LSPR characteristics can greatly improve the sensitivity of SPR through resonance coupling effect. The plasma resonance response and optical properties of film coupling nanoparticle systems largely depends on the ingenious design of gap structures. Nucleic acid nanostructures have good stability, flexibility, and high biocompatibility, making them ideal materials for gap construction. 2D MOF (Cu-Tcpp) has a large conjugated surface similar to graphene, which can provide a stable substrate for the directional fixation of nucleic acid nanostructures. However, research on gap coupling plasmon based on nucleic acid nanostructures and 2D MOF is still rarely reported. By integrating the advantages of Cu-Tcpp assembled film and DNA tetrahedron immobilization, a nano gap with porous scaffold structure between the gold film and gold nanorod was build. The rigidity of DNA tetrahedron can precisely control the gap size, and its unique programmability allows us to give the coupling structure greater flexibility through the design of nucleic acid chain. The experimental results and FDTD simulation show that the film coupling nanoparticle systems constructed with DNA tetrahedrons greatly enhance the electric field strength near the chip surface and effectively improve the sensitivity of SPR. This research shows the huge potential of nucleic acid nanomaterials in the construction of SPR chip surface microstructures.

Free PCR virus detection via few-layer bismuthene and tetrahedral DNA nanostructured assemblies

In this work we describe a highly sensitive method based on a biocatalyzed electrochemiluminescence approach. The system combines, for the first time, the use of few-layer bismuthene (FLB) as a platform for the oriented immobilization of tetrahedral DNA nanostructures (TDNs) specifically designed and synthetized to detect a specific SARS-CoV-2 gene sequence. In one of its vertices, these TDNs contain a DNA capture probe of the open reading frame 1 ab (ORF1ab) of the virus, available for the biorecognition of the target DNA/RNA. At the other three vertices, there are thiol groups that enable the stable anchoring/binding to the FLB surface. This novel geometry/approach enables not only the binding of the TDNs to surfaces, but also the orientation of the capture probe in a direction normal to the bismuthine surface so that it is readily accessible for binding/recognition of the specific SARS-CoV-2 sequence. The analytical signal is based on the anodic electrochemiluminescence (ECL) intensity of luminol which, in turn, arises as a result of the reaction with H2O2, generated by the enzymatic reaction of glucose oxidation, catalyzed by the biocatalytic label avidin-glucose oxidase conjugate (Av-GOx), which acts as co-reactant in the electrochemiluminescent reaction. The method exhibits a limit of detection (LOD) of 4.31 aM and a wide linear range from 14.4 aM to 1.00 μM, and its applicability was confirmed by detecting SARS-CoV-2 in nasopharyngeal samples from COVID-19 patients without the need of any amplification process.

Construction of a New Probe Based on Copper Chaperone Protein for Detecting Cu2+ in Cells

Biomacromolecular probes have been extensively employed in the detection of metal ions for their prominent biocompatibility, water solubility, high selectivity, and easy modification of fluorescent groups. In this study, a fluorescent probe FP was constructed. The probe FP exhibited high specificity recognition for Cu2+. With the combination of Cu2+, the probe was subjected to fluorescence quenching. The research suggested that the probe FP carried out the highly sensitive detection of Cu2+ with detection limits of 1.7 nM. The fluorescence quenching of fluorescamine was induced by Cu2+ perhaps due to the PET (photoinduced electron transfer) mechanism. The FP-Cu2+ complex shows weak fluorescence, which is likely due to the PET quenching effect from Cu2+ to fluorescamine fluorophore. Moreover, the probe FP can be employed for imaging Cu2+ in living cells. The new fluorescent probe developed in this study shows the advantages of good biocompatibility and low cytotoxicity. It can be adopted for the targeted detection of Cu2+ in cells, and it has promising applications in the mechanism research and diagnosis of Cu2+-associated diseases.

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.

Decorated DNA-Based Scaffolds as Lateral Flow Biosensors

Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA-based structures decorated with reporter tags and recognition elements. We have rationally re-engineered tile-based DNA tubular structures that can act as scaffolds and can be decorated with recognition elements of different nature (i.e. antigens, aptamers or proteins) and with orthogonal fluorescent dyes. As a proof-of-principle we have developed sandwich and competitive multiplex lateral flow platforms for the detection of several targets, ranging from small molecules (digoxigenin, Dig and dinitrophenol, DNP), to antibodies (Anti-Dig, Anti-DNP and Anti-MUC1/EGFR bispecific antibodies) and proteins (thrombin). Coupling the advantages of functional DNA-based scaffolds together with the simplicity of LFAs, our approach offers the opportunity to detect a wide range of targets with nanomolar sensitivity and high specificity.

Laser induced graphene electrochemical aptasensor based on tetrahedral DNA for ultrasensitive on-site detection of microcystin-LR

The development of accurate and reliable sensor for on-site detection of microcystin-LR (MC-LR), one of hazardous environmental pollutants, is highly required. Herein, a laser induced graphene (LIG)-based electrochemical aptasensor for sensitive on-site detection of MC-LR was reported. LIG electrode, the substrate of aptasensor, was prepared via thermal transfer with ethylene-vinyl acetate copolymer, and LIG acted as quasi-reference electrode to replace conventional Ag/AgCl electrode for better operability and robustness. LIG electrode provided large surface area to assemble tetrahedral DNA to absorb methylene blue (MB) for the signal amplification. For detection, the specific recognition of MC-LR with aptamer led to the stripping of tetrahedral DNA complex and further the decreased redox current of MB (IMB). Consequently, the fabricated aptasensor offered high analytical performance for MC-LR detection with a linear range of 1 × 10-2-1 × 105 pM and a detection limit of 3 × 10-3 pM, which was successfully used for water sample analysis with comparable reliability and accuracy of standard method. Furthermore, a portable detection platform by coupling of LIG-based electrochemical aptasensor with electrochemical workstation was constructed for on-site detection of MC-LR. This work offers a novel method for the on-site monitoring of MC-LR, which promotes the investigation of LIG-based electrochemical biosensing in the field of environmental analysis.

Precise Control of Trypsin Immobilization by a Programmable DNA Tetrahedron Designed for Ultrafast Proteome Digestion and Accurate Protein Quantification

In proteomics research, with advantages including short digestion times and reusable applications, immobilized enzyme reactors (IMERs) have been paid increasing attention. However, traditional IMERs ignore the reasonable spatial arrangement of trypsin on the supporting matrixes, resulting in the partial overlapping of the active domain on trypsin and reducing digesting efficiency. In this work, a DNA tetrahedron (DNA TET)-based IMER Fe3O4-GO-AuNPs-DNA TET-Trypsin was designed and prepared. The distance between vertices of DNA TETs effectively controls the distribution of trypsin on the nanomaterials; thus, highly efficient protein digestion and accurate quantitative results can be achieved. Compared to the in-solution digestion (12-16 h), the sequence coverage of bovine serum albumin was up to 91% after a 2-min digestion by the new IMER. In addition, 3328 proteins and 18,488 peptides can be identified from HeLa cell protein extract after a 20-min digestion. For the first time, human growth hormone reference material was rapidly and accurately quantified after a 4-h digestion by IMER. Therefore, this new IMER has great application potential in proteomics research and SI traceable quantification.

Tetrahedral DNA nanostructure-corbelled click chemistry-based large-scale assembly of nanozymes for ratiometric fluorescence assay of DNA methyltransferase activity

Ligation efficiency in a surface-based DNA click chemistry (CuAAC) reaction is extremely restricted by the orientation and density of probes arranged on a heterogeneous surface. Herein, we engineer DNA tetrahedral nanostructure (DTN)-corbelled click chemistry to trigger a hybridization chain reaction (HCR) assembling a large-scale of nanozymes for ratiometric fluorescence detection of DNA adenine methyltransferase (Dam). In this study, a DNA tetrahedron structure with an alkynyl modifying pendant DNA probe (Alk-DTN) is designed and assembled on a magnetic bead (MB) as a scaffold for click chemistry. When a CuO NP-encoded magnetic nanoparticle (CuO-MNP) substrate was methylated by Dam, CuO NPs were released and turned into a mass of Cu+. The Cu+ droves azido modifying lDNA (azide-lDNA) to connect with the Alk-DTN probe on the MB through the click reaction, forming an intact primer to initiate the HCR. The HCR product, a rigid structure double-stranded DNA, periodically assembles glucose oxidase mimicking gold nanoparticles (GNPs) into a large-scale of nanozymes for catalyzing the oxidation of glucose to H2O2. NH2-MIL-101 MOFs, a fluorescent indicator and a biomimetic catalyst, activated the product H2O2 to oxidize o-phenylenediamine (oPD) into visually detectable 2,3-diaminophenazine (DAP). The change of the signal ratio between DAP and NH2-MIL-101 is proportional to the methylation event corresponding to the MTase activity. In this study, the DTN enhances the efficiency of the surface-based DNA click reaction and maintains the catalytic activities of gold nanoparticle nanozymes due to the intrinsic nature of mechanical rigidity and well-controlled orientation and well-adjusted size. Large-scale assembly of nanozymes circumvents the loss of natural enzyme activity caused by chemical modification and greatly improves the amplification efficiency. The proposed biosensor displayed a low detection limit of 0.001 U mL-1 for Dam MTase due to multiple amplification and was effective in real samples and methylation inhibitor screening, providing a promising modular platform for bioanalysis.

Synergistically remodulating H+/Ca2+ gradients to induce mitochondrial depolarization for enhanced synergistic cancer therapy

The remodulation of H+/Ca2+ gradients in the mitochondria matrix could be effective to induce mitochondria depolarization for the enhancement of cancer therapy. However, it is still challenged by H+ homeostasis, insufficient Ca2+, uncoordinated regulations, and inefficient loading/delivery strategies. Herein, a supramolecular DNA nanocomplex (Ca@DNA-MF) was prepared to synergistically remodulate H+/Ca2+ gradients for mitochondrial depolarization. Upon targeted functionalization and TME-triggered delivery, multiple reagents were released in cancer cells for synergistic three-channel mitochondrial depolarization: the gene reagent of siMCT4 blocked the LA metabolism to induce mitochondrial acidification by downregulating monocarboxylate transporter 4 (MCT4); released Ca2+ disrupted Ca2+ homeostasis to facilitate Ca2+-based mitochondrial depolarization; specifically, TME-activated glutathione (GSH) depletion facilitated efficient generation of hydroxyl radicals (˙OH), further enhancing the mitochondrial depolarization. The remodulation not only triggered apoptosis but also led to ferroptosis to generate abundant ROS for efficient LPO-based apoptosis, providing a synergistic strategy for enhanced synergistic cancer therapy.

Methylation specific enzyme-linked oligonucleotide assays (MS-ELONA) for ultrasensitive DNA methylation analysis

Methylation of the promoter region of cancer related genes plays a crucial role in the occurrence and development of cancer, and the degree of methylation has great potential for the early cancer diagnosis. At present, the technology used to quantify DNA methylation is mainly based on the DNA sequencing which are time-consuming and high-cost in the relating application. We have developed an ultrasensitive method of methylation specific enzyme-linked oligonucleotide assays (MS-ELONA) to detect and quantify the level of DNA methylation. We could detect as little as 2 pg of methylated DNA in the 100000-fold excess of unmethylated genes, and discriminate prostate cancer from benign prostatic hyperplasia (BPH) and control with serum samples. We also demonstrate the reversibility of DNA methylation modification by treatment with demethylation drugs. With 16-channel electrochemical work station, our research reveals a simple and inexpensive method to quantify the methylation level of specially appointed genes, and have the potential to be applied in the clinical research.

Intellectualized Visualization of Single-Particle Raman Spectra for Sensitive Detection and Simultaneous Multianalysis of Heavy Metal Ions

Easy-to-use, reliable, and real-time methods for detecting heavy metal ion contamination are urgently required, which is a primary concern for water pollution control and human health. However, present methods for this aim are still unable to achieve simultaneous multianalysis for complex real sample detection. Herein, an intellectualized vision-based single-nanoparticle Raman imaging strategy combined with ion-responsive functional nucleic acids (FNAs) was proposed to address these issues. We reported a correspondence between the concentration of the analytes and the density of particles (DOP) of specifically captured nanoparticles to achieve sensitive detection and simultaneous multianalysis of heavy metal ions. The specific detection of Pb2+ (Hg2+) was obtained with a detection linear range from 100 pM to 100 nM (from 500 fM to 100 nM) and limit of detections low to 1 pM (100 fM), with the advantages of good specificity, excellent homogeneity, and reproducibility. Furthermore, the differentiation of different heavy metal ions (Pb2+/Hg2+) was achieved, i.e., the simultaneous multianalysis, based on Raman imaging of the single particle and intelligent machine vision method. Finally, the Raman imaging assay was utilized for real sample analysis, and it provided a powerful and reliable tool for detecting trace Pb2+/Hg2+ in real water samples and facilitated the portable on-site monitoring of heavy metal ions.

Enhancing the Reliability of SERS Detection in Ampicillin Using Oriented Tetrahedral Framework Nucleic Acid Probes and a Long-Range SERS Substrate

Indirect surface-enhanced Raman scattering (SERS)-based methods are highly efficient in detecting and quantitatively analyzing trace antibiotics in complex samples. However, the poor reproducibility of indirect SERS assays caused by the diffusion and orientation changes of the probing molecules on SERS substrates still presents a significant challenge. To address this issue, this study reports the construction of a novel SERS sensing platform using tetrahedral framework nucleic acid (tFNA) as SERS probes in conjunction with a long-range SERS (LR-SERS) substrate. The tFNA was modified with sulfhydryl groups at three vertices and appended with a probing DNA at the remaining vertex, anchored on the substrate surface with a well-ordered orientation and stable coverage density, resulting in highly reproducible SERS signals. Owing to the weak SERS signal of tFNA inherited from its size being larger than the effective range of the enhancing electric field (E-field) of conventional SERS substrates, we utilized an LR-SERS substrate to enhance the signal of tFNA probes by capitalizing on its extended E-field. Correspondingly, the LR-SERS substrate demonstrated a 54-fold increase in the intensity of tFNA probes compared to the conventional substrate. Using this novel platform, we achieved a highly reliable detection of the antibiotic ampicillin with a wide linear range (10 fM to 1 nM), low detection limit (3.1 fM), small relative standard deviation (3.12%), and yielded quantitative recoveries of 97-102% for ampicillin in water, milk, and human serum samples. These findings, therefore, effectively demonstrate the achievement of highly reliable SERS detection of antibiotics using framework nucleic acids and an LR-SERS substrate.

Straightforward fabrication of electrochemical aptasensors with outstanding antifouling performance

Self-assembled monolayers (SAMs) are popular tools for many different applications - SAMs of commercially available chemicals that convincingly inhibit unspecific binding for electrochemical sensors, however, have yet to be developed. While adsorption of foulants prohibits the reliable analysis of biological samples, unspecific binding of the analyte similarly impedes the investigation of binding characteristics from buffer solutions. In this communication, diglycolamine is introduced for the modification of electrodes with outstanding antifouling performance. The presented sensor design, solely consisting of diglycolamine and an aptamer of choice, convinces with its ease of preparation, low cost, and, most importantly, an exceptional specificity. The latter was found to rely on a gentle but potent cleaning of the electrodes, as only our optimized cleaning procedure granted the diglycolamine layer its excellent fouling minimization performance, while literature standard protocols failed to do so. Each step of the sensor fabrication protocol was optimized by electrochemical impedance spectroscopy, while square-wave voltammetry, surface-enhanced Raman spectroscopy, and zeta potential measurement were performed for further characterization. The presented approach of surface modification with diglycolamine is a versatile method applicable not just to electrochemical measurements, but to a variety of other detection techniques, too, and has the potential to change the way we investigate binding characteristics and fabricate sensors for the analysis of complex biological samples.

Harnessing Nucleic Acids Nanotechnology for Bone/Cartilage Regeneration

The effective regeneration of weight-bearing bone defects and critical-sized cartilage defects remains a significant clinical challenge. Traditional treatments such as autologous and allograft bone grafting have not been successful in achieving the desired outcomes, necessitating the need for innovative therapeutic approaches. Nucleic acids have attracted significant attention due to their ability to be designed to form discrete structures and programmed to perform specific functions at the nanoscale. The advantages of nucleic acid nanotechnology offer numerous opportunities for in-cell and in vivo applications, and hold great promise for advancing the field of biomaterials. In this review, the current abilities of nucleic acid nanotechnology to be applied in bone and cartilage regeneration are summarized and insights into the challenges and future directions for the development of this technology are provided.

Analytical device miniaturization for the detection of circulating biomarkers

Diverse (sub)cellular materials are secreted by cells into the systemic circulation at different stages of disease progression. These circulating biomarkers include whole cells, such as circulating tumour cells, subcellular extracellular vesicles and cell-free factors such as DNA, RNA and proteins. The biophysical and biomolecular state of circulating biomarkers carry a rich repertoire of molecular information that can be captured in the form of liquid biopsies for disease detection and monitoring. In this Review, we discuss miniaturized platforms that allow the minimally invasive and rapid detection and analysis of circulating biomarkers, accounting for their differences in size, concentration and molecular composition. We examine differently scaled materials and devices that can enrich, measure and analyse specific circulating biomarkers, outlining their distinct detection challenges. Finally, we highlight emerging opportunities in biomarker and device integration and provide key future milestones for their clinical translation.

Programmable Nanostructures Based on Framework-DNA for Applications in Biosensing

DNA has been actively utilized as bricks to construct exquisite nanostructures due to their unparalleled programmability. Particularly, nanostructures based on framework DNA (F-DNA) with controllable size, tailorable functionality, and precise addressability hold excellent promise for molecular biology studies and versatile tools for biosensor applications. In this review, we provide an overview of the current development of F-DNA-enabled biosensors. Firstly, we summarize the design and working principle of F-DNA-based nanodevices. Then, recent advances in their use in different kinds of target sensing with effectiveness have been exhibited. Finally, we envision potential perspectives on the future opportunities and challenges of biosensing platforms.

DNA tetrahedron-based CRISPR bioassay for treble-self-amplified and multiplex HPV-DNA detection with elemental tagging

Sensitive quantification of multiple analytes of interest is of great significance for clinical diagnosis. CRISPR Cas platforms offer a strategy for improving the specificity, sensitivity, and speed of nucleic acid-based diagnostics, while their multiplex analysis capability is still limited and challenging. Herein, we develop a novel DNA Tetrahedron (DTN)-supported biosensor based on the spatially separated CRISPR Cas self-amplification strategy and multiple-metal-nanoparticle tagging coupled with inductively coupled plasma mass spectrometry (ICP-MS) detection to improve the sensitivity and feasibility of the platform for multiplex detection of HPV-DNA (HPV-16, HPV-18 and HPV-52). Given target DNA induces robust trans-cleavage activity of the Cas12a/crRNA duplex, and the surrounding corresponding single-stranded DNA (ssDNA) linker are cleaved into short fragments that are unable to bond metal-nanoparticle probes (¹⁹⁷Au, ¹⁰⁷Ag, ¹⁹⁵Pt) onto DTN modified magnetic beads probe (MBs-DTN), resulting in obvious ICP-MS signal change. Of note, compared with ssDNA functionalized MBs, a higher Signal-to-Noise Ratio was obtained by using MBs-DTN in our system, further amplifying the signal by regulating probes on the surface of MBs. As expected, the HPV-DNA could be detected with detection limits as low as 218 fM and be multiplexed assayed at one test with high accuracy and specificity by this proposed strategy. Furthermore, we demonstrated that the HPV-DNA in cervical swab samples could be detected, showing high consistency with DNA sequencing results. We believe that this work provides a promising option in designing CRISPR based multiplex detection system for high sensitivity, good specificity, and clinical molecular diagnostics.

Tetrahedral DNA Nanostructure-Engineered Paper-Based Sensor with an Enhanced Antifouling Ability for Photoelectrochemical Sensing

Herein, a newly designed two-in-one tetrahedral DNA (TDN) nanostructure with an antifouling surface and backbone-rigidified interfacial tracks was developed for highly sensitive and selective detection of miRNA-182-5p. The well-regulated TDN tracks were assembled onto the surface of the TiO₂/MIL-125-NH₂-functionalized paper electrode, which efficiently avoided the obstacle of DNA strand tangling and decreased the probability of suspension during the walking process, thus greatly promoting the moving efficiency of DNA walkers. More interestingly, the TDN-modified sensing interfaces demonstrated incomparable antifouling ability against protein samples and interfering miRNAs due to the strong hydrophilic capacity and special molecular conformations, which addressed the dilemma of low sensitivity from traditional antifouling coating strategies. As a proof of concept, the designed bifunctional tetrahedron-modified paper-based photoelectrochemical sensor was successfully used to quantify miRNA-182-5p with a low detection limit of 0.09 fM and high specificity and was validated for monitoring of miRNA-182-5p in real samples. This TDN-engineered biointerface could be used as a universal platform for tracking various targets by substituting the biorecognition events, providing great promise for bioanalysis and clinical diagnosis.

Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles

Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (R_CT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.

The role of size in biostability of DNA tetrahedra

The potential for using DNA nanostructures for drug delivery applications requires understanding and ideally tuning their biostability. Here we investigate how biological degradation varies with size of a DNA nanostructure. We designed DNA tetrahedra of three edge lengths ranging from 13 to 20 bp and analyzed nuclease resistance for two nucleases and biostability in fetal bovine serum. We found that DNase I had similar digestion rates across sizes but appeared to incompletely digest the smallest tetrahedron, while T5 exonuclease was notably slower to digest the largest tetrahedron. In fetal bovine serum, the 20 bp tetrahedron was degraded ~four times faster than the 13 bp. These results show that DNA nanostructure size can influence nuclease degradation, but suggest a complex relationship that is nuclease specific.

Application of aptamer-drug delivery system in the therapy of breast cancer

Despite significant treatment advances, breast cancer remains the leading cause of cancer death in women. From the current treatment situation, in addition to developing chemoresistant tumours, distant organ metastasis, and recurrences, patients with breast cancer often have a poor prognosis. Aptamers as "chemical antibodies" may be a way to resolve this dilemma. Aptamers are single-stranded, non-coding oligonucleotides (DNA or RNA), resulting their many advantages, including stability for long-term storage, simplicity of synthesis and function, and low immunogenicity, a high degree of specificity and antidote. Aptamers have gained popularity as a method for diagnosing and treating specific tumors in recent years. This article introduces the application of ten different aptamer delivery systems in the treatment and diagnosis of breast cancer, and systematically reviews their latest research progress in breast cancer treatment and diagnosis. It provides a new direction for the clinical treatment of breast cancer.

Bioorthogonal Disassembly of Hierarchical DNAzyme Nanogel for High-Performance Intracellular microRNA Imaging

Rolling circle amplification (RCA) enables the facile construction of compact and versatile DNA nanoassemblies which are yet rarely explored for intracellular analysis. This is might be ascribed to the uncontrollable and inefficient probe integration/activation. Herein, by encoding with tandem allosteric deoxyribozyme (DNA-cleaving DNAzyme), a multifunctional RCA nanogel was established for realizing the efficient intracellular microRNA imaging via the successive activation of the RCA-disassembly module and signal amplification module. The endogenous microRNA stimulates the precise degradation of DNA nanocarriers, thus leading to the efficient exposure of RCA-entrapped DNAzyme biocatalyst for an amplified readout signal. Our bioorthogonal DNAzyme disassembly strategy achieved the robust analysis of intracellular biomolecules, thus showing more prospects in clinical diagnosis.

Tetrahedral DNA framework assisted rotational paper-based analytical device for differential detection of SARS-CoV-2 and influenza A H1N1 virus

Coronavirus disease 2019 (COVID-19) and influenza A are two respiratory infectious diseases with similar clinical manifestations. Because of the complex global epidemic situation of COVID-19, the distinction and diagnosis of COVID-19 and influenza A infected persons is crucial for epidemic prevention and control. In this study, tetrahedral DNA framework (TDF) was combined with a rotational paper-based analytical device, and the color change generated by the reaction between horseradish peroxidase (HRP) and 3,3'5,5'-tetramethylbenzidine (TMB)-H₂O₂ was used for grayscale signal analysis by ImageJ software. The quantitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A H1N1 virus were realized simultaneously. Under the optimal conditions, the paper-based analytical device showed a good linear relationship between the two viruses in the range of 10^-14-10^-8g/mL, and the two viruses were not affected by cross reaction. This sensor provides a convenient and reliable method for clinical rapid differentiation and diagnosis of COVID-19 and influenza A.