A DNA Tetrahedron Nanoprobe with Controlled Distance of Dyes for Multiple Detection in Living Cells and in Vivo

Adoption of a Tetrahedral DNA Nanostructure as a Multifunctional Biomaterial for Drug Delivery

DNA nanostructures have been widely researched in recent years as emerging biomedical materials for drug delivery, biosensing, and cancer therapy, in addition to their hereditary function. Multiple precisely designed single-strand DNAs can be fabricated into complex, three-dimensional DNA nanostructures through a simple self-assembly process. Among all of the synthetic DNA nanostructures, tetrahedral DNA nanostructures (TDNs) stand out as the most promising biomedical nanomaterial. TDNs possess the merits of structural stability, cell membrane permeability, and natural biocompatibility due to their compact structures and DNA origin. In addition to their inherent advantages, TDNs were shown to have great potential in delivering therapeutic agents through multiple functional modifications. As a multifunctional material, TDNs have enabled innovative pharmaceutical applications, including antimicrobial therapy, anticancer treatment, immune modulation, and cartilage regeneration. Given the rapid development of TDNs in the biomedical field, it is critical to understand how to successfully produce and fine-tune the properties of TDNs for specific therapeutic needs and clinical translation. This article provides insights into the synthesis and functionalization of TDNs and summarizes the approaches for TDN-based therapeutics delivery as well as their broad applications in the field of pharmaceutics and nanomedicine, challenges, and future directions.

Strategy, Design, and Fabrication of Electrochemical Biosensors: A Tutorial

Advanced healthcare requires novel technologies capable of real-time sensing to monitor acute and long-term health. The challenge relies on converting a real-time quantitative biological and chemical signal into a desired measurable output. Given the success in detecting glucose and the commercialization of glucometers, electrochemical biosensors continue to be a mainstay of academic and industrial research activities. Despite the wealth of literature on electrochemical biosensors, reports are often specific to a particular application (e.g., pathogens, cancer markers, glucose, etc.), and most fail to convey the underlying strategy and design, and if it is transferable to detection of a different analyte. Here we present a tutorial review for those entering this research area that summarizes the basic electrochemical techniques utilized as well as discusses the designs and optimization strategies employed to improve sensitivity and maximize signal output.

A two-step electrochemical biosensor based on Tetrazyme for the detection of fibrin

In this study, an electrochemical biosensor was constructed for the detection of fibrin, specifically by a simple two-step approach, with a novel artificial enzyme (Tetrazyme) based on the DNA tetrahedral framework as signal probe. The multichannel screen-printed electrode with the activated surface cannot only remove some biological impurities, but also serve as a carrier to immobilize a large number of antigen proteins. The DNA tetrahedral nanostructure was employed to ensure the high sensitivity of the probe for biological analysis. The hemin was chimeric into the G-quadruplex to constitute the complex with peroxidase catalytic activity (hemin/G4-DNAzyme), subsequently, Tetrazyme was formed through combining of this complex and DNA tetrahedral nucleic acid framework. The artificial enzyme signal probe formed by the covalent combination of the homing peptide (Cys-Arg-Glu-Lys-Ala, CREKA), which is the aptamer of fibrin and the new artificial enzyme is fixed on the surface of the multichannel carbon electrode by CREKA-specific recognition, so as to realize the sensitive detection of fibrin. The feasibility of sensing platform was validated by cyclic voltammetry (CV) and amperometric i-t curve (IT) methods. Effects of Tetrazyme concentration, CREKA concentrations and hybridization time on the sensor were explored. Under the best optimal conditions of 0.6 μmol/L Tetrazyme, 80 μmol/L CREKA, and 2.5 h reaction time, the immunosensor had two linear detection ranges, 10-40 nmol/L, with linear regression equation Y = 0.01487X - 0.011 (R2 = 0.992), and 50-100 nmol/L, with linear regression equation Y = 0.00137X + 0.6405 (R2 = 0.998), the detection limit was 9.4 nmol/L, S/N ≥ 3. The biosensor could provide a new method with great potential for the detection of fibrin with good selectivity, stability, and reproducibility.

DNA-Based Nanomaterials as Drug Delivery Platforms for Increasing the Effect of Drugs in Tumors

DNA nanotechnology has significantly advanced and might be used in biomedical applications, drug delivery, and cancer treatment during the past few decades. DNA nanomaterials are widely used in biomedical research involving biosensing, bioimaging, and drug delivery since they are remarkably addressable and biocompatible. Gradually, modified nucleic acids have begun to be employed to construct multifunctional DNA nanostructures with a variety of architectural designs. Aptamers are single-stranded nucleic acids (both DNAs and RNAs) capable of self-pairing to acquire secondary structure and of specifically binding with the target. Diagnosis and tumor therapy are prospective fields in which aptamers can be applied. Many DNA nanomaterials with three-dimensional structures have been studied as drug delivery systems for different anticancer medications or gene therapy agents. Different chemical alterations can be employed to construct a wide range of modified DNA nanostructures. Chemically altered DNA-based nanomaterials are useful for drug delivery because of their improved stability and inclusion of functional groups. In this work, the most common oligonucleotide nanomaterials were reviewed as modern drug delivery systems in tumor cells.

Imaging strategies for receptor tyrosine kinase dimers in living cells

Receptor tyrosine kinases (RTKs) are the essential regulators of cell signal transduction pathways and play important roles in biological processes. RTK dimerization is generally considered the first step in receptor activation and cell communication. And the abnormal expression of RTK dimers is closely related to the occurrence and development of many diseases. Therefore, the visualization of RTK dimerization is of great significance for monitoring physiological processes. The genetic and nongenetic imaging strategies have attracted widespread attention due to their high efficiency and high sensitivity. In this review, the RTKs and their dimers as well as the advances in strategies for imaging RTK dimers are introduced. Furthermore, we analyze the limitations of existing imaging strategies and put forward suggestions for the future development of imaging probes. We expect that this review will inspire more in-depth investigation of RTK dimers, which will also broaden the application of strategies of RTK dimers in biomedical areas.

Apurinic/apyrimidinic endonuclease triggered doxorubicin-releasing DNA nanoprism for target therapy

Drug delivery and triggered release in tumor cells would realize the ultimate goal of precise cancer treatment. An APE1 triggered DNA nanoprism was designed, aiming at the applications of both drug delivery and precise triggered drug release in cancer cell. We demonstrate that the AP-Prism was successfully used as a vehicle based on the intracellular endogenous enzyme APE1 triggered for controlled drug delivery and triggered release. The box like DNA prism was self-assembled by annealing process and Doxorubicin molecules were then inserted into the GC base pairs. The reaction of AP-Prism enzymolysis and stability of DNA prism were investigated. Encouraged by the demonstration of AP-Prism as a drug delivery carrier, the cellular uptake and Dox release were with investigated in a human cervical cancer cell HeLa and human embryonic kidney cell HEK-293 T. Thanks to the overexpression level of APE1 in cancer cells, DNA prism could selectively release the trapped doxorubicin in response to APE1 activity in cancer cells, and provide a new strategy for the development of precision medicine.

Getting drugs to the brain: advances and prospects of organic nanoparticle delivery systems for assisting drugs to cross the blood-brain barrier

The blood-brain barrier (BBB) plays an irreplaceable role in protecting the central nervous system (CNS) from bloodborne pathogens. However, the BBB complicates the treatment of CNS diseases because it prevents almost all therapeutic drugs from getting into the CNS. With the growing understanding of the physiological characteristics of the BBB and the development of nanotechnology, nanomaterial-based drug delivery systems have become promising tools for delivering drugs across the BBB to the CNS. Herein, we systematically summarize the recent progress in organic-nanoparticle delivery systems for treating CNS diseases and evaluate their mechanisms in overcoming the BBB with the aim to provide a comprehensive understanding of the advantages, disadvantages, and challenges of organic nanoparticles in delivering drugs across the BBB. This review may inspire new research ideas and directions for applying nanotechnology to treat CNS diseases.

Construction of Fast-Walking Tetrahedral DNA Walker with Four Arms for Sensitive Detection and Intracellular Imaging of Apurinic/Apyrimidinic Endonuclease 1

Herein, a novel tetrahedral DNA walker with four arms was engineered to travel efficiently on the 3D-tracks via catalyzed hairpin assembly autonomously, realizing the sensitive detection and activity assessment as well as intracellular imaging of apurinic/apyrimidinic endonuclease 1 (APE1). In contrast to traditional DNA walkers, the tetrahedral DNA walker with the rigid 3D framework structure and nonplanar multi-sites walking arms endowed with high collision efficiency, showing a fast walking rate and high nuclease resistance. Impressively, the initial rate of the tetrahedral DNA walker with four arms was 4.54 times faster than that of the free bipedal DNA walker and produced a significant fluorescence recovery in about 40 min, achieving a sensitive detection of APE1 with a low detection limit of 5.54× 10^-6 U/μL as well as ultrasensitive intracellular APE1 fluorescence activation imaging. This strategy provides a novel DNA walker for accurate identification of low-abundance cancer biomarker and potential medical diagnosis.

Advances in Immunomodulation and Immune Engineering Approaches to Improve Healing of Extremity Wounds

Delayed healing of traumatic wounds often stems from a dysregulated immune response initiated or exacerbated by existing comorbidities, multiple tissue injury or wound contamination. Over decades, approaches towards alleviating wound inflammation have been centered on interventions capable of a collective dampening of various inflammatory factors and/or cells. However, a progressive understanding of immune physiology has rendered deeper knowledge on the dynamic interplay of secreted factors and effector cells following an acute injury. There is a wide body of literature, both in vitro and in vivo, abstracted on the immunomodulatory approaches to control inflammation. Recently, targeted modulation of the immune response via biotechnological approaches and biomaterials has gained attention as a means to restore the pro-healing phenotype and promote tissue regeneration. In order to fully realize the potential of these approaches in traumatic wounds, a critical and nuanced understanding of the relationships between immune dysregulation and healing outcomes is needed. This review provides an insight on paradigm shift towards interventional approaches to control exacerbated immune response following a traumatic injury from an agonistic to a targeted path. We address such a need by (1) providing a targeted discussion of the wound healing processes to assist in the identification of novel therapeutic targets and (2) highlighting emerging technologies and interventions that utilize an immunoengineering-based approach. In addition, we have underscored the importance of immune engineering as an emerging tool to provide precision medicine as an option to modulate acute immune response following a traumatic injury. Finally, an overview is provided on how an intervention can follow through a successful clinical application and regulatory pathway following laboratory and animal model evaluation.

Amplified Fluorescence in Situ Hybridization by Small and Bright Dye-Loaded Polymeric Nanoparticles

Detection and imaging of RNA at the single-cell level is of utmost importance for fundamental research and clinical diagnostics. Current techniques of RNA analysis, including fluorescence in situ hybridization (FISH), are long, complex, and expensive. Here, we report a methodology of amplified FISH (AmpliFISH) that enables simpler and faster RNA imaging using small and ultrabright dye-loaded polymeric nanoparticles (NPs) functionalized with DNA. We found that the small size of NPs (below 20 nm) was essential for their access to the intracellular mRNA targets in fixed permeabilized cells. Moreover, proper selection of the polymer matrix of DNA-NPs minimized nonspecific intracellular interactions. Optimized DNA-NPs enabled sequence-specific imaging of different mRNA targets (survivin, actin, and polyA tails), using a simple 1 h staining protocol. Encapsulation of cyanine and rhodamine dyes with bulky counterions yielded green-, red-, and far-red-emitting NPs that were 2-100-fold brighter than corresponding quantum dots. These NPs enabled multiplexed detection of three mRNA targets simultaneously, showing distinctive mRNA expression profiles in three cancer cell lines. Image analysis confirmed the single-particle nature of the intracellular signal, suggesting single-molecule sensitivity of the method. AmpliFISH was found to be semiquantitative, correlating with RT-qPCR. In comparison with the commercial locked nucleic acid (LNA)-based FISH technique, AmpliFISH provides 8-200-fold stronger signal (dependent on the NP color) and requires only three steps vs ∼20 steps together with a much shorter time. Thus, combination of bright fluorescent polymeric NPs with FISH yields a fast and sensitive single-cell transcriptomic analysis method for RNA research and clinical diagnostics.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

Proteomic Exploration of Endocytosis of Framework Nucleic Acids

Efficient cell internalization of framework nucleic acid nanostructures free of transfection agents provides new opportunities for developing biocompatible and intelligent nanoprobes and drug delivery carriers. Here, a proteomic identification method to screen target proteins that interact with tetrahedral DNA nanostructures (TDNs) during the process of endocytosis by combining drug affinity responsive target stability (DARTS) with liquid chromatography/tandem mass spectrometry (LC-MS/MS) techniques, is reported. It is found that that caveolin-1 (CAV1) and macropinocytosis-related protein sorting nexin5 (SNX5) are associated with the endocytosis of TNDs, which is further validated by microscale thermophoresis (MST) analysis. CAV1- and SNX5- knockout experiments reveal that both caveolae-mediated endocytosis and macropinocytosis mediate the cellular uptake of TDNs, which complement previous findings with fluorescence tracing methods. This method provides a generic strategy to analyze cellular internalization process of DNA nanostructures for biomedical applications.

DNA Nanostructures: Current Challenges and Opportunities for Cellular Delivery

DNA nanotechnology has produced a wide range of self-assembled structures, offering unmatched possibilities in terms of structural design. Because of their programmable assembly and precise control of size, shape, and function, DNA particles can be used for numerous biological applications, including imaging, sensing, and drug delivery. While the biocompatibility, programmability, and ease of synthesis of nucleic acids have rapidly made them attractive building blocks, many challenges remain to be addressed before using them in biological conditions. Enzymatic hydrolysis, low cellular uptake, immune cell recognition and degradation, and unclear biodistribution profiles are yet to be solved. Rigorous methodologies are needed to study, understand, and control the fate of self-assembled DNA structures in physiological conditions. In this review, we describe the current challenges faced by the field as well as recent successes, highlighting the potential to solve biology problems or develop smart drug delivery tools. We then propose an outlook to drive the translation of DNA constructs toward preclinical design. We particularly believe that a detailed understanding of the fate of DNA nanostructures within living organisms, achieved through thorough characterization, is the next required step to reach clinical maturity.

Recent Advances of DNA Tetrahedra for Therapeutic Delivery and Biosensing

The chemical and self-assembly properties of nucleic acids make them ideal for the construction of discrete structures and stimuli-responsive devices for a diverse array of applications. Amongst the various three-dimensional assemblies, DNA tetrahedra are of particular interest, as these structures have been shown to be readily taken up by the cell, by the process of caveolin-mediated endocytosis, without the need for transfection agents. Moreover, these structures can be readily modified with a diverse range of pendant groups to confer greater functionality. This minireview highlights recent advances related to applications of this interesting DNA structure including the delivery of therapeutic agents ranging from small molecules to oligonucleotides in addition to its use for sensing and imaging various species within the cell.

Electrochemiluminescence platform for transcription factor diagnosis by using CRISPR-Cas12a trans-cleavage activity

Herein, we exploited the double-stranded DNA (dsDNA) binding property of transcription factor (TF), combined with the trans cleavage characteristic of CRISPR-Cas12a, for the detection of NF-κB p50.

Emerging applications at the interface of DNA nanotechnology and cellular membranes: Perspectives from biology, engineering, and physics

DNA nanotechnology has proven exceptionally apt at probing and manipulating biological environments as it can create nanostructures of almost arbitrary shape that permit countless types of modifications, all while being inherently biocompatible. Emergent areas of particular interest are applications involving cellular membranes, but to fully explore the range of possibilities requires interdisciplinary knowledge of DNA nanotechnology, cell and membrane biology, and biophysics. In this review, we aim for a concise introduction to the intersection of these three fields. After briefly revisiting DNA nanotechnology, as well as the biological and mechanical properties of lipid bilayers and cellular membranes, we summarize strategies to mediate interactions between membranes and DNA nanostructures, with a focus on programmed delivery onto, into, and through lipid membranes. We also highlight emerging applications, including membrane sculpting, multicell self-assembly, spatial arrangement and organization of ligands and proteins, biomechanical sensing, synthetic DNA nanopores, biological imaging, and biomelecular sensing. Many critical but exciting challenges lie ahead, and we outline what strikes us as promising directions when translating DNA nanostructures for future in vitro and in vivo membrane applications.

Four-in-One: Advanced Copper Nanocomposites for Multianalyte Assays and Multicoding Logic Gates

The usage of non-noble-metal nanomaterials for nanoprobes or functional modules is still a big challenge because of their poor stability, functionality, and surface plasmon resonance property. In this work, copper ion, mercaptosuccinic acid, and nanocrystalline cellulose are combined for facile one-step synthesis and self-assembly of ultrasmall copper nanoparticles to produce supercolloidal particles (NCC@MSA-Cu SPs). Cu SPs show advanced multifunctionality for fast point-of-care tests (POCTs) of four metal ions (Hg²⁺, Pb²⁺, Ag⁺, and Zr⁴⁺). These selective recognitions integrate four different chemical reaction mechanisms (ion etching, core-shell deposition, templated synthesis, and precipitation) to produce four distinct readout signals. The multisignal mode-guided multianalyte sensing strategy can effectively avoid interference that affects single signal mode-based sensing. Benefiting from the creative multi-input and multireadout abilities, the visual multicoding logic gates of OR, NOR, AND, and INHIBIT are built based on optical responses of Cu SPs.

Tetrahedral DNA nanostructures as drug delivery and bioimaging platforms in cancer therapy

Structural DNA nanotechnology enables DNA to be used as nanomaterials for novel nanostructure construction with unprecedented functionalities. Artificial DNA nanostructures can be designed and generated with precisely controlled features, resulting in its utility in bionanotechnological and biomedical applications. A tetrahedral DNA nanostructure (TDN), the most popular DNA nanostructure, with high stability and simple synthesis procedure, is a promising candidate as nanocarriers in drug delivery and bioimaging platforms, particularly in precision medicine as well as diagnosis for cancer therapy. Recent evidence collectively indicated that TDN successfully enhanced cancer therapeutic efficiency both in vitro and in vivo. Here, we summarize the development of TDN and highlight various aspects of TDN applications in cancer therapy based on previous reports, including anticancer drug loading, photodynamic therapy, therapeutic oligonucleotides, bioimaging platforms, and other molecules and discuss a perspective in opportunities and challenges for future TDN‐based nanomedicine.

Penetrating the Blood-Brain Barrier by Self-Assembled 3D DNA Nanocages as Drug Delivery Vehicles for Brain Cancer Therapy

The development of biocompatible drug delivery vehicles for cancer therapy in the brain remains a big challenge. In this study, we designed self-assembled DNA nanocages functionalized with or without blood-brain barrier (BBB)-targeting ligands, d and we investigated their penetration across the BBB. Our DNA nanocages were not cytotoxic and they were substantially taken up in brain capillary endothelial cells and Uppsala 87 malignant glioma (U-87 MG) cells. We found that ligand modification is not essential for this DNA system as the ligand-free DNA nanocages (LF-NCs) could still cross the BBB by endocytosis inin vitro and in vivo models. Our spherical DNA nanocages were more permeable across the BBB compared with tubular DNA nanotubes. Remarkably, in vivo studies revealed that DNA nanocages could carry anticancer drugs across the BBB and inhibit the tumor growth in a U-87 MG xenograft mouse model. This is the first example showing the potential of DNA nanocages as innovative delivery vehicles to the brain for cancer therapy. Unlike other delivery systems, our work suggest that a DNA nanocage-based platform provides a safe and cost-effective tool for targeted delivery to the brain and therapy for brain tumors.

Dual-Wavelength Electrochemiluminescence Ratiometric Biosensor for NF-κB p50 Detection with Dimethylthiodiaminoterephthalate Fluorophore and Self-Assembled DNA Tetrahedron Nanostructures Probe

In this work, we fabricated a dual-wavelength electrochemiluminescence ratiometric biosensor based on electrochemiluminescent resonance energy transfer (ECL-RET). In this biosensor, Au nanoparticle-loaded graphitic phase carbon nitride (Au-g-C₃N₄) as a donor and Au-modified dimethylthiodiaminoterephthalate (TAT) analogue (Au@TAT) as an acceptor were investigated for the first time. Besides, tetrahedron DNA probe was immobilized onto Au-g-C₃N₄ to improve the binding efficiency of the transcription factor and ECL ratiometric changes on the basis of the ratio of ECL intensities at 595 and 460 nm, which were obtained through the formation of a sandwich structure of DNA probe-antigen-antibody. Our biosensor achieved the assay of NF-κB p50 with a detection limit of 5.8 pM as well as high stability and specificity.

A label-free homogeneous electrochemical cytosensor for the ultrasensitive detection of cancer cells based on multiaptamer-functionalized DNA tetrahedral nanostructures

We developed a label-free homogeneous electrochemical cytosensor for ultrasensitive detection of cancer cells based on multiaptamer-functionalized DNA tetrahedral nanostructures, which avoided expensive labeling and sophisticated immobilization procedures, providing opportunities for precisely detecting cancer cells in clinical applications.

An integrated electrochemical biosensor based on target-triggered strand displacement amplification and "four-way" DNA junction towards ultrasensitive detection of PIK3CA gene mutation

A novel electrochemical biosensor was constructed for specific and ultrasensitive detection of PIK3CA^H1047R gene mutation based on NsbI restriction enzyme-mediated strand displacement amplification (NsbI-SDA) and four-way DNA junction for the first time. In this biosensor, the NsbI restriction enzyme combined with strand displacement amplification (SDA) was able to specifically distinguish PIK3CA^H1047R gene mutation and increase the number of DNA copies to improve electrochemical response. In the presence of target mutation gene, DNA fragments produced by the cleavage event of NsbI restriction enzyme could trigger the SDA reaction to generate massive linker chains. When the linker chains were captured on the electrode, the four-way DNA junction was then attached at the end of linker chain. By integrating electroactive molecules of methylene blue (MB) into four-way DNA junction, this sandwich-like electrochemical biosensor was able to determine the specific distinction of target mutation gene with a low detection limit of 0.001%. Finally, this strategy could be used to analyze mutation gene spiked into human serum samples, indicating the potential application in genetic analysis and clinical disease diagnosis.

A gold-selenium-bonded nanoprobe for real-time in situ imaging of the upstream and downstream relationship between uPA and MMP-9 in cancer cells

A novel Au-Se nanoprobe with remarkable anti-interference ability for glutathione was developed for real-time in situ monitoring of the upstream and downstream regulatory relationship between uPA and MMP-9 proteins in the pathway.

Ultrasensitive Biosensor for Detection of Mercury(II) Ions Based on DNA-Cu Nanoclusters and Exonuclease III-assisted Signal Amplification

This paper describes a novel method for label-free mercury(II) ion detection based on exonuclease III-induced target signal recycling amplification using double-stranded DNA templated copper nanoclusters. The synthesized DNA-Cu nanoclusters were used with exonuclease III loop amplification technology for ultra-high sensitivity detection of mercury(II) ions, which were detected by significantly decreased fluorescence intensity. Under the optimal experimental conditions, there was a clear linear relationship between Hg²⁺ concentration in the range of 0.04 to 8 nM and fluorescence intensity. The detection limit for Hg²⁺ was 4 pM. In addition, the interference of other metal ions on the mercury(II) ion detection was also studied. To confirm the application of the fluorescent sensor, it was applied to determine the concentrations of mercury(II) ions in tap water, and the results showed that the method can be used to detect mercury(II) ions in water samples successfully.

Enhancement of mitochondrial ROS accumulation and radiotherapeutic efficacy using a Gd-doped titania nanosensitizer

Radiotherapy is an extensively used treatment modality in the clinic and can kill malignant cells by generating cytotoxic reactive oxygen species (ROS). Unfortunately, excessive dosages of radiation are typically required because only a small proportion of the radiative energy is adsorbed by the soft tissues of a tumor, which results in the nonselective killing of normal cells and severe systemic side effects. An efficient nanosensitizer that makes cancer cells more sensitive to radiotherapy under a relatively low radiation dose would be highly desirable.

Methods: In this study, we developed a Gd-doped titania nanosensitizer that targets mitochondria to achieve efficient radiotherapy. Upon X-ray irradiation, the nanosensitizer triggers a “domino effect” of ROS accumulation in mitochondria. This overabundance of ROS leads to mitochondrial permeability transition and ultimately irreversible cell apoptosis. Confocal laser imaging, western blotting and flow cytometry analysis were used to explore the biological process of intrinsic apoptosis induced by the nanosensitizer. Clonogenic survival assay, cell migration and invasion experiments were employed to evaluate the radiosensitizing effect of the nanosensitizer in vitro. Finally, to evaluate the therapeutic outcome of the nanosensitizer in vivo, MCF-7 tumor model was used.

Results: Confocal laser images and western blotting data demonstrated that the nanosensitizer in conjunction with X-ray irradiation could induce cell apoptosis in ROS-mediated apoptotic signal pathways. A clonogenic survival assay revealed that cells treated with the prepared nanosensitizer exhibited a lower number of viable cell colonies than that of the nontargeted group under X-ray irradiation. Notably, with only a single dose of radiotherapy, the mitochondria-targeted nanosensitizer elicited the complete ablation of tumors in a mouse model.

Conclusion: The designed nanosensitizer in combination with X-ray radiation exposure could be used for radiotherapy against cancer in living cells and in vivo. Moreover, the nanosensitizer with mitochondria targeting played a pivotal role in triggering a “domino effect” of ROS and cell apoptosis. The current strategy could provide new opportunities in designing efficient radiosensitizers for future cancer therapy.

FRET investigation toward DNA tetrahedron-based ratiometric analysis of intracellular telomerase activity

Ratiometric sensing of telomerase activity is realized at a single-cell level based on a novel DNA nanoprobe reconciling an extension primer, a DNA tetrahedron and a flare probe.

Chimeric DNA-Functionalized Titanium Carbide MXenes for Simultaneous Mapping of Dual Cancer Biomarkers in Living Cells

Acquiring multilayer information on diverse biomarkers with different spatial distributions at the cellular level is crucial for monitoring the progression of cancers. Herein, a dual-signal-tagged chimeric DNA-functionalized titanium carbide MXenes nanoprobe (dcDNA-Ti₃C₂) that responds to biomarkers with different cellular locations from plasma membrane to cytoplasm was designed toward this end. In the presence of cancer biomarkers, including transmembrane glycoprotein mucin 1 (MUC1) and cytoplasmic microRNA-21 (miR-21), the recognition between MUC1 and its aptamer in the dcDNA-Ti₃C₂ probe induces the separation of TAMRA-MUC1 aptamer from Ti₃C₂ MXenes, thereby resulting in an increase in red fluorescence; and the hybridization of miR-21 with the hairpin probe triggers the increase of green fluorescence. As a result, dual analysis of MUC1 and miR-21 at low-nanomolar concentrations in vitro, as well as in situ simultaneous imaging of the biomarkers within MCF-7 breast cancer cells, was achieved. The feasibility of the nanoprobe was further demonstrated by monitoring the expression changes of both the biomarkers in cancer cells under different inhibitor combinations. Therefore, this strategy allows us to acquire the expression levels and spatial distributions of different biomarkers in living cells, providing a helpful tool for reliable diagnosis of cancers and basic understanding their progression.

Overview of DNA Self-Assembling: Progresses in Biomedical Applications

Molecular self-assembling is ubiquitous in nature providing structural and functional machinery for the cells. In recent decades, material science has been inspired by the nature's assembly principles to create artificially higher-order structures customized with therapeutic and targeting molecules, organic and inorganic fluorescent probes that have opened new perspectives for biomedical applications. Among these novel man-made materials, DNA nanostructures hold great promise for the modular assembly of biocompatible molecules at the nanoscale of multiple shapes and sizes, designed via molecular programming languages. Herein, we summarize the recent advances made in the designing of DNA nanostructures with special emphasis on their application in biomedical research as imaging and diagnostic platforms, drug, gene, and protein vehicles, as well as theranostic agents that are meant to operate in-cell and in-vivo.

"Trojan Horse" DNA Nanostructure for Personalized Theranostics: Can It Knock on the Door of Preclinical Practice?

Nanotheranostics, combing diagnostic and therapeutic components in an all-in-one nanomaterial, possess exciting potentials for precision nanomedicine. However, a major obstacle for current nanotheranostics to enter preclinical and/or clinical trials is the intrinsic toxicities of these nanomaterials. As an emerging biomaterial, the bioinspired DNA nanostructure shows advantages for constructing better nanotheranostics due to its excellent features, including native biocompatibility, full programmability, and ready accessibility. In this feature article, we highlight recent advances in the design of DNA-nanostructure-based diagnostics and/or therapeutics capable of specifically responding to biological stimuli in a dynamic way, with a particular focus on the design mechanism, responsive performance, and potential for preclinical and/or clinical trials in personalized theranostics.

Highly Efficient Target Recycling-Based Netlike Y-DNA for Regulation of Electrocatalysis toward Methylene Blue for Sensitive DNA Detection

In this work, the highly efficient target recycling-based netlike Y-shaped DNA (Y-DNA), which regulated the electrocatalysis of Fe₃O₄@CeO₂-Pt nanoparticles (Fe₃O₄@CeO₂-PtNPs) toward methylene blue (MB) for signal amplification, was developed to prepare a sensitive DNA biosensor for detecting the DNA associated with oral cancer. Specifically, with the help of highly efficient enzyme-assisted target recycling (EATR) amplification strategy, one target DNA input was converted to corresponding plenty of DNA strands S1-Fe₃O₄@CeO₂-Pt and S2-MB output, which could be employed to interact with HP2 immobilized on the electrode surface to form stable netlike Y-DNA without any waste of recycling products. Meanwhile, the formation of netlike Y-DNA could regulate electrocatalytic efficiency of Fe₃O₄@CeO₂-PtNPs, inducing the proximity of Fe₃O₄@CeO₂-PtNPs to MB and significantly enhancing electrochemical signal. Further, the signal could also be amplified by Fe₃O₄@CeO₂-PtNPs modified on the electrode surface. By virtue of this ingenious design, a novel netlike Y-DNA structure based on highly efficient EATR was simply constructed and successfully applied to an electrochemical DNA biosensor along with electrocatalysis of Fe₃O₄@CeO₂-PtNPs, achieving the sensitive detection of target DNA ranging from 10 fM to 50 nM with a detection limit of 3.5 fM. Impressively, the biosensor here demonstrates an admirable method for regulating the electrocatalysis of NPs toward substrates to enhance signal, and we believe that this biosensor is a potential candidate for the sensitive detection of target DNA or other disease-related nucleic acids.

Framework-Nucleic-Acid-Enabled Biosensor Development

Nucleic acids have been actively exploited to develop various exquisite nanostructures due to their unparalleled programmability. Especially, framework nucleic acids (FNAs) with tailorable functionality and precise addressability hold great promise for biomedical applications. In this review, we summarize recent progress of FNA-enabled biosensing in homogeneous solutions, on heterogeneous surfaces, and inside cells. We describe the strategies to translate the structural order and rigidity of FNAs to interfacial engineering with high controllability, and approaches to realize multiplexing for highly parallel in vitro detection. We also envision the marriage of the currently available FNA tool sets with other emerging technologies to develop a new generation of biosensors for precision diagnosis and bioimaging.

Collapse of DNA Tetrahedron Nanostructure for "Off-On" Fluorescence Detection of DNA Methyltransferase Activity

As a potential detection technique, highly rigid and versatile functionality of DNA tetrahedron nanostructures is often used in biosensing systems. In this work, a novel multifunctional nanostructure has been developed as an "off-on" fluorescent probe for detection of target methyltransferase by integrating the elements of DNA tetrahedron, target recognition, and dual-labeled reporter. This sensing system is initially in an "OFF" state owing to the close proximity of fluorophores and quenchers. After the substrate is recognized by target methyltransferase, the DNA tetrahedron can be methylated to produce methylated DNA sites. These sites can be recognized and cut by the restriction endonuclease DpnI to bring about the collapse of the DNA tetrahedron, which leads to the separation of the dual-labeled reporters from the quenchers, and thus the recovery of fluorescence signal to produce an "ON" state. The proposed DNA tetrahedron-based sensing method can detect Dam methyltransferase in the range of 0.1-90 U mL^-1 with a detection limit of 0.045 U mL^-1 and shows good specificity and reproducibility for detection of Dam methyltransferase in a real sample. It has been successfully applied for screening various methylation inhibitors. Thus, this work possesses a promising prospect for detection of DNA methyltransfrase in the field of clinical diagnostics.

Fluorescence Resonance Energy Transfer-Based DNA Nanoprism with a Split Aptamer for Adenosine Triphosphate Sensing in Living Cells

We have developed a DNA nanoprobe for adenosine triphosphate (ATP) sensing in living cells, based on the split aptamer and the DNA triangular prism (TP). In which nucleic acid aptamer was split into two fragments, the stem of the split aptamer was respectively labeled donor and acceptor fluorophores that underwent a fluorescence resonance energy transfer if two ATP molecules were bound as target molecule to the recognition module. Hence, ATP as a target induced the self-assembly of split aptamer fragments and thereby brought the dual fluorophores into close proximity for high fluorescence resonance energy transfer (FRET) efficiency. In the in vitro assay, an almost 5-fold increase in F_A/F_D signal was observed, the fluorescence emission ratio was found to be linear with the concentration of ATP in the range of 0.03-2 mM, and the nanoprobe was highly selective toward ATP. For the strong protecting capability to nucleic acids from enzymatic cleavage and the excellent biocompatibility of the TP, the DNA TP nanoprobe exhibited high cellular permeability, fast response, and successfully realized "FRET-off" to "FRET-on" sensing of ATP in living cells. Moreover, the intracellular imaging experiments indicated that the DNA TP nanoprobe could effectively detect ATP and distinguish among changes of ATP levels in living cells. More importantly, using of the split aptamer and the FRET-off to FRET-on sensing mechanism could efficiently avoid false-positive signals. This design provided a strategy to develop biosensors based on the DNA nanostructures for intracellular molecules analysis.

DNA tetrahedron nanostructures for biological applications: biosensors and drug delivery

Herein, we review and summarise the development and biological applications of DNA tetrahedron, including cellular biosensors and drug delivery systems.

Tuning of resonance energy transfer from 4′,6-diamidino-2-phenylindole to an ultrasmall silver nanocluster across the lipid bilayer

Liposome mediated efficient tuning of FRET between photoexcited 4′,6-diamidino-2-phenylindole (DAPI) and an ultrasmall silver nanocluster (Ag NC) has been demonstrated using steady-state and time-resolved fluorescence spectroscopy.