A Telomerase-Responsive DNA Icosahedron for Precise Delivery of Platinum Nanodrugs to Cisplatin-Resistant Cancer

Recent advances in the applications of DNA frameworks in liquid biopsy: A review

Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.

Targeting Telomere Dynamics as an Effective Approach for the Development of Cancer Therapeutics

Telomere is a protective structure located at the end of chromosomes of eukaryotes, involved in maintaining the integrity and stability of the genome. Telomeres play an essential role in cancer progression; accordingly, targeting telomere dynamics emerges as an effective approach for the development of cancer therapeutics. Targeting telomere dynamics may work through multifaceted molecular mechanisms; those include the activation of anti-telomerase immune responses, shortening of telomere lengths, induction of telomere dysfunction and constitution of telomerase-responsive drug release systems. In this review, we summarize a wide variety of telomere dynamics-targeted agents in preclinical studies and clinical trials, and reveal their promising therapeutic potential in cancer therapy. As shown, telomere dynamics-active agents are effective as anti-cancer chemotherapeutics and immunotherapeutics. Notably, these agents may display efficacy against cancer stem cells, reducing cancer stem levels. Furthermore, these agents can be integrated with the capability of tumor-specific drug delivery by the constitution of related nanoparticles, antibody drug conjugates and HSA-based drugs.

Construction of Smart DNA-Based Drug Delivery Systems for Cancer Therapy

Due to the disadvantages of poor targeting, slow action, and low effectiveness of current commonly used cancer treatments, including surgery, chemotherapy, and radiotherapy, researchers have turned to DNA as a biomaterial for constructing drug delivery nanocarriers. DNA is favored for its biocompatibility and programmability. In order to overcome the limitations associated with traditional drug delivery systems (DDSs), researchers have developed smart-responsive DNA DDSs that can control drug release in response to specific physical or chemical stimuli at targeted sites. In this review, a summary of multiple targeted ligand structures is provided, various shapes of stable DNA nanomaterials, and different stimuli-responsive drug release strategies in DNA DDSs. Specifically, targeted cell recognition, in vivo stable transport, and controlled drug release of smart DDSs are focused. Finally, the further development prospects and challenges of clinical application of DNA nanomaterials in the field of smart drug delivery are discussed. The objective of this review is to enhance researchers' comprehension regarding the potential application of DNA nanomaterials in precision drug delivery, with the aim of expediting the clinical implementation of intelligent DDSs.

Telomerase-Mediated Self-Assembly of DNA Network in Cancer Cells Enabling Mitochondrial Interference

The precise control of the artificially induced reactions inside living cells is emerging as an effective strategy for the regulation of cell functions. Nevertheless, the manipulation of the assembly of exogenous molecules into artificial architectures in response to intracellular-specific signals remains a grand challenge. Herein, we achieve the precise self-assembly of deoxyribonucleic acid (DNA) network inside cancer cells, specifically responding to telomerase, and realize effective mitochondrial interference and the consequent regulation of cellular behaviors. Two functional DNA modules were designed: a mitochondria-targeting branched DNA and a telomerase-responsive linear DNA. Upon uptake by cancer cells, the telomerase primer in linear DNA responded to telomerase, and a strand displacement reaction was triggered by the reverse transcription of telomerase, thus releasing a linker DNA from the linear DNA. The linker DNA afterward hybridized with the branched DNA to form a DNA network on mitochondria. The DNA network interfered with the function of mitochondria, realizing the apoptosis of cancer cells. This system was further administered in a nude mouse tumor model, showing remarkable suppression of tumor growth. We envision that the telomerase-mediated intracellular self-assembly of the DNA network provides a promising route for cancer therapy.

Intracellular spatiotemporal metabolism in connection to target engagement

The metabolism in eukaryotic cells is a highly ordered system involving various cellular compartments, which fluctuates based on physiological rhythms. Organelles, as the smallest independent sub-cell unit, are important contributors to cell metabolism and drug metabolism, collectively designated intracellular metabolism. However, disruption of intracellular spatiotemporal metabolism can lead to disease development and progression, as well as drug treatment interference. In this review, we systematically discuss spatiotemporal metabolism in cells and cell subpopulations. In particular, we focused on metabolism compartmentalization and physiological rhythms, including the variation and regulation of metabolic enzymes, metabolic pathways, and metabolites. Additionally, the intricate relationship among intracellular spatiotemporal metabolism, metabolism-related diseases, and drug therapy/toxicity has been discussed. Finally, approaches and strategies for intracellular spatiotemporal metabolism analysis and potential target identification are introduced, along with examples of potential new drug design based on this.

Molecularly or atomically precise nanostructures for bio-applications: how far have we come?

A huge variety of nanostructures are promising for biomedical applications, but only a few have been practically applied. Among the various reasons, the limited structural preciseness is a critical one, as it increases the difficulty in product quality control, accurate dosing, and ensuring the repeatability of material performance. Constructing nanoparticles with molecule-like preciseness is becoming a new research field. In this review, we focus on the artificial nanomaterials that can currently be molecularly or atomically precise, including DNA nanostructures, some metallic nanoclusters, dendrimer nanoparticles and carbon nanostructures, describing their syntheses, bio-applications and limitations, in view of up-to-date studies. A perspective on their potential for clinical translation is also given. This review is expected to provide a particular rationale for the future design of nanomedicines.

Advanced applications of DNA nanostructures dominated by DNA origami in antitumor drug delivery

DNA origami is a cutting-edge DNA self-assembly technique that neatly folds DNA strands and creates specific structures based on the complementary base pairing principle. These innovative DNA origami nanostructures provide numerous benefits, including lower biotoxicity, increased stability, and superior adaptability, making them an excellent choice for transporting anti-tumor agents. Furthermore, they can considerably reduce side effects and improve therapy success by offering precise, targeted, and multifunctional drug delivery system. This comprehensive review looks into the principles and design strategies of DNA origami, providing valuable insights into this technology's latest research achievements and development trends in the field of anti-tumor drug delivery. Additionally, we review the key function and major benefits of DNA origami in cancer treatment, some of these approaches also involve aspects related to DNA tetrahedra, aiming to provide novel ideas and effective solutions to address drug delivery challenges in cancer therapy.

Reversing immune evasion using a DNA nano-orchestrator for pancreatic cancer immunotherapy

Immune evasion caused by the paucity of MHCI is a prominent characteristic of pancreatic adenocarcinoma (PAAD), which is thought to underlie dysfunctional even absent adaptive T cell immunity and is responsible for ineffective immunotherapy. Here, we report a ROS-responsive DNA nano-orchestrator to cascade reverse MHC I-associated immune evasion and boost anti-tumor T cell stimulation, stimulating the activation of tumoricidal immunity against PAAD. Chloroquine phosphate (CQP) as an autophagy inhibitor was first encapsulated with ferritin, and via DNA modular self-assembly technology, the generated ferritin nanocores (FNC) were then caged into ROS-responsive CpG-DNA nanoframe. After systemic injection, the FNC-laden DNA nanoframe (FNC@NF) was passively enriched in tumor tissues in which the DNA nanoframe was cleaved upon the ROS stimulation. Oligodeoxynucleotide (ODN) with CpG motifs was detached and functioned as a TLR9 agonist. The liberated FNC was then endocytosed in an actively targeted manner by binding to transferrin receptor 1. In the lysosome, CQP was burst released from FNC due to acid-triggering. Through CQP-mediated autophagy abrogation, MHC-I molecules were preserved. We demonstrated that cascade inhibiting autophagy and boosting TLR9 stimulation via our proposed DNA-based hybrid nanosystem restored MHC I on the tumor cell surface and reshaped the antigen presentation of DCs, and ultimately reversed immune evasion and synergistically reinforced the activation of cytotoxic T cells against PAAD cells. In sum, our work provides an alternative strategy for cascade reversing immune evasion and boosting anti-tumor T cell stimulation and holds great potential for pancreatic cancer immunotherapy. STATEMENT OF SIGNIFICANCE: A DNA nano-orchestrator was created by sequentially assembling chloroquine phosphate-laden ferritin nanocores with ROS-responsive CpG-DNA nanoframe. Through cascade inhibiting autophagy and boosting TLR9 stimulation, the nano-orchestrator efficiently reversed MHC I-associated immune evasion and augmented anti-tumor T cell stimulation, which ultimately activated tumoricidal immunity against pancreatic adenocarcinoma.

DNA framework-engineered chimeras platform enables selectively targeted protein degradation

A challenge in developing proteolysis targeting chimeras (PROTACs) is the establishment of a universal platform applicable in multiple scenarios for precise degradation of proteins of interest (POIs). Inspired by the addressability, programmability, and rigidity of DNA frameworks, we develop covalent DNA framework-based PROTACs (DbTACs), which can be synthesized in high-throughput via facile bioorthogonal chemistry and self-assembly. DNA tetrahedra are employed as templates and the spatial position of each atom is defined. Thus, by precisely locating ligands of POI and E3 ligase on the templates, ligand spacings can be controllably manipulated from 8 Å to 57 Å. We show that DbTACs with the optimal linker length between ligands achieve higher degradation rates and enhanced binding affinity. Bispecific DbTACs (bis-DbTACs) with trivalent ligand assembly enable multi-target depletion while maintaining highly selective degradation of protein subtypes. When employing various types of warheads (small molecules, antibodies, and DNA motifs), DbTACs exhibit robust efficacy in degrading diverse targets, including protein kinases and transcription factors located in different cellular compartments. Overall, utilizing modular DNA frameworks to conjugate substrates offers a universal platform that not only provides insight into general degrader design principles but also presents a promising strategy for guiding drug discovery.

DNA Nanoclusters Combined with One-Shot Radiotherapy Augment Cancer Immunotherapy Efficiency

Immunotherapy shows immense promise for improving cancer treatment. Combining immunotherapy with radiotherapy provides a conspicuous advantage due to its enhanced abscopal effect. However, established immune tolerance mechanisms in the tumor microenvironment can hamper the generation of a sufficient abscopal effect. Herein, a type of DNA nanocluster (DNAnc) that is self-assembled by a CpG-ODNs-loaded Y-shaped double-stranded DNA vector based on the unique complementary base-pairing rules is designed. The unique structure of DNAnc makes it load more than ≈8125.5 ± 822.5 copies of CpG ODNs within one single nanostructure, which effectively increases resistance to nuclease degradation and elevates the efficiency of repolarizing macrophages to an M1-like phenotype. Mechanistic studies reveal that more DNAncs are endocytosed by macrophages in the cancer tissue and repolarized macrophages to elicit a robust abscopal effect with the accumulation of macrophages induced by radiotherapy, generating potent, long-term, and durable antitumor immunity for the inhibition of tumor metastasis and the prevention of tumor recurrence, which provides a novel strategy to boost cancer immunotherapy.

Center backbone-rigidified DNA polygonal nanostructures and bottom face-templated polyhedral pyramids with structural stability in a complex biological medium

Due to the sequence programmability, good biocompatibility, versatile functionalities and vast sequence space, DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures in one, two and three dimensions that are capable of engineering of multiple functional nucleic acids into a useful tool to implement intended tasks in biological and medical field. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging mainly because of the molecular flexibility-based uncontrollability of size and shape. In this contribution, utilizing gel electrophoretic analysis and atomic force microscopy, we demonstrate the modeling assembly technique for the construction of wireframe DNA nanostructures that can be divided into two categories: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the construction of DNA polygons and polyhedral pyramids, respectively. The highest assembly efficiency (AE) is about 100%, while the lowest AE is not less than 50%. Moreover, when adding one edge for polygons or one side face for pyramids, we only need to add one oligonucleotide strand. Especially, the advanced polygons (e.g., pentagon and hexagon) of definite shape are for the first time constructed. Along this line, introduction of cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours even if the vulnerable nicks are not sealed. The proposed modeling assembly technique represents important progress toward the development of DNA nanotechnology and is expected to promote the application of DNA nanostructures in biological and biomedical fields. STATEMENT OF SIGNIFICANCE: DNA oligonucleotides are considered to be ideal building blocks for the assembly of diverse nanostructures. However, the construction of wireframe nanostructures consisting of only a few DNA strands remains quite challenging. In this contribution, we demonstrate the modeling technique for the construction of different wireframe DNA nanostructures: rigid center backbone-guided modeling (RBM) and bottom face-templated assembly (BTA) that are responsible for the assembly of DNA polygons and polyhedral pyramids, respectively. Moreover, cross-linking strands enables the hierarchical assembly of polymer polygons and polymer pyramids. These wireframe DNA nanostructures exhibit the substantially enhanced resistance to nuclease degradation and maintain their structural integrity in fetal bovine serum for several hours, promoting the application of DNA nanostructures in biological and biomedical fields.

Self-Assembled Artificial DNA Nanocompartments and Their Bioapplications

Compartmentalization is the strategy evolved by nature to control reactions in space and time. The ability to emulate this strategy through synthetic compartmentalization systems has rapidly evolved in the past years, accompanied by an increasing understanding of the effects of spatial confinement on the thermodynamic and kinetic properties of the guest molecules. DNA nanotechnology has played a pivotal role in this scientific endeavor and is still one of the most promising approaches for the construction of nanocompartments with programmable structural features and nanometer-scaled addressability. In this review, the design approaches, bioapplications, and theoretical frameworks of self-assembled DNA nanocompartments are surveyed. From DNA polyhedral cages to virus-like capsules, the construction principles of such intriguing architectures are illustrated. Various applications of DNA nanocompartments, including their use for programmable enzyme scaffolding, single-molecule studies, biosensing, and as artificial nanofactories, ending with an ample description of DNA nanocages for biomedical purposes, are then reported. Finally, the theoretical hypotheses that make DNA nanocompartments, and nanosystems in general, a topic of great interest in modern science, are described and the progresses that have been done until now in the comprehension of the peculiar phenomena that occur within nanosized environments are summarized.

A nuclease-mimetic platinum nanozyme induces concurrent DNA platination and oxidative cleavage to overcome cancer drug resistance

Platinum (Pt) resistance in cancer almost inevitably occurs during clinical Pt-based chemotherapy. The spontaneous nucleotide-excision repair of cancer cells is a representative process that leads to Pt resistance, which involves the local DNA bending to facilitate the recruitment of nucleotide-excision repair proteins and subsequent elimination of Pt-DNA adducts. By exploiting the structural vulnerability of this process, we herein report a nuclease-mimetic Pt nanozyme that can target cancer cell nuclei and induce concurrent DNA platination and oxidative cleavage to overcome Pt drug resistance. We show that the Pt nanozyme, unlike cisplatin and conventional Pt nanoparticles, specifically induces the nanozyme-catalyzed cleavage of the formed Pt-DNA adducts by generating in situ reactive oxygen species, which impairs the damage recognition factors-induced DNA bending prerequisite for nucleotide-excision repair. The recruitment of downstream effectors of nucleotide-excision repair to DNA lesion sites, including xeroderma pigmentosum groups A and F, is disrupted by the Pt nanozyme in cisplatin-resistant cancer cells, allowing excessive accumulation of the Pt-DNA adducts for highly efficient cancer therapy. Our study highlights the potential benefits of applying enzymatic activities to the use of the Pt nanomedicines, providing a paradigm shift in DNA damaging chemotherapy.

Platinum-based drug-induced depletion of amino acids in the kidneys and liver

Cisplatin (cis-diamminedichloroplatinum II; CDDP) is a widely used cytostatic agent; however, it tends to promote kidney and liver disease, which are a major signs of drug-induced toxicity. Platinum compounds are often presented as alternative therapeutics and subsequently easily dispersed in the environment as contaminants. Due to the major roles of the liver and kidneys in removing toxic materials from the human body, we performed a comparative study of the amino acid profiles in chicken liver and kidneys before and after the application of CDDP and platinum nanoparticles (PtNPs-10 and PtNPs-40). The treatment of the liver with the selected drugs affected different amino acids; however, Leu and Arg were decreased after all treatments. The treatment of the kidneys with CDDP mostly affected Val; PtNPs-10 decreased Val, Ile and Thr; and PtNPs-40 affected only Pro. In addition, we tested the same drugs on two healthy cell lines, HaCaT and HEK-293, and ultimately explored the amino acid profiles in relation to the tricarboxylic acid cycle (TCA) and methionine cycle, which revealed that in both cell lines, there was a general increase in amino acid concentrations associated with changes in the concentrations of the metabolites of these cycles.

Delivery of DNA octahedra enhanced by focused ultrasound with microbubbles for glioma therapy

DNA nanostructures, with good biosafety, highly programmable assembly, flexible modification, and precise control, are tailored as drug carriers to deliver therapeutic agents for cancer therapy. However, they face considerable challenges regarding their delivery into the brain, mainly due to the blood-brain barrier (BBB). By controlling the acoustic parameters, focused ultrasound combined with microbubbles (FUS/MB) can temporarily, noninvasively, and reproducibly open the BBB in a localized region. We investigated the delivery outcome of pH-responsive DNA octahedra loading Epirubicin (Epr@DNA-Octa) via FUS/MB and its therapeutic efficiency in a mouse model bearing intracranial glioma xenograft. Using FUS/MB to locally disrupt the BBB or the blood-tumor barrier (BTB) and systemic administration of Epr@DNA-Octa (Epr@DNA-Octa + FUS/MB) (2 mg/kg of loaded Epr), we achieved an Epr concentration of 292.3 ± 10.1 ng/g tissue in glioma, a 4.4-fold increase compared to unsonicated animals (p < 0.001). The in vitro findings indicated that Epr released from DNA strands accumulated in lysosomes and induced enhanced cytotoxicity compared to free Epr. Further two-photon intravital imaging of spatiotemporal patterns of the DNA-Octa leakage revealed that the FUS/MB treatment enhanced DNA-Octa delivery across several physiological barriers at microscopic level, including the first extravasation across the BBB/BTB and then deep penetration into the glioma center and engulfment of DNA-Octa into the tumor cell body. Longitudinal in vivo bioluminescence imaging and histological analysis indicated that the intracranial glioma progression in nude mice treated with Epr@DNA-Octa + FUS/MB was effectively retarded compared to other groups. The beneficial effect on survival was most significant in the Epr@DNA-Octa + FUS/MB group, with a 50% increase in median survival and a 73% increase in the maximum survival compared to control animals. Our work demonstrates the potential viability of FUS/MB as an alternative strategy for glioma delivery of anticancer drugs using DNA nanostructures as the drug delivery platform for brain cancer therapy.

Reconfiguration of DNA nanostructures induced by enzymatic ligation treatment

Enzymatic ligation is a popular method in DNA nanotechnology for structural enforcement. When employed as stability switch for chosen components, ligation can be applied to induce DNA nanostructure reconfiguration. In this study, we investigate the reinforcement effect of ligation on addressable DNA nanostructures assembled entirely from short synthetic strands as the basis of structural reconfiguration. A careful calibration of ligation efficiency is performed on structures with programmable nicks. Systematic investigation using comparative agarose gel electrophoresis enables quantitative assessment of enhanced survivability with ligation treatment on a number of unique structures. The solid ligation performance sets up the foundation for the ligation-based structural reconfiguration. With the capability of switching base pairing status between permanent and transient (ON and OFF) by a simple round of enzymatic treatment, ligation induced reconfiguration can be engineered for DNA nanostructures accordingly.

Spatio-Temporal Controlled Gene-Chemo Drug Delivery in a DNA Nanocomplex to Overcome Multidrug Resistance of Cancer Cells

Multidrug resistance (MDR) in cancer cells is a substantial limitation to the success of chemotherapy. The spatio-temporal controlled gene-chemo therapeutics strategy is expected to surmount the limitation of MDR. We herein develop a DNA nanocomplex to achieve intrinsic stimuli-responsive spatio-temporal controlled gene-chemo drug delivery, overcoming MDR of cancer cells. The drug delivery system consisted of a restriction endonuclease (HhaI)-degradable DNA hydrogel layer, an acid-responsive HhaI nanocapsule (HhaI-GDA), and a glutathione (GSH)-sensitive dendritic mesoporous organosilica nanoparticle (DMON). The DNA hydrogel layer consisted of a DNA network formed through interfacial assembly from ultralong single-stranded DNA (ssDNA), which contained multiple tandem repeated antisense oligonucleotides (ASOs). DMON had dendritic mesopores for enhanced loading of anti-tumor drug doxorubicin (DOX). Upon cellular uptake of the DNA nanocomplex, the GDA shell was degraded at a lysosomal microenvironment, and the activity of HhaI was activated, leading to accurate cleavage ultralong ssDNA to release ASO as gene drugs, which down-regulated the expression of MDR-related P glycoprotein. Spatio-temporal sequentially, DMONs containing disulfide bonds responded to intracellular GSH to release DOX for enhanced chemotherapy.

Application Perspectives of Nanomedicine in Cancer Treatment

Cancer is a disease that seriously threatens human health. Based on the improvement of traditional treatment methods and the development of new treatment modes, the pattern of cancer treatment is constantly being optimized. Nanomedicine plays an important role in these evolving tumor treatment modalities. In this article, we outline the applications of nanomedicine in three important tumor-related fields: chemotherapy, gene therapy, and immunotherapy. According to the current common problems, such as poor targeting of first-line chemotherapy drugs, easy destruction of nucleic acid drugs, and common immune-related adverse events in immunotherapy, we discuss how nanomedicine can be combined with these treatment modalities, provide typical examples, and summarize the advantages brought by the application of nanomedicine.

Simultaneous Imaging of Dual microRNAs in Cancer Cells through Catalytic Hairpin Assembly on a DNA Tetrahedron

Accurate detection and imaging of tumor-related microRNA (miRNA) in living cells hold great promise for early cancer diagnosis and prognosis. One of the challenges is to develop methods that enable the identification of multiple miRNAs simultaneously to further improve the detection accuracy. Herein, a simultaneous detection and imaging method of two miRNAs was established by using a programmable designed DNA tetrahedron nanostructure (DTN) probe that includes a nucleolin aptamer (AS1411), two miRNA capture strands, and two pairs of metastable catalytic hairpins at different vertexes. The DTN probe exhibited enhanced tumor cell recognition ability, excellent stability and biocompatibility, and fast miRNA recognition and reaction kinetics. It was found that the DTN probe could specifically enter tumor cells, in which the capture strand could hybridize with miRNAs and initiate the catalytic hairpin assembly (CHA) only when the overexpressed miR-21 and miR-155 existed simultaneously, resulting in a distinct fluorescence resonance energy transfer signal and demonstrating the feasibility of this method for tumor diagnosis.

Pharmaceutical applications of framework nucleic acids

DNA is a biological polymer that encodes and stores genetic information in all living organism. Particularly, the precise nucleobase pairing inside DNA is exploited for the self-assembling of nanostructures with defined size, shape and functionality. These DNA nanostructures are known as framework nucleic acids (FNAs) for their skeleton-like features. Recently, FNAs have been explored in various fields ranging from physics, chemistry to biology. In this review, we mainly focus on the recent progress of FNAs in a pharmaceutical perspective. We summarize the advantages and applications of FNAs for drug discovery, drug delivery and drug analysis. We further discuss the drawbacks of FNAs and provide an outlook on the pharmaceutical research direction of FNAs in the future.

Advances and prospects of dynamic DNA nanostructures in biomedical applications

With the rapid development of DNA nanotechnology, the emergence of stimulus-responsive dynamic DNA nanostructures (DDNs) has broken many limitations of static DNA nanostructures, making precise, remote, and reversible control possible. DDNs are intelligent nanostructures with certain dynamic behaviors that are capable of responding to specific stimuli. The responsible stimuli of DDNs include exogenous metal ions, light, pH, etc., as well as endogenous small molecules such as GSH, ATP, etc. Due to the excellent stimulus responsiveness and other superior physiological characteristics of DDNs, they are now widely used in biomedical fields. For example, they can be applied in the fields of biosensing and bioimaging, which are able to detect biomarkers with greater spatial and temporal precision to help disease diagnosis and live cell physiological function studies. Moreover, they are excellent intelligent carriers for drug delivery in treating cancer and other diseases, achieving controlled release of drugs. And they can promote tissue regeneration and regulate cellular behaviors. Although some challenges need further study, such as the practical value in clinical applications, DDNs have shown great potential applications in the biomedical field.

With the rapid development of DNA nanotechnology, the emergence of stimulus-responsive dynamic DNA nanostructures (DDNs) has great potential applications in the biomedical field.

Topological DNA Tetrahedron Encapsulated Gold Nanoparticle Enables Precise Ligand Engineering for Targeted Cell Imaging

Ligand-functionalized plasmonic nanoparticles have been widely used for targeted imaging in living systems. However, ligand presentation and encoding on the nanoparticle's surface in a stoichiometrically controllable manner remains a great challenge. Herein, we propose a method to construct ligand-engineered plasmonic nanoprobes by using nanoparticle encapsulation with topological DNA tetrahedrons, which enables the programmed ligand loading for precise regulation of targeting efficiency of nanoprobes in biorelated applications. With this method, we demonstrated the preparation of functionalized plasmonic nanoprobes by programmed loading of RGD peptides and aptamers onto the DNA tetrahedron encapsulated gold nanoparticles with controllable stoichiometric ratios. The cell imaging and particle counting assays suggested that the targeting efficiency of the nanoprobes could be readily modulated by tailoring the number and stoichiometric ratios of the loaded ligands, respectively. It can be anticipated that this robust strategy could provide new opportunities for the construction of efficacious nanoprobes and delivery systems for versatile bioapplications.

Insights into nucleic acid-based self-assembling nanocarriers for targeted drug delivery and controlled drug release

Over the past few decades, rapid advances of nucleic acid nanotechnology always drive the development of nanoassemblies with programmable design, powerful functionality, excellent biocompatibility and outstanding biosafety. Nowadays, nucleic acid-based self-assembling nanocarriers (NASNs) play an increasingly greater role in the research and development in biomedical studies, particularly in drug delivery, release and targeting. In this review, NASNs are systematically summarized the strategies cooperated with their broad applications in drug delivery. We first discuss the self-assembling methods of nanocarriers comprised of DNA, RNA and composite materials, and summarize various categories of targeting media, including aptamers, small molecule ligands and proteins. Furthermore, drug release strategies by smart-responding multiple kinds of stimuli are explained, and various applications of NASNs in drug delivery are discussed, including protein drugs, nucleic acid drugs, small molecule drugs and nanodrugs. Lastly, we propose limitations and potential of NASNs in the future development, and expect that NASNs enable facilitate the development of new-generation drug vectors to assist in solving the growing demands on disease diagnosis and therapy or other biomedicine-related applications in the real world.

DNA Nanodevice-Based Drug Delivery Systems

DNA, a natural biological material, has become an ideal choice for biomedical applications, mainly owing to its good biocompatibility, ease of synthesis, modifiability, and especially programmability. In recent years, with the deepening of the understanding of the physical and chemical properties of DNA and the continuous advancement of DNA synthesis and modification technology, the biomedical applications based on DNA materials have been upgraded to version 2.0: through elaborate design and fabrication of smart-responsive DNA nanodevices, they can respond to external or internal physical or chemical stimuli so as to smartly perform certain specific functions. For tumor treatment, this advancement provides a new way to solve the problems of precise targeting, controllable release, and controllable elimination of drugs to a certain extent. Here, we review the progress of related fields over the past decade, and provide prospects for possible future development directions.

Oxidative Cleavage-Based Three-Dimensional DNA Biosensor for Ratiometric Detection of Hypochlorous Acid and Myeloperoxidase

Methods to detect and quantify disease biomarkers with high specificity and sensitivity in biological fluids play a key role in enabling clinical diagnosis, including point-of-care testing. Myeloperoxidase (MPO) is an emerging biomarker for the detection of inflammation, neurodegenerative diseases, and cardiovascular disease, where excess MPO can lead to oxidative damage to biomolecules in homeostatic systems. While numerous methods have been developed for MPO analysis, most techniques are challenging in clinical applications due to the lack of amplification methods, high cost, or other practical drawbacks. Enzyme-linked immunosorbent assays are currently used for the quantification of MPO in clinical practice, which is often limited by the availability of antibodies with high affinity and specificity and the significant nonspecific binding of antibodies to the analytical surface. In contrast, nucleic acid-based biosensors are of interest because of their simplicity, fast response time, low cost, high sensitivity, and low background signal, but detection targets are limited to nucleic acids and non-nucleic acid biomarkers are rare. Recent studies reveal that the modification of a genome in the form of phosphorothioate is specifically sensitive to the oxidative effects of the MPO/H₂O₂/Cl^- system. We developed an oxidative cleavage-based three-dimensional DNA biosensor for rapid, ratiometric detection of HOCl and MPO in a "one-pot" method, which is simple, stable, sensitive, specific, and time-saving and does not require a complex reaction process, such as PCR and enzyme involvement. The constructed biosensor has also been successfully used for MPO detection in complex samples. This strategy is therefore of great value in disease diagnosis and biomedical research.

Multimodules integrated functional DNA nanomaterials for intelligent drug delivery

Deoxyribonucleic acid (DNA) has been an emerging building block to construct functional biomaterials. Due to their programmable sequences and rich responsiveness, DNA has attracted rising attention in the construction of intelligent nanomaterials with predicable nanostructure and adjustable functions, which has shown great potential in drug delivery. On the one hand, the DNA sequences with molecule recognition, responsiveness, and therapeutic efficacy can be easily integrated to the framework of DNA nanomaterials by sequence designing; on the other hand, the rich chemical groups on DNA molecules provide binding points for other functional units. In this review, we divided the functionalization modules in the construction of DNA nanomaterials into three types, including targeting modules, responsive modules, and therapeutic modules. Based on these modules, five DNA kinds of representative nanomaterials applied in drug delivery were introduced, including DNA nanogel, DNA origami, DNA framework, DNA nanoflower, and DNA hybrid nanosphere. Finally, we discussed the challenges in the transition of DNA materials to clinical applications. We expect that this review can help readers to obtain a deeper understanding of DNA materials, and further promote the development of these intelligent materials to real world's application. This article is categorized under: Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology.

DNA Nanotechnology-Based Biosensors and Therapeutics

Over the past few decades, DNA nanotechnology engenders a vast variety of programmable nanostructures utilizing Watson-Crick base pairing. Due to their precise engineering, unprecedented programmability, and intrinsic biocompatibility, DNA nanostructures cannot only interact with small molecules, nucleic acids, proteins, viruses, and cancer cells, but also can serve as nanocarriers to deliver different therapeutic agents. Such addressability innate to DNA nanostructures enables their use in various fields of biomedical applications such as biosensors and cancer therapy. This review is begun with a brief introduction of the development of DNA nanotechnology, followed by a summary of recent applications of DNA nanostructures in biosensors and therapeutics. Finally, challenges and opportunities for practical applications of DNA nanotechnology are discussed.

Triple-Layered Metal-Organic Framework Hybrid for Tandem Response-Driven Enhanced Chemotherapy

The precise release of drugs is essential to improve cancer therapeutic efficacy. In this work, a tandem responsive strategy was developed based on a triple-layered metal-organic framework (MOF) hybrid. The MOF nanoprobe was stepwise fabricated with a telomerase-responsive inner, a pH-sensitive MOF filling and H₂ O₂ -responsive coordination complex shell of Fe³⁺ and eigallocatechin gallate (EGCG). In the tumor microenvironment, the shell was dissociated by endogenous H₂ O₂ and simultaneously produced highly reactive hydroxyl radicals by a Fenton reaction. Meanwhile, the released EGCG could downregulate the expression of P-glycoprotein responsible for drug resistance. After the dissociation of the framework by protons, telomerase could trigger the release of the drug from the DNA duplex on the exposed inner shell. By integrating confined drug release, inhibited efflux pump and chemodynamic therapy, the all-in-one chemotherapy strategy was identified with enhanced therapeutic efficacy in drug-resistant cancer cells.

Tetrahedral DNA Nanostructures Inhibit Ferroptosis and Apoptosis in Cisplatin-induced Renal Injury

Acute kidney injury (AKI) is the most serious adverse reaction during cisplatin chemotherapy, which limits the drug's clinical effects. Therefore, effective strategies for protective therapy need to be developed. In the current study, we verified that tetrahedral DNA nanostructures (TDNs), promising DNA nano biomaterials, played protective roles against cisplatin-induced death of renal tubular cells. Herein, we observed that TDNs decreased the generation of lipid reactive oxygen species (ROS), restored the down-regulation of glutathione peroxidase 4 (GPX4), and hence inhibited ferroptosis induced by RSL3, a typical inducer of ferroptosis. In addition, we proved that TDNs attenuated cisplatin-induced ferroptosis by reversing the down-regulation of GPX4 and attenuated apoptosis induced by cisplatin via reducing the cleavage of poly(ADP-ribose) polymerase (PARP). Taking this all into account, our investigation suggested the potential of TDNs for cisplatin-induced AKI therapy.

Nucleic acid-driven aggregation-induced emission of Au nanoclusters for visualizing telomerase activity in living cells and in vivo

Visual monitoring of telomerase activity in living cancer cells and in vivo is essential for clinical diagnosis and treatment. However, most detection methods were performed in vitro due to the difficulty of probes entering cells and the interferences from complex biological environments. Herein, we developed a novel probe based on Au nanoclusters (AuNCs) with a nucleic acid-driven aggregation-induced emission (AIE) property for the first time. The probe was applied for detection of telomerase with high sensitivity. Importantly, the probe could achieve telomerase imaging in living cells and in solid tumor tissue in vivo. The study provided a specific connection fashion of metal nanoclusters for AIE generation. It holds great potential for the development of AIE-active metal nanoclusters as a diagnostic tool for disease detection in vitro as well as in vivo.

DNA nanostructure-based nucleic acid probes: construction and biological applications

In recent years, DNA has been widely noted as a kind of material that can be used to construct building blocks for biosensing, in vivo imaging, drug development, and disease therapy because of its advantages of good biocompatibility and programmable properties. However, traditional DNA-based sensing processes are mostly achieved by random diffusion of free DNA probes, which were restricted by limited dynamics and relatively low efficiency. Moreover, in the application of biosystems, single-stranded DNA probes face challenges such as being difficult to internalize into cells and being easily decomposed in the cellular microenvironment. To overcome the above limitations, DNA nanostructure-based probes have attracted intense attention. This kind of probe showed a series of advantages compared to the conventional ones, including increased biostability, enhanced cell internalization efficiency, accelerated reaction rate, and amplified signal output, and thus improved in vitro and in vivo applications. Therefore, reviewing and summarizing the important roles of DNA nanostructures in improving biosensor design is very necessary for the development of DNA nanotechnology and its applications in biology and pharmacology. In this perspective, DNA nanostructure-based probes are reviewed and summarized from several aspects: probe classification according to the dimensions of DNA nanostructures (one, two, and three-dimensional nanostructures), the common connection modes between nucleic acid probes and DNA nanostructures, and the most important advantages of DNA self-assembled nanostructures in the applications of biosensing, imaging analysis, cell assembly, cell capture, and theranostics. Finally, the challenges and prospects for the future development of DNA nanostructure-based nucleic acid probes are also discussed.

A stepwise recognition strategy for the detection of telomerase activity via direct electrochemical analysis of metal-organic frameworks

The detection of telomerase is of great significance for monitoring cell canceration. The conventional methods depend on the extension of telomerase towards its primer to conduct signal transduction. Herein, a specific and reliable detection strategy based on stepwise recognition was developed for tandem detection of metal ions and enzymes. We first synthesized an electrically active metal-organic framework (MIL-101(Fe)), which can act directly as a signal reporter in phosphate buffered saline after being modified with capture DNA (cDNA). When the zinc ion is added as a coenzyme factor, the modified hairpin DNA on the electrode is cleaved by DNAzyme to yield the activated primer. After the addition of telomerase, the cleaved DNA strand would be extended, and the resulting sequence will be hybridized with the signal label of MIL-101(Fe)-cDNA. Therefore, a signal-on strategy for the detection of telomerase was achieved based on the direct electrochemical analysis of MIL-101(Fe). Moreover, this electrochemical biosensor can discriminate telomerase activity among different cell lines. The stepwise recognition ensured the advantages of an electrochemical biosensor such as high sensitivity and specificity during the detection process, providing a novel method for monitoring and diagnosis of diseases.

DNA Transformations for Diagnosis and Therapy

Due to its unique physical and chemical characteristics, DNA, which is known only as genetic information, has been identified and utilized as a new material at an astonishing rate. The role of DNA has increased dramatically with the advent of various DNA derivatives such as DNA-RNA, DNA-metal hybrids, and PNA, which can be organized into 2D or 3D structures by exploiting their complementary recognition. Due to its intrinsic biocompatibility, self-assembly, tunable immunogenicity, structural programmability, long stability, and electron-rich nature, DNA has generated major interest in electronic and catalytic applications. Based on its advantages, DNA and its derivatives are utilized in several fields where the traditional methodologies are ineffective. Here, the present challenges and opportunities of DNA transformations are demonstrated, especially in biomedical applications that include diagnosis and therapy. Natural DNAs previously utilized and transformed into patterns are not found in nature due to lack of multiplexing, resulting in low sensitivity and high error frequency in multi-targeted therapeutics. More recently, new platforms have advanced the diagnostic ability and therapeutic efficacy of DNA in biomedicine. There is confidence that DNA will play a strong role in next-generation clinical technology and can be used in multifaceted applications.

Nucleolin-Targeted DNA Nanotube for Precise Cancer Therapy through Förster Resonance Energy Transfer-Indicated Telomerase Responsiveness

Precise drug delivery holds great promise in cancer treatment but still faces challenges in controllable drug release in tumor cells specifically. Herein, a nucleolin-targeted and telomerase-responsive DNA nanotube for drug release was developed. First, a DNA nanosheet with four capture strands on its surface was prepared, which could bind and load ricin A chain (RTA). The RTA-loaded nanosheet was further converted into a DNA nanotube with a high Förster resonance energy transfer (FRET) efficiency in the presence of a Cy3-modified DNA fastener by hybridizing with the Cy5-modified DNA and another DNA-containing telomerase primer sequence along the long sides. Moreover, the aptamer of nucleolin was assembled on the DNA nanotube by combining with the hybrid chain at the terminal. The aptamer-functionalized and RTA-loaded DNA nanotube displayed enhanced tumor permeability and precise drug release in response to the telomerase in tumor cells, following the change of the FRET signal and RTA-induced cell death. Moreover, the DNA nanotube was applied successfully in vivo, and there was an obvious inhibition of tumor growth on xenograft-bearing mice following systemic administration, indicating that the constructed DNA nanotube represents a promising platform for precise RTA delivery in target cancer therapy.

Chemotherapeutic drug-DNA hybrid nanostructures for anti-tumor therapy

Compared to traditional drug delivery systems, DNA nanostructure-based drug delivery systems have several advantages including programmable sequences, precise size and shape, high drug payloads, excellent biocompatibility and biodegradability. To date, a wide range of chemotherapeutic drug-DNA hybrid nanostructures have been developed for anti-tumor therapy. In this review, the constructions of various DNA nanostructures for anticancer drug delivery are firstly summarized. Next, the anticancer drug loading methods for DNA nanostructures are presented. Then, the recent applications of chemotherapeutic drug-DNA hybrid nanostructures for drug delivery are highlighted. In the end, the challenges and opportunities of the chemotherapeutic drug-DNA hybrid nanostructure-based delivery system are discussed. The designs of drug-DNA hybrid systems, including the constructions of nanostructures and the strategies for drug loading, largely influence the efficiency of drug delivery. Recent studies have focused on the development of novel drug-DNA hybrid systems to acquire more precise and efficient therapy for various diseases. A systematic review of the design strategies of chemotherapeutic drug-DNA hybrid nanostructures will benefit the innovation and development of the chemotherapeutic drug-based chemotherapy in clinics.

Molecular micromanagement: DNA nanotechnology establishes spatio-temporal control for precision medicine

Current advances in DNA nanotechnology pinpoint exciting perspectives for the design of customized, patient-specific treatments. This advance is made possible by the exceptionally high precision and specificity that are typical for DNA base pairing on the one hand and our growing ability to harness those features in synthetic, DNA-based constructs on the other hand. Modern medicine may soon benefit from recent developments in this field, especially regarding the targeted delivery of drugs and the rational interference of synthetic DNA strands with cellular oligonucleotides. In this Review, we summarize selected examples from the area of DNA nanotechnology, where the development of precisely controlled, advanced functional mechanisms was achieved. To demonstrate the high versatility of these rationally designed structures, we categorize the dynamic DNA-based materials suggested for precision medicine according to four fundamental tasks: "hold & release," "heal," "detect & measure," as well as "guide & direct." In all the biomedical applications we highlight, DNA strands not only constitute structural building blocks but allow for creating stimuli-responsive objects, serve as an active cargo, or act as molecular control/guidance tools. Moreover, we discuss several issues that need to be considered when DNA-based structures are designed for applications in the field of precision medicine. Even though the majority of DNA-based objects have not been used in clinical settings yet, recent progress regarding the stability, specificity, and control over the dynamic behavior of synthetic DNA structures has advanced greatly. Thus, medical applications of those nanoscopic objects should be feasible in the near future.

Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems

DNA nanotechnology is a unique field that provides simple yet robust design techniques for self-assembling nanoarchitectures with extremely high potential for biomedical applications. Though the field began to exploit DNA to build various nanoscale structures, it has now taken a different path, diverging from the creation of complex structures to functional DNA nanodevices that explore various biological systems and mechanisms. Here, we present a brief overview of DNA nanotechnology, summarizing the key strategies for construction of various DNA nanodevices, with special focus on three-dimensional (3D) nanocages or polyhedras. We then discuss biological applications of 3D DNA nanocages, particularly tetrahedral DNA cages, in their ability to program and modulate cellular systems, in biosensing, and as tools for targeted therapeutics. We conclude with a final discussion on challenges and perspectives of 3D DNA nanodevices in biomedical applications.

A facile and efficient approach for hypertrophic scar therapy via DNA-based transdermal drug delivery

The transdermal drug delivery approach has been considered a potential therapy for human hypertrophic scars (HSs) instead of current uncomfortable surgical excision, local injection and laser therapy. However, a facile and efficient drug delivery method is urgently needed to overcome the skin barrier of transdermal administration. Herein, we employed a DNA-Fe nanoparticle delivery system via Fe ion driven self-assembly to satisfy the requirement of transdermal administration for HS therapy. Doxorubicin hydrochloride (DOX) as one of the widely used anticancer drugs was employed to treat the hyperplasia of abnormal skin fibrous tissue. Both in vitro and in vivo experiments of the DOX loaded DNA-Fe nanoparticles (DOX@DNA-Fe NPs) were performed to demonstrate the penetration ability, rapid drug release, and scar-inhibiting effects. This facile and efficient approach for HS therapy via a DNA-based transdermal drug delivery system may provide more possibilities for the development of transdermal administration.

Rationally Designed DNA Nanostructures for Drug Delivery

DNA is an excellent biological material that has received growing attention in the field of nanotechnology due to its unique capability for precisely engineering materials via sequence specific interactions. Self-assembled DNA nanostructures of prescribed physicochemical properties have demonstrated potent drug delivery efficiency in vitro and in vivo. By using various conjugation techniques, DNA nanostructures may be precisely integrated with a large diversity of functional moieties, such as targeting ligands, proteins, and inorganic nanoparticles, to enrich their functionalities and to enhance their performance. In this review, we start with introducing strategies on constructing DNA nanostructures. We then summarize the biological barriers ahead of drug delivery using DNA nanostructures, followed by introducing existing rational solutions to overcome these biological barriers. Lastly, we discuss challenges and opportunities for DNA nanostructures toward real applications in clinical settings.

DNA Nanostructures as Pt(IV) Prodrug Delivery Systems to Combat Chemoresistance

Cisplatin is a first-line drug in clinical cancer treatment but its efficacy is often hindered by chemoresistance in cancer cells. Reduced intracellular drug accumulation is revealed to be a major mechanism of cisplatin resistance. Nanoscale drug delivery systems could help to overcome this problem because of their more active cellular uptake and more accurate tumor localization. DNA nanostructures have emerged as promising drug delivery systems because of their intrinsic biocompatibility and structural programmability. Herein, three diverse DNA nanostructures are constructed and their potential for cisplatin prodrug delivery is investigated. Results found that these DNA nanostructures could remarkably enhance the cellular internalization of platinum drugs and thus increase the anticancer activity, not only to regular lung cancer cells (A549), but more importantly to cisplatin-resistant cancer cells (A549cisR). Further, in vivo studies also demonstrate that cisplatin prodrug loaded DNA nanostructures could effectively suppress tumor growth in both regular and cisplatin-resistant tumor models. This study suggests that DNA nanostructures are effective carriers for platinum prodrug delivery to combat chemoresistance.

Construction and Analysis of Double Helix for Triangular Bipyramid and Pentangular Bipyramid

DNA cages can be joined together to make larger 3D nanostructures on which molecular electronic circuits and tiny containers are built for drug delivery. The mathematical models for these promising nanomaterials play important roles in clarifying their assembly mechanism and understanding their structures. In this study, we propose a mathematical and computer method to construct permissible topological structures with double-helical edges for a triangular bipyramid and pentangular bipyramid. Furthermore, we remove the same topological links, without eliminating the nonrepeated ones for a triangular bipyramid and pentangular bipyramid. By analyzing characteristics of these unique links, some self-assembly and statistic rules are discussed. This study may obtain some new insights into the DNA assembly from the viewpoint of mathematics, promoting the comprehending and design efficiency of DNA polyhedra with required topological structures.

Tumor-Oriented Telomerase-Terminated Nanoplatform as Versatile Strategy for Multidrug Resistance Reversal in Cancer Treatment

Multidrug resistance is one of the major problems in chemotherapy, and exploiting impactful targets to reverse drug resistance of most tumors remains a difficult problem. In this study, the tumor-oriented nanoparticle, BIBR1532-loaded peptide dendrimeric prodrug nanoassembly (B-PDPN), is used to assist telomerase inhibition for multidrug resistance reversal. B-PDPN possesses the characteristics of an acid-activated histidine to promote cellular uptake, a redox-sensitive poly(ethylene glycol) (PEG) layer to actualize endosomal escape and telomerase inhibitor release, and an acid sensitive chemical bond to facilitate chemotherapeutic drug release. Telomerase termination weakens the protective effect of hTERT protein on mitochondria and enhances reactive oxygen species (ROS) production, which increases DNA damage and apoptosis. The tumor-oriented nanoparticle B-PDPN achieves a broad-spectrum telomerase inhibition to combat multidrug resistance. In vivo experiments support the evidence that B-PDPN accumulates in the tumor site and reduces the expression of hTERT in tumor tissues to inhibit drug resistant tumor growth. This work introduces an innovative strategy of utilizing features of tumor-activated nanoplatform to assist telomerase termination. The nanoplatform enhances intracellular drug concentration and nucleus delivery of doxorubicin (DOX), and promotes DNA damage to combat multidrug resistance.