Precision-Guided Missile-Like DNA Nanostructure Containing Warhead and Guidance Control for Aptamer-Based Targeted Drug Delivery into Cancer Cells in Vitro and in Vivo

Self-folding RCA product into a parallel monolayer DNA nanoribbon and woven into a nano-fence structure by a short bridge strand

The universal programmed construction of patterned periodic self-assembled nanostructures is a technical challenge in DNA origami nanotechnology but has numerous potential applications in biotechnology and biomedicine. In order to circumvent the dilemma that traditional DNA origami requires a long unusual single-stranded virus DNA as the scaffold and hundreds or even thousands of short strands as staples, we report a method for constructing periodically-self-folded rolling circle amplification products (RPs). The repeating unit is designed to have 3 intra-unit duplexes (inDP1,2,3) and 2 between-unit duplexes (buDP1,2). Based on the complementary pairing of bases, RPs each can self-fold into a periodic grid-patterned ribbon (GR) without the help of any auxiliary oligonucleotide staple. Moreover, by using only an oligonucleotide bridge strand, the GRs are connected together into the larger and denser planar nano-fence-shaped product (FP), which substantially reduces the number of DNA components compared with DNA origami and eliminates the obstacles in the practical application of DNA nanostructures. More interestingly, the FP-based DNA framework can be easily functionalized to offer spatial addressability for the precise positioning of nanoparticles and guest proteins with high spatial resolution, providing a new avenue for the future application of DNA assembled framework nanostructures in biology, material science, nanomedicine and computer science that often requires the ordered organization of functional moieties with nanometer-level and even molecular-level precision.

Aptamer-controlled stimuli-responsive drug release

Aptamers have been widely researched and applied in nanomedicine due to their programmable, activatable, and switchable properties. However, there are few reviews on aptamer-controlled stimuli-responsive drug delivery. This article highlights the mechanisms and advantages of aptamers in the construction of stimuli-responsive drug delivery systems. We summarize the assembly/reconfiguration mechanisms of aptamers in controlled release systems. The assembly and drug release strategies of drug delivery systems are illustrated. Specifically, we focus on the binding mechanisms to the target and the factors that induce/inhibit the binding to the stimuli, such as strand, pH, light, and temperature. The applications of aptamer-based stimuli-responsive drug release are elaborated. The challenges are discussed, and the future directions are proposed.

Advancements in DNA computing: exploring DNA logic systems and their biomedical applications

DNA computing is regarded as one of the most promising candidates for the next generation of molecular computers, utilizing DNA to execute Boolean logic operations. In recent decades, DNA computing has garnered widespread attention due to its powerful programmable and parallel computing capabilities, demonstrating significant potential in intelligent biological analysis. This review summarizes the latest advancements in DNA logic systems and their biomedical applications. Firstly, it introduces recent DNA logic systems based on various materials such as functional DNA sequences, nanomaterials, and three-dimensional DNA nanostructures. The material innovations driving DNA computing have been summarized, highlighting novel molecular reactions and analytical performance metrics like efficiency, sensitivity, and selectivity. Subsequently, it outlines the biomedical applications of DNA computing-based multi-biomarker analysis in cellular imaging, clinical diagnosis, and disease treatment. Additionally, it discusses the existing challenges and future research directions for the development of DNA computing.

Breast Tumor Diagnosis Based on Molecular Learning Vector Quantization Neural Networks

DNA nanotechnology plays a crucial role in precise cancer medicine. Currently, molecular logic circuits are applied to detect tumor-specific biomarkers and control the release of therapeutic drugs. However, these systems lack self-learning capabilities for intelligent diagnostics in biological samples, and their data processing capabilities are limited. Here, a molecular learning vector quantization neural network (LVQNN) model based on DNA strand displacement (DSD) technology for breast tumor diagnosis is developed. Compared to previous work, the molecular LVQNN boasts powerful computing abilities, handling high-dimensional data for intelligent cancer diagnosis. To verify the feasibility and versatility of the network, two distinct typical datasets are selected: one from a single source with cell morphology data from 569 cases, and a more extensive one spanning different populations and ages, with miRNA gene expression data from 1881 cases. By using the molecular LVQNN, diagnostic experiments are conducted on 50 and 120 public individuals from these two datasets, respectively, achieving accuracy rates of 94% and 97.5%. This study demonstrates that the LVQNN model exhibits significant advantages in breast cancer diagnosis and enhances diagnostic accuracy while introducing new approaches for intelligent cancer diagnosis, anticipated to bring significant breakthroughs and application prospects to precise cancer medicine.

Mirror-Image DNA Nanobox for Enhancing Environment Resistance of Nucleic Acid Probes

Degradation and interference of the nucleic acid probes in complex biological environments like cytoplasm or body fluid can cause obvious false-positive signals and inefficient bioregulation in biosensing and biomedicine. To solve this problem, here, we proposed a universal strategy, termed L-DNA assembly mirror-image box-based environment resistance (L-AMBER), to protect nucleic acid probes from degradation and maintain their responsive activity in complex biological environments. Strand displacement reaction (SDR), aptamer, or DNAzyme-based D-DNA probes were encapsulated into an L-DNA box by using an L-D-L block DNA carrier strand to construct different kinds of L-AMBER probes. We proved that the L-DNA box could effectively protect the encapsulated D-DNA probes by shielding the interference of complex biological environments and only allowing small target molecules to enter for recognition. Compared with the D-AMBER probes, the L-AMBER probes can realize DNase I-assisted amplification detection of biological samples, low false-positive bioimaging, and highly efficient miRNA silence in living cells. Therefore, L-AMBER provided a universal and effective strategy for enhancing the resistance to environmental interference of nucleic acid probes in biosensing and biomedicine applications.

Construction of Multiply Guaranteed DNA Sensors for Biological Sensing and Bioimaging Applications

Nucleic acids exhibit exceptional functionalities for both molecular recognition and catalysis, along with the capability of predictable assembly through strand displacement reactions. The inherent programmability and addressability of DNA probes enable their precise, on-demand assembly and accurate execution of hybridization, significantly enhancing target detection capabilities. Decades of research in DNA nanotechnology have led to advances in the structural design of functional DNA probes, resulting in increasingly sensitive and robust DNA sensors. Moreover, increasing attention has been devoted to enhancing the accuracy and sensitivity of DNA-based biosensors by integrating multiple sensing procedures. In this review, we summarize various strategies aimed at enhancing the accuracy of DNA sensors. These strategies involve multiple guarantee procedures, utilizing dual signal output mechanisms, and implementing sequential regulation methods. Our goal is to provide new insights into the development of more accurate DNA sensors, ultimately facilitating their widespread application in clinical diagnostics and assessment.

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

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

DNA response element-based smart drug delivery systems for precise drug release

Smart drug delivery systems (DDSs) that respond to, interact with, or are actuated by biological signals or pathological abnormalities (e.g., the tumor microenvironment) for controllable drug release are appealing therapeutic platforms for cancer treatment. Owing to their inherent self-assembled nature, nucleic acids have emerged as programmable materials for the development of multifunctional structures. In response to external environmental stimuli, DNA response elements can serve as switches to trigger conformational changes in DNA structures. Their stimulus-responsive properties make them promising candidates for constructing smart DDSs, and advancements in DNA response element-based DDSs in the field of biomedicine have been made. This review summarizes different types of DNA response elements, including DNA aptamers, DNAzymes, disulfide bond-modified DNA, pH-responsive DNA motifs, and photocleavable DNA building blocks, and highlights the advancements in DNA response element-based smart DDSs for precise drug release. Finally, future challenges and perspectives in this field are discussed.

Advancements in Aptamer-Driven DNA Nanostructures for Precision Drug Delivery

DNA nanostructures exhibit versatile geometries and possess sophisticated capabilities not found in other nanomaterials. They serve as customizable nanoplatforms for orchestrating the spatial arrangement of molecular components, such as biomolecules, antibodies, or synthetic nanomaterials. This is achieved by incorporating oligonucleotides into the design of the nanostructure. In the realm of drug delivery to cancer cells, there is a growing interest in active targeting assays to enhance efficacy and selectivity. The active targeting approach involves a "key-lock" mechanism where the carrier, through its ligand, recognizes specific receptors on tumor cells, facilitating the release of drugs. Various DNA nanostructures, including DNA origami, Tetrahedral, nanoflower, cruciform, nanostar, nanocentipede, and nanococklebur, can traverse the lipid layer of the cell membrane, allowing cargo delivery to the nucleus. Aptamers, easily formed in vitro, are recognized for their targeted delivery capabilities due to their high selectivity for specific targets and low immunogenicity. This review provides a comprehensive overview of recent advancements in the formation and modification of aptamer-modified DNA nanostructures within drug delivery systems.

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.

Persistent Targeting DNA Nanocarrier Made of 3D Structural Unit Assembled from Only One Basic Multi-Palindromic Oligonucleotide for Precise Gene Cancer Therapy

Construction of a simple, reconfigurable, and stimuli-responsive DNA nanocarrier remains a technical challenge. In this contribution, by designing three palindromic fragments, a simplest four-sticky end-contained 3D structural unit (PS-unit) made of two same DNA components is proposed. Via regulating the rotation angle of central longitudinal axis of PS-unit, the oriented assembly of one-component spherical architecture is accomplished with high efficiency. Introduction of an aptamer and sticky tail warehouse into one component creates a size-change-reversible targeted siRNA delivery nanovehicle. Volume swelling of 20 nm allows one carrier to load 1987 siPLK1s. Once entering cancer cells and responding to glutathione (GSH) stimuli, siPLK1s are almost 100% released and original size of nanovehicle is restored, inhibiting the expression of PLK1 protein and substantially suppressing tumor growth (superior to commercial transfection agents) in tumor-bearing mice without systemic toxicity.

Chemically Modified Platforms for Better RNA Therapeutics

RNA-based therapies have catalyzed a revolutionary transformation in the biomedical landscape, offering unprecedented potential in disease prevention and treatment. However, despite their remarkable achievements, these therapies encounter substantial challenges including low stability, susceptibility to degradation by nucleases, and a prominent negative charge, thereby hindering further development. Chemically modified platforms have emerged as a strategic innovation, focusing on precise alterations either on the RNA moieties or their associated delivery vectors. This comprehensive review delves into these platforms, underscoring their significance in augmenting the performance and translational prospects of RNA-based therapeutics. It encompasses an in-depth analysis of various chemically modified delivery platforms that have been instrumental in propelling RNA therapeutics toward clinical utility. Moreover, the review scrutinizes the rationale behind diverse chemical modification techniques aiming at optimizing the therapeutic efficacy of RNA molecules, thereby facilitating robust disease management. Recent empirical studies corroborating the efficacy enhancement of RNA therapeutics through chemical modifications are highlighted. Conclusively, we offer profound insights into the transformative impact of chemical modifications on RNA drugs and delineates prospective trajectories for their future development and clinical integration.

Y-Shaped Backbone-Rigidified DNA Tiles for the Construction of Supersized Nondeformable Tetrahedrons for Precise Cancer Therapies

While engineered DNA nanoframeworks have been extensively exploited for delivery of diagnostic and therapeutic regents, DNA tiling-based DNA frameworks amenable to applications in living systems lag much behind. In this contribution, by developing a Y-shaped backbone-based DNA tiling technique, we assemble Y-shaped backbone-rigidified supersized DNA tetrahedrons (RDT) with 100% efficiency for precisely targeted tumor therapy. RDT displays unparalleled rigidness and unmatched resistance to nuclease degradation so that it almost does not deform under the force exerted by the atomic force microscopy tip, and the residual amount is not less than 90% upon incubating in biological media for 24 h, displaying at least 11.6 times enhanced degradation resistance. Without any targeting ligand, RDT enters the cancer cell in a targeted manner, and internalization specificity is up to 15.8. Moreover, 77% of RDT objects remain intact within living cells for 14 h. The drug loading content of RDT is improved by 4-8 times, and RDT almost 100% eliminates the unintended drug leakage in a stimulated physiological medium. Once systemically administrated into HeLa tumor-bearing mouse models, doxorubicin-loaded RDTs preferentially accumulate in tumor sites and efficiently suppress tumor growth without detectable off-target toxicity. The Y-DNA tiling technique offers invaluable insights into the development of structural DNA nanotechnology for precise medicine.

A hairpin-contained i-motif guided DNA nanoantenna for sensitive and specific sensing of tumor extracellular pH gradients

Antenna, as a converter, could receive and convert signals from the outside world flexibly. Inspired by the behavior of antennas receiving external signals, we developed a pH-stimulated and aptamer-anchored Y-shaped DNA nanoantenna (termed pH-Apt-YNA) for sensitive and specific sensing of tumor extracellular pH gradients. The nanoantenna consisted of three functional nucleic acid sequences, an I-strand, Apt-Y-R and Y-L-G, where the I-strand endowed the DNA nanoantenna with the ability to receive and convert signals, the Apt-Y-R containing an aptamer fragment gave the DNA nanoantenna the ability to specifically anchor target tumor cells, and the complementarity of Y-L-G with the other two sequences ensured the stability of the DNA nanoantenna. Initially, the DNA nanoantenna was in a "silent" state, and rhodamine green was close to BHQ2, leading to suppressed signal emission. When the DNA nanoantenna anchored on the surface of target cancer cells through the aptamer recognition domain, the I-strand tended to fold into a hairpin-contained i-motif tetramer structure owing to the extracellular low pH stimuli, resulting in the DNA nanoantenna changing into an "active" state. In the meantime, rhodamine green moved far away from BHQ2, resulting in a strong signal output. The results demonstrate that the pH-Apt-YNA presents a sensitive pH sensing capacity within a narrow pH range of 6.2-7.4 and exhibits excellent specificity for the imaging of target cancer cell extracellular pH. Based on these advantages, we therefore anticipate that our facile design of the DNA nanoantenna with sensitive responsiveness provides a new way and great promise in the application of sensing pH-related physiological and pathological processes.

Recent Advances in Biomedical Nanotechnology Related to Natural Products

Natural product processing via nanotechnology has opened the door to innovative and significant applications in medical fields. On one hand, plants-derived bioactive ingredients such as phenols, pentacyclic triterpenes and flavonoids exhibit significant pharmacological activities, on another hand, most of them are hydrophobic in nature, posing challenges to their use. To overcome this issue, nanoencapsulation technology is employed to encapsulate these lipophilic compounds and enhance their bioavailability. In this regard, various nano-sized vehicles, including degradable functional polymer organic compounds, mesoporous silicon or carbon materials, offer superior stability and retention for bioactive ingredients against decomposition and loss during delivery as well as sustained release. On the other hand, some naturally occurring polymers, lipids and even microorganisms, which constitute a significant portion of Earth's biomass, show promising potential for biomedical applications as well. Through nano-processing, these natural products can be developed into nano-delivery systems with desirable characteristics for encapsulation a wide range of bioactive components and therapeutic agents, facilitating in vivo drug transport. Beyond the presentation of the most recent nanoencapsulation and nano-processing advancements with formulations mainly based on natural products, this review emphasizes the importance of their physicochemical properties at the nanoscale and their potential in disease therapy.

Thermodynamic and cellular studies of doxorubicin/daunorubicin loaded by a DNA tetrahedron for diagnostic imaging, chemotherapy, and gene therapy

The combined diagnostic imaging, chemotherapy, and gene therapy based on DNA nanocarriers can reduce the toxic side effects and overcome multidrug resistance (MDR). In this study, we designed an antisense oligonucleotides (ASOs)-linked DNA tetrahedron (ASOs-TD). The detection limit of ASOs-TD for MDR1 mRNA was 0.05 μM. By using fluorescence spectroscopy and isothermal titration calorimetry (ITC), the interactions between doxorubicin (DOX) /daunorubicin (DAU) and ASOs-TD were investigated. The number of binding sites (n), binding constant (Ka), entropy change (ΔSo), enthalpy change (ΔHo) and Gibbs free energy change (ΔGo) were obtained. The intercalation of DOX/DAU with ASOs-TD was demonstrated by differential scanning calorimetry (DSC) and quenching researches of potassium ferricyanide K4[Fe(CN)6]. The in vitro release rate of DOX/DAU loaded in ASOs-TD was accelerated by deoxyribonuclease I (DNase I). In vitro cytotoxicity proved the good gene therapy effect of ASOs-TD and the increased cytotoxicity of DOX/DAU to MCF-7/ADR cells. The results of confocal laser scanning microscope (CLSM) suggested that ASOs-TD could effectively identify drug-resistant cells due to its good imaging ability for MDR1 mRNA. This work offers theoretical significance for overcoming MDR using DNA nanostructures which combine diagnostic imaging, chemotherapy, and gene therapy.

Aptamers: Features, Synthesis and Applications

Aptamers have become a topic of interest among the researchers and scientists since they not only possess all of the benefits of antibodies but also possess special qualities including heat stability, low cost, and limitless uses⋅ Here we give a review about the features, applications, and challenges of aptamers and also how they are beneficial over the antibodies for biomedical applications. Their unique features make aptamers a prominent tool in therapeutics, diagnostics, biosensors and targeted drug delivery. In conclusion, aptamers represent exciting materials for a variety of applications and can be modified to improve their properties and to extend their applications in biomedical field.

Engineered Plant-Derived Nanovesicles Facilitate Tumor Therapy: Natural Bioactivity Plus Drug Controlled Release Platform

Tumors are the second-most common disease in the world, killing people at an alarming rate. As issues with drug resistance, lack of targeting, and severe side effects are revealed, there is a growing demand for precision-targeted drug delivery systems. Plant-derived nanovesicles (PDNVs), which arecomposed of proteins, lipids, RNA, and metabolites, are widely distributed and readily accessible. The potential for anti-proliferative, pro-apoptotic, and drug-resistant-reversing effects on tumor cells, as well as the ability to alter the tumor microenvironment (TME) by modulating tumor-specific immune cells, make PDNVs promising anti-tumor therapeutics. With a lipid bilayer structure that allows drug loading and a transmembrane capacity readily endocytosed by cells, PDNVs are also expected to become a new drug delivery platform. Exogenous modifications of PDNVs enhance their circulating stability, tumor targeting ability, high cell endocytosis rate, and controlled-release capacity. In this review, we summarize PDNVs' natural antitumor activity, as well as engineered PDNVs as efficient precision-targeted drug delivery tools that enhance therapeutic effects. Additionally, we discuss critical considerations related to the issues raised in this area, which will encourage researchers to improve PDNVs as better anti-tumor therapeutics for clinic applications.

Addressing the in vivo delivery of nucleic-acid nanostructure therapeutics

DNA and RNA nanostructures are being investigated as therapeutics, vaccines, and drug delivery systems. These nanostructures can be functionalized with guests ranging from small molecules to proteins with precise spatial and stoichiometric control. This has enabled new strategies to manipulate drug activity and to engineer devices with novel therapeutic functionalities. Although existing studies have offered encouraging in vitro or pre-clinical proof-of-concepts, establishing mechanisms of in vivo delivery is the new frontier for nucleic-acid nanotechnologies. In this review, we first provide a summary of existing literature on the in vivo uses of DNA and RNA nanostructures. Based on their application areas, we discuss current models of nanoparticle delivery, and thereby highlight knowledge gaps on the in vivo interactions of nucleic-acid nanostructures. Finally, we describe techniques and strategies for investigating and engineering these interactions. Together, we propose a framework to establish in vivo design principles and advance the in vivo translation of nucleic-acid nanotechnologies.

Advances of medical nanorobots for future cancer treatments

Early detection and diagnosis of many cancers is very challenging. Late stage detection of a cancer always leads to high mortality rates. It is imperative to develop novel and more sensitive and effective diagnosis and therapeutic methods for cancer treatments. The development of new cancer treatments has become a crucial aspect of medical advancements. Nanobots, as one of the most promising applications of nanomedicines, are at the forefront of multidisciplinary research. With the progress of nanotechnology, nanobots enable the assembly and deployment of functional molecular/nanosized machines and are increasingly being utilized in cancer diagnosis and therapeutic treatment. In recent years, various practical applications of nanobots for cancer treatments have transitioned from theory to practice, from in vitro experiments to in vivo applications. In this paper, we review and analyze the recent advancements of nanobots in cancer treatments, with a particular emphasis on their key fundamental features and their applications in drug delivery, tumor sensing and diagnosis, targeted therapy, minimally invasive surgery, and other comprehensive treatments. At the same time, we discuss the challenges and the potential research opportunities for nanobots in revolutionizing cancer treatments. In the future, medical nanobots are expected to become more sophisticated and capable of performing multiple medical functions and tasks, ultimately becoming true nanosubmarines in the bloodstream.

Tools and techniques for the discovery of therapeutic aptamers: recent advances

INTRODUCTION

The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers.

AREAS COVERED

The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility.

EXPERT OPINION

The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.

Quantitative Measurement of Drug Release Dynamics within Targeted Organelles Using Förster Resonance Energy Transfer

Measuring the release dynamics of drug molecules after their delivery to the target organelle is critical to improve therapeutic efficacy and reduce side effects. However, it remains challenging to quantitatively monitor subcellular drug release in real time. To address the knowledge gap, a novel gemini fluorescent surfactant capable of forming mitochondria-targeted and redox-responsive nanocarriers is designed. A quantitative Förster resonance energy transfer (FRET) platform is fabricated using this mitochondria-anchored fluorescent nanocarrier as a FRET donor and fluorescent drugs as a FRET acceptor. The FRET platform enables real-time measurement of drug release from organelle-targeted nanocarriers. Moreover, the obtained drug release dynamics can evaluate the duration of drug release at the subcellular level, which established a new quantitative method for organelle-targeted drug release. This quantitative FRET platform can compensate for the absent assessment of the targeted release performances of nanocarriers, offering in-depth understanding of the drug release behaviors at the subcellular targets.

Sustainable Nanomaterials for Biomedical Applications

Significant progress in nanotechnology has enormously contributed to the design and development of innovative products that have transformed societal challenges related to energy, information technology, the environment, and health. A large portion of the nanomaterials developed for such applications is currently highly dependent on energy-intensive manufacturing processes and non-renewable resources. In addition, there is a considerable lag between the rapid growth in the innovation/discovery of such unsustainable nanomaterials and their effects on the environment, human health, and climate in the long term. Therefore, there is an urgent need to design nanomaterials sustainably using renewable and natural resources with minimal impact on society. Integrating sustainability with nanotechnology can support the manufacturing of sustainable nanomaterials with optimized performance. This short review discusses challenges and a framework for designing high-performance sustainable nanomaterials. We briefly summarize the recent advances in producing sustainable nanomaterials from sustainable and natural resources and their use for various biomedical applications such as biosensing, bioimaging, drug delivery, and tissue engineering. Additionally, we provide future perspectives into the design guidelines for fabricating high-performance sustainable nanomaterials for medical applications.

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.

Study on Sgc8 Aptamer-mediated Nucleic Acid Nanomaterial-doxorubicin Complex for Tumor Targeted Therapy

Chemotherapy is one of the most important treatments for malignant cancers, but most chemotherapeutic drugs are poorly targeted, highly toxic and expensive, resulting in unsatisfactory treatment results for cancer patients. Therefore, intelligent drug delivery platforms are needed to be explored urgently to enhance drug treatment and reduce toxicity on normal cells. Nucleic acid nanomaterials are a class of nanomaterials developed on the basis of the "base complementary pairing principle", which have the advantages of good programmability, high stability, good biocompatibility, and strong targeting. Herein, we present a simple Sgc8 aptamer-modified nucleic acid nanomaterial (Sgc8NM) for the targeted delivery of Doxorubicin (Dox), a widely used chemotherapy drug in clinic. Studies have shown the Sgc8NM-Dox performed a precise treatment effect on target cells and low toxicity on non-target cells, providing a new strategy for the potential application of nanocomposite drugs in targeted cancer delivery.

Nucleolin recognizing silica nanoparticles inhibit cell proliferation by activating the Bax/Bcl-2/caspase-3 signalling pathway to induce apoptosis in liver cancer

Multifunctional nanocarrier platforms have shown great potential for the diagnosis and treatment of liver cancer. Here, a novel nucleolin-responsive nanoparticle platform was constructed for the concurrent detection of nucleolin and treatment of liver cancer. The incorporation of AS1411 aptamer, icaritin (ICT) and FITC into mesoporous silica nanoparticles, labelled as Atp-MSN (ICT@FITC) NPs, was the key to offer functionalities. The specific combination of the target nucleolin and AS1411 aptamer caused AS1411 to separate from mesoporous silica nanoparticles surface, allowing FITC and ICT to be released. Subsequently, nucleolin could be detected by monitoring the fluorescence intensity. In addition, Atp-MSN (ICT@FITC) NPs can not only inhibit cell proliferation but also improve the level of ROS while activating the Bax/Bcl-2/caspase-3 signalling pathway to induce apoptosis in vitro and in vivo. Moreover, our results demonstrated that Atp-MSN (ICT@FITC) NPs had low toxicity and could induce CD3⁺ T-cell infiltration. As a result, Atp-MSN (ICT@FITC) NPs may provide a reliable and secure platform for the simultaneous identification and treatment of liver cancer.

A Thermal and Enzymatic Dual-Stimuli Responsive DNA-Based Nanomachine for Controlled mRNA Delivery

The extreme instability of mRNA makes the practical application of mRNA-based vaccines heavily rely on efficient delivery system and cold chain transportation. Herein, a DNA-based nanomachine, which achieves programmed capture, long-term storage without cryopreservation, and efficient delivery of mRNA in cells, is developed. The polythymidine acid (Poly-T) functionalized poly(N-isopropylacrylamide) (DNA-PNIPAM) is synthesized and assembled as the central compartment of the nanomachine. The DNA-PNIPAM nano-assembly exhibits reversible thermal-responsive dynamic property: when lower than the low critical solution temperature (LCST, ≈32 °C) of PNIPAM, the DNA-PNIPAM transforms into extension state to expose the poly-T, facilitating the hybridization with polyadenylic acid (Poly-A) tail of mRNA; when higher than LCST, DNA-PNIPAM re-assembles and achieves an efficient encapsulation of mRNA. It is remarkable that the DNA-PNIPAM nano-assembly realizes long-term storage of mRNA (≈7 days) at 37 °C. Biodegradable 2-hydroxypropyltrimethyl ammonium chloride chitosan is assembled on the outside of DNA-PNIPAM to facilitate the endocytosis of mRNA, RNase-H mediating mRNA release occurs in cytoplasm, and efficient mRNA translation is achieved. This work provides a new disign principle of nanosystem for mRNA delivery.

Self-assembly of DNA nanospheres with controllable size and self-degradable property for enhanced antitumor chemotherapy

Controllable size, self-degradability and targeting property are important for a precise improvement of anticancer effects and reduction of side effects of drug vehicles. Here, a series of DNA nanospheres with controllable size and self-degradation ability were constructed through the hybridization of two i-motif strands and two linker strands for targeted cancer therapy. DNA nanospheres with different sizes were fabricated by regulating the linker sequence, and their pH-responsive self-degradation property was realized by the introduction of the i-motif strand. Moreover, the ZY11 aptamer was introduced to endow the DNA nanospheres with targeting property toward SMMC-7721 cancer cells. The results revealed that the appropriate size of DNA nanospheres (80 nm) highly promoted the internalization by mammalian cells. The results of DLS, AFM and CD spectra showed that the DNA nanospheres were stable in a physiological environment but they self-degraded in a slightly acidic environment due to the existence of the i-motif strand. Moreover, the fluorescence of DOX@AP-NSs2 was triple at pH = 5.0 than at pH = 7.4, which further confirmed the pH-responsive drug release performance. The above results proved that the use of DOX@AP-NSs2 is a promising approach to accelerate the rapid release of drugs into the tumors and avoid drug leakage into the normal tissue. The results at a cellular level and in vivo confirmed the pH-responsive targeted antitumor effect. Hence, the novel DNA nanospheres with controllable size and self-degradable property represent a potential tool for targeted drug delivery and cancer therapy.

Reconfigurable DNA triplex structure for pH responsive logic gates†

The DNA triplex is a special DNA structure often used as a logic gate substrate due to its high stability, programmability, and pH responsiveness. However, multiple triplex structures with different C−G−C⁺ proportions must be introduced into existing triplex logic gates due to the numerous logic calculations involved. This requirement complicates circuit design and results in many reaction by-products, greatly restricting the construction of large-scale logic circuits. Thus, we designed a new reconfigurable DNA triplex structure (RDTS) and constructed the pH-responsive logic gates through its conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. The use of these logic calculations necessitates fewer substrates, further enhancing the extensibility of the logic circuit. This result is expected to promote the development of the triplex in molecular computing and facilitate the completion of large-scale computing networks.

We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.

Current perspectives and trend of nanomedicine in cancer: A review and bibliometric analysis

The limitations of traditional cancer treatments are driving the creation and development of new nanomedicines. At present, with the rapid increase of research on nanomedicine in the field of cancer, there is a lack of intuitive analysis of the development trend, main authors and research hotspots of nanomedicine in the field of cancer, as well as detailed elaboration of possible research hotspots. In this review, data collected from the Web of Science Core Collection database between January 1st, 2000, and December 31st, 2021, were subjected to a bibliometric analysis. The co-authorship, co-citation, and co-occurrence of countries, institutions, authors, literature, and keywords in this subject were examined using VOSviewer, Citespace, and a well-known online bibliometrics platform. We collected 19,654 published papers, China produced the most publications (36.654%, 7204), followed by the United States (29.594%, 5777), and India (7.780%, 1529). An interesting fact is that, despite China having more publications than the United States, the United States still dominates this field, having the highest H-index and the most citations. Acs Nano, Nano Letters, and Biomaterials are the top three academic publications that publish articles on nanomedicine for cancer out of a total of 7580 academic journals. The most significant increases were shown for the keywords "cancer nanomedicine", "tumor microenvironment", "nanoparticles", "prodrug", "targeted nanomedicine", "combination", and "cancer immunotherapy" indicating the promising area of research. Meanwhile, the development prospects and challenges of nanomedicine in cancer are also discussed and provided some solutions to the major obstacles.

Self-assembly of DNA nanostructure containing cell-specific aptamer as a precise drug delivery system for cancer therapy in non-small cell lung cancer

Background

As the most common subtype in lung cancer, the precise and efficient treatment for non-small cell lung cancer (NSCLC) remains an outstanding challenge owing to early metastasis and poor prognosis. Chemotherapy, the most commonly used treatment modality, is a difficult choice for many cancer patients due to insufficient drug accumulation in tumor sites and severe systemic side-effects. In this study, we constructed a cell-specific aptamer-modified DNA nanostructure (Apt-NS) as a targeting drug delivery system achieving the precision therapy for lung cancer.

Methods

The synthesis of DNA nanostructure and its stability were evaluated using gel electrophoresis. The targeting properties and internalization mechanism were investigated via flow cytometry and confocal analyses. Drug loading, release, and targeted drug delivery were determined by fluorescence detection, Zeta potentials assay, and confocal imaging. CCK8 assays, colony formation, cell apoptosis, metastasis analyses and in vivo experiments were conducted to assess the biological functions of DNA nanostructure.

Results

Self-assembled DNA nanoparticles (Apt-NS) had excellent stability to serum and DNase I and the ability to specifically recognize A549 cells. Upon specific binding, the drug-loaded nanoparticles (Apt-NS-DOX) were internalized into target cells by clathrin-mediated endocytosis. Subsequently, DOX could be released from Apt-NS-DOX based on the degradation of the lysosome. Apt-NS-DOX exerted significant suppression of cell proliferation, invasion and migration, and also enhanced cell apoptosis due to the excellent performance of drug delivery and intracellular release, while maintaining a superior biosafety. In addition, the antitumor effects of Apt-NS-DOX were further confirmed using in vivo models.

Conclusions

Our study provided cell-specific aptamer-modified DNA nanostructures as a drug-delivery system targeting A549 cells, which could precisely and efficiently transport chemotherapeutic drug into tumor cells, exerting enhanced antineoplastic efficacy. These findings highlight that DNA nanostructure serving as an ideal drug delivery system in cancer treatment appears great promise in biomedical applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01701-5.

Outward Movement of Targeting Ligands from a Built-In Reserve Pool in Nuclease-Resistant 3D Hierarchical DNA Nanocluster for in Vivo High-Precision Cancer Therapy

Nanostructures made entirely of DNAs display great potential as chemotherapeutic drug carriers but so far cannot achieve sufficient clinic therapy outcomes due to off-target toxicity. In this contribution, an aptamer-embedded hierarchical DNA nanocluster (Apt-eNC) is constructed as an intelligent carrier for cancer-targeted drug delivery. Specifically, Apt-eNC is designed to have a built-in reserve pool in the interior cavity from which aptamers may move outward to function as needed. When surface aptamers are degraded, ones in reserve pool can move outward to offer the compensation, thereby magically preserving tumor-targeting performance in vivo. Even if withstanding extensive aptamer depletion, Apt-eNC displays a 115-fold enhanced cell targeting compared with traditional counterparts and at least 60-fold improved tumor accumulation. Moreover, one Apt-eNC accommodates 5670 chemotherapeutic agents. As such, when systemically administrated into HeLa tumor-bearing BALB/c nude mouse model, drug-loaded Apt-eNC significantly inhibits tumor growth without systemic toxicity, holding great promise for high precision therapy.

Size-Controllable and Self-Assembled DNA Nanosphere for Amplified MicroRNA Imaging through ATP-Fueled Cyclic Dissociation

Visualizing intracellular microRNA (miRNA) is of great importance for revealing its roles in the development of disease. However, cell membrane barrier, complex intracellular environment and low abundance of target miRNA are three main challenges for efficient imaging of intracellular miRNA. Here, we report a size-controllable and self-assembled DNA nanosphere with ATP-fueled dissociation property for amplified miRNA imaging in live cells and mice. The DNA nanosphere was self-assembled from Y-shaped DNA (Y-DNA) monomers through predesigned base pair hybridization, and the size could be easily controlled by varying the concentration of Y-DNA. Once the nanosphere was internalized into cells, the intracellular specific target miRNA would trigger the cyclic dissociation of the DNA nanosphere driven by ATP, resulting in amplified FRET signal. The programmable DNA nanosphere has been proven to work well for detecting the expression of miRNA in cancer cells and in mice, which demonstrates its fairish cell penetration, stability and sensitivity.

Endogenous Stimuli-Responsive Autonomous Separation of Dual-Targeting DNA Guided Missile from Nanospacecraft for Intelligent Targeted Cancer Therapy

Most conventional chemotherapeutics indiscriminately kill both cancerous and healthy cells and cause toxic side effects, limiting the maximum tolerated dose and thereby compromising therapeutic efficacy. To address this challenge, here dual-targeting intelligent DNA guided missile (GM)-integrated nanospacecraft (NSC) (abbreviated as GM-NSC) is demonstrated for staged chemotherapeutic drug delivery exclusively into cancer cells and then mitochondria (not into healthy cells). GM-NSC is essentially a core/shell nanocomposite composed of gold nanoparticles (AuNPs) surrounded by a high-density multilayer DNA crown that is self-assembled from DNA tetrahedral units (DNA Tetra) in a highly ordered manner. Each tetrahedral structural unit is equipped with three functional components: a cancer cell-targeting aptamer pointing toward the outside environment, a hidden mitochondria-targeting triphenylphosphonium (TPP), and an explosive bolt (E-bolt). GM-NSC can remain intact in fetal bovine serum solution over 12 h and has 53-fold improved systemic stability. Each GM-NSC accommodates 1250 anticancer doxorubicin (Dox), achieving a 48-63-fold improved drug payload capacity. When systemically administrated into a tumor-bearing xenograft murine model, Dox-loaded GM-NSC enters into tumor sites with 18-fold improved specificity followed by autonomous separation of GMs from the NSC core and specific mitochondrial accumulation due to the explosion of E-bolt upon stimuli of endogenous miRNAs. About 80% of Dox uptaken is transferred into mitochondria and induces mitochondria-mediated apoptosis. As a result, the growth of malignant tumor is almost 100% inhibited without detectable toxicity to healthy tissues. Due to the desirable systemic stability, good biocompatibility, high cargo loading capability, satisfactory in vivo biodistribution, and therapeutic efficacy without adverse effects, intelligible GM-NSC is expected to become an alternative drug delivery system for precision cancer therapy.

Systematic bio-fabrication of aptamers and their applications in engineering biology

Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.

"Willow Branch" DNA Self-Assembly for Cancer Dual-Target and Proliferation Inhibition

DNA nanotechnology is beginning to yield unique advantages in the area of drug delivery. For the dual-targeting and proliferation suppression of cancer cells, a "willow branch" DNA assembly based on rolling circle amplification (RCA) was built. Three single-stranded DNAs, including antibody modified cDNAs, aptamer cDNAs, and simple cDNAs, were employed in the DNA self-assembly, along with the RCA scaffolds (every 63 bases is a repeat unit). "Willow branch" DNA (WB DNA) assembly successfully linked multiple antibodies and aptamers together to achieve dual targeting of cancer cells. Binding of CD44 antibodies and S2.2 aptamers to receptors on the cell membrane inhibits both pathways, β-catenin signaling and nuclear factor-kappa B-specific transcription activity, through feedback regulation. Results demonstrated that WB DNA assembly could effectively exert multivalency clustering cell-surface receptors, modulating signal pathways and inhibiting proliferation. This study proposes a new approach for cancer dual-target and proliferation inhibition by clustering multivalent receptors.

Functionalized-DNA nanostructures as potential targeted drug delivery systems for cancer therapy

Seeman's pioneer idea has led to the foundation of DNA nanostructures, resulting in a remarkable advancement in DNA nanotechnology. Over the last few decades, remarkable advances in drug delivery techniques have resulted in the self-assembly of DNA for encapsulating candidate drug molecules. The nuclear targeting capability of DNA nanostructures is lies within their high spatial addressability and tremendous potential for active targeting. However, effective programming and assembling those DNA molecules remains a challenge, making the path to DNA nanostructures for real-world applications difficult. Because of their small size, most nanostructures are self-capable of infiltrating into the tumor cellular environment. Furthermore, to enable controlled and site-specific delivery of encapsulated drug molecules, DNA nanostructures are functionalized with special moieties that allow them to bind specific targets and release cargo only at targeted sites rather than non-specific sites, resulting in the prevention/limitation of cellular toxicity. In light of this, the current review seeks to shed light on the versatility of the DNA molecule as a targeting and encapsulating moiety for active drugs in order to achieve controlled and specific drug release with spatial and temporal precision. Furthermore, this review focused on the challenges associated with the construction of DNA nanostructures as well as the most recent advances in the functionalization of DNA nanostructures using various materials for controlled and targeted delivery of medications for cancer therapy.

Advances in aptamer-based drug delivery vehicles for cancer therapy

Overall, aptamers are special classes of nucleic acid-based macromolecules that are beginning to investigate because of their capability of avidity binding to a specific target for clinical use. Taking advantage of target-specific medicine led to more effective therapeutic and limitation of side effects of drugs. Herein, we discuss several aptamers and their binding capability and capacity for selecting tumor biomarkers and usage of them as targeting ligands for the functionalization of nanomaterials. We review recent applications based on aptamers and several nanoparticles to rise efficacy and develop carrier systems such as graphene oxide, folic acid, gold, mesopores silica, and various polymers and copolymer, polyethylene glycol, cyclodextrin, chitosan. The nanocarriers have been characterized by particle size, zeta potential, aptamer conjugation, and drug encapsulation efficiency. Hydrodynamic diameter and Zeta potential can used in order to monitor aptamers' crosslinking, in-vitro drug release, intracellular delivery of nanocarriers, and cellular cytotoxicity assay. Also, they are studied for cellular uptake and internalization to types of cancer cell lines such as colorectal, breast, prostate, leukemia and etc. The results are investigated in in-vivo cytotoxicity assay and cell viability assay. Targeted cancer therapy seems a good and promising strategy to overcome the systemic toxicity of chemotherapy.

Preparation, applications, and challenges of functional DNA nanomaterials

As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.

Self-Assembled ATP-Responsive DNA Nanohydrogel for Specifically Activated Fluorescence Imaging and Chemotherapy in Cancer Cells

Tumor marker-responsive drug delivery systems have been developed for cancer imaging and chemotherapy. However, improving their ability of controlled drug release remains a challenge. In this study, we have developed an adenosine triphosphate (ATP)-responsive DNA nanohydrogel for specifically activated fluorescence imaging and chemotherapy in cancer cells. Acrylamide and acrydite-modified DNAs were polymerized to obtain DNA-grafted polyacrylamide copolymers. Then, the copolymers acted as the backbone of the nanohydrogel and were assembled by base complementation with ATP aptamer linkers to construct an ATP-responsive nanohydrogel. Meanwhile, the chemotherapeutic drug doxorubicin (DOX) was added and loaded into the ATP-responsive nanohydrogel during the assembly process. After endocytosis by cancer cells and response to a high intracellular ATP level, the DOX-loaded nanohydrogel disassembled due to the formation of aptamer/ATP complexes. Subsequently, the released DOX played a role in fluorescence imaging and chemotherapy of cancer cells. Through the ATP-responsive property and satisfying drug delivery capability, this nanohydrogel realized fluorescence imaging and specific cancer cell killing capabilities due to different intracellular ATP levels in normal and cancer cell lines. In summary, this study has provided a novel strategy of constructing a tumor microenvironment-responsive drug delivery system triggered by the tumor markers for tumor intracellular imaging and chemotherapy.

In silico SELEX screening and statistical analysis of newly designed 5mer peptide-aptamers as Bcl-xl inhibitors using the Taguchi method

Drug development for cancer treatment is a complex process that requires special efforts. Targeting crucial proteins is the most essential purpose of drug design in cancers. Bcl-xl is an anti-apoptotic protein that binds to pro-apoptotic proteins and interrupts their signals. Pro-apoptotic Bcl-xl effectors are short BH3 sequences that form an alpha helix and bind to anti-apoptotic proteins to inhibit their activity. Computational systematic evolution of ligands by exponential enrichment (SELEX) is an exclusive approach for developing peptide aptamers as potential effectors. Here, the amino acids with a high tendency for constructing an alpha-helical structure were selected. Due to the enormous number of pentapeptides, Taguchi method was used to study a selected number of peptides. The binding affinity of the peptides to Bcl-xl was assessed using molecular docking, and after analysis of the obtained results, a final set of optimized peptides was arranged and constructed. For a better comparison, three chemical compounds with approved anti-Bcl-xl activity were selected for comparison with the top-ranked 5mer peptides. The optimized peptides showed considerable binding affinity to Bcl-xl. The molecular dynamics (MD) simulation indicated that the designed peptide (PO5) could create considerable interactions with the BH3 domain of Bcl-xl. The MM/GBSA calculations revealed that these interactions were even stronger than those created by chemical compounds. In silico SELEX is a novel approach to design and evaluate peptide-aptamers. The experimental design improves the SELEX process considerably. Finally, PO5 could be considered a potential inhibitor of Bcl-xl and a potential candidate for cancer treatment.

Structure-switchable aptamer-arranged reconfigurable DNA nanonetworks for targeted cancer therapy

The structural DNA nanotechnology holds great potential application in bioimaging, drug delivery and cancer therapy. Herein, an intelligent aptamer-incorporated DNA nanonetwork (Apt-Nnes) is demonstrated for cancer cell imaging and targeted drug delivery, which essentially is a micron-scale pattern with the thickness of double-stranded monolayer. Cancer cell-surface receptors can make it perform magical transformation into small size of nanosheet intermediates and specifically enter target cells. The binding affinity of Apt-Nnes is increased by 3-fold due to multivalent binding effect of aptamers and it can maintain the structural integrity in fetal bovine serum (FBS) for 8 h. More interestingly, target cancer cells can cause the structural disassembly, and each resulting unit transports 4963 doxorubicin (Dox) into target cells, causing the specific cellular cytotoxicity. The cell surface receptor-mediated disassembly of large size of DNA nanostructures into small size of fractions provides a valuable insight into developing intelligent DNA nanostructure suitable for biomedical applications.

Calcium-Differentiated Cellular Internalization of Allosteric Framework Nucleic Acids for Targeted Payload Delivery

Target delivery systems have extensively shown promising applications in cancer therapy, and many of them function smartly by responding to the cancer cell microenvironment. Here, we for the first time report Ca²⁺-differentiated cellular internalization of 2D/3D framework nucleic acids (FNAs), enabling the engineering of a conceptually new target delivery system using an allosteric FNA nanovehicle. The FNA vehicle is subject to a 2D-to-3D transformation on the cancer cell surface via G-quadruplexes responding to environmental K⁺ and thereby allows its cell entry to be more efficiently promoted by Ca²⁺. This design enables the FNA vehicle to target cancer cells and selectively deliver an antisense strand-containing cargo for live-cell mRNA imaging. It would open new avenues toward targeted drug delivery and find extensive applications in precise disease treatment.

Design and application of DNA nanostructures for organelle-targeted delivery of anticancer drugs

INTRODUCTION

DNA nanostructures targeting organelles are of great significance for the early diagnosis and precise therapy of human cancers. This review is expected to promote the development of DNA nanostructure-based cancer treatment with organelle-level precision in the future.

AREAS COVERED

In this review, we introduce the different principles for targeting organelles, summarize the progresses in the development of organelle-targeting DNA nanostructures, highlight their advantages and applications in disease treatment, and discuss current challenges and future prospects.

EXPERT OPINION

Accurate targeting is a basic problem for effective cancer treatment. However, current DNA nanostructures cannot meet the actual needs. Targeting specific organelles is expected to further improve the therapeutic effect and overcome tumor cell resistance, thereby holding great practical significance for tumor treatment in the clinic. With the deepening of the research on the molecular mechanism of disease development, especially on tumorigenesis and tumor progression, and increasing understanding of the behavior of biological materials in living cells, more versatile DNA nanostructures will be constructed to target subcellular organelles for drug delivery, essentially promoting the early diagnosis of cancers, classification, precise therapy and the estimation of prognosis in the future.