DNA Nanostructure-Based Systems for Intelligent Delivery of Therapeutic Oligonucleotides

Supramolecular Modulator Assisted Cryo-Engineered Porous Cu-DNA Nano-Vehicles for Versatile Theranostic Agent Delivery

DNA nanotechnology combines structural design with therapeutic functions via programmable DNA motifs, but faces challenges in drug loading capacity. Herein a pore-engineering strategy is reported to develop a highly porous, universal DNA nano-vehicle through coordination self-assembly, cryo-engineering, and supramolecular chemistry, adapting to diverse cargo loading with desired theranostic agents. Thus, the complex synthesis and compatibility challenges typically associated with switching between different drug carriers are avoided. To this end, Cu2+ and nucleic acid therapeutic G3139 self-assemble into a prefabricated solid nanostructure, which subsequently undergoes ultrafast freezing and sublimation to introduce porosity, forming highly porous Cu-G3139 nanoparticles (CG NPs). The porous CG NPs efficiently accommodate diverse therapeutic molecules, from chemotherapeutics to non-chemotherapeutic agents, facilitated by positively-charged cyclodextrin. As a proof-of-concept, the photosensitizer indocyanine green (ICG) is loaded and coated with tannic acid (TA) to form CICG@TA, enabling remarkable photothermal and fluorescence imaging-guided synergistic tumor ablation. This work represents the first demonstration of sublimation-induced pore formation in metal-DNA hybrid nanoparticles without chemical etching, offering a scalable "plug-and-play" platform for personalized cancer therapy without redesign. This versatile pore-engineering strategy, merging supramolecular chemistry with cryo-engineered porosity, opens up new avenues for efficient, customized multidrug delivery for diverse tumor theranostic applications.

Targeted delivery of CEBPA-saRNA for the treatment of pancreatic ductal adenocarcinoma by transferrin receptor aptamer decorated tetrahedral framework nucleic acid

Pancreatic cancer, predominantly pancreatic ductal adenocarcinoma (PDAC), remains a highly lethal malignancy with limited therapeutic options and a dismal prognosis. By targeting the underlying molecular abnormalities responsible for PDAC development and progression, gene therapy offers a promising strategy to overcome the challenges posed by conventional radiotherapy and chemotherapy. This study sought to explore the therapeutic potential of small activating RNAs (saRNAs) specifically targeting the CCAAT/enhancer-binding protein alpha (CEBPA) gene in PDAC. To overcome the challenges associated with saRNA delivery, tetrahedral framework nucleic acids (tFNAs) were rationally engineered as nanocarriers. These tFNAs were further functionalized with a truncated transferrin receptor aptamer (tTR14) to enhance targeting specificity for PDAC cells. The constructed tFNA-based saRNA formulation demonstrated exceptional stability, efficient saRNA release ability, substantial cellular uptake, biocompatibility, and nontoxicity. In vitro experiments revealed successful intracellular delivery of CEBPA-saRNA utilizing tTR14-decorated tFNA nanocarriers, resulting in significant activation of tumor suppressor genes, namely, CEBPA and its downstream effector P21, leading to notable inhibition of PDAC cell proliferation. Moreover, in a mouse model of PDAC, the tTR14-decorated tFNA-mediated delivery of CEBPA-saRNA effectively upregulated the expression of the CEBPA and P21 genes, consequently suppressing tumor growth. These compelling findings highlight the potential utility of saRNA delivered via a designed tFNA nanocarrier to induce the activation of tumor suppressor genes as an innovative therapeutic approach for PDAC.

Enhancing Neuronal Cell Uptake of Therapeutic Nucleic Acids with Tetrahedral DNA Nanostructures

The successful translation of therapeutic nucleic acids (NAs) for the treatment of neurological disorders depends on their safe and efficient delivery to neural cells, in particular neurons. DNA nanostructures can be a promising NAs delivery vehicle. Nonetheless, the potential of DNA nanostructures for neuronal cell delivery of therapeutic NAs is unexplored. Here, tetrahedral DNA nanostructures (TDN) as siRNA delivery scaffolds to neuronal cells, exploring the influence of functionalization with two different reported neuronal targeting ligands: C4-3 RNA aptamer and Tet1 peptide are investigated. Nanostructures are characterized in vitro, as well as in silico using molecular dynamic simulations to better understand the overall TDN structural stability. Enhancement of neuronal cell uptake of TDN functionalized with the C4-3 Aptamer (TDN-Apt), not only in neuronal cell lines but also in primary neuronal cell cultures is demonstrated. Additionally, TDN and TDN-Apt nanostructures carrying siRNA are shown to promote silencing in a process aided by chloroquine-induced endosomal disruption. This work presents a thorough workflow for the structural and functional characterization of the proposed TDN as a nano-scaffold for neuronal delivery of therapeutic NAs and for targeting ligands evaluation, contributing to the future development of new neuronal drug delivery systems based on DNA nanostructures.

Programmable Tetrahedral DNA-RNA Nanocages Woven with Stimuli-Responsive siRNA for Enhancing Therapeutic Efficacy of Multidrug-Resistant Tumors

Multidrug resistance (MDR) is a major obstacle limiting the effectiveness of chemotherapy against cancer. The combination strategy of chemotherapeutic agents and siRNA targeting drug efflux has emerged as an effective cancer treatment to overcome MDR. Herein, stimuli-responsive programmable tetrahedral DNA-RNA nanocages (TDRN) have been rationally designed and developed for dynamic co-delivery of the chemotherapeutic drug doxorubicin and P-glycoprotein (P-gp) siRNA. Specifically, the sense and antisense strand sequences of the P-gp siRNA, which are programmable bricks with terminal disulfide bond conjugation, are precisely embedded in one edge of the DNA tetrahedron. TDRN provides a stimuli-responsive release element for dynamic control of functional cargo P-gp siRNA that is significantly more stable than the "tail-like" TDN nanostructures. The stable and highly rigid 3D nanostructure of the siRNA-organized TDRN nanocages demonstrated a notable improvement in the stability of RNase A and mouse serum, as well as long-term storage stability for up to 4 weeks, as evidenced by this study. These biocompatible and multifunctional TDRN nanocarriers with gold nanocluster-assisted delivery (TDRN@Dox@AuNCp) are successfully used to achieve synergistic RNAi/Chemo-therapy in vitro and in vivo. This programmable TDRN drug delivery system, which integrates RNAi therapy and chemotherapy, offers a promising approach for treating multidrug-resistant tumors.

Framework nucleic acids as promising reactive oxygen species scavengers for anti-inflammatory therapy

Reactive oxygen species (ROS) are an array of derivatives of molecular oxygen that participate in multiple physiological processes under the control of redox homeostasis. However, under pathological conditions, the over-production of ROS often leads to oxidative stress and inflammatory reactions, indicating a potential therapeutic target. With the rapid development of nucleic acid nanotechnology, scientists have exploited various DNA nanostructures with remarkable biocompatibility, programmability, and structural stability. Among these novel organic nanomaterials, a group of skeleton-like framework nucleic acid (FNA) nanostructures attracts the most interest due to their outstanding self-assembly, cellular endocytosis, addressability, and functionality. Surprisingly, different FNAs manifest similarly satisfactory antioxidative and anti-inflammatory effects during their biomedical application process. First, they are intrinsically endowed with the ability to neutralize ROS due to their DNA nature. Therefore, they are extensively involved in the complicated inflammatory signaling network. Moreover, the outstanding editability of FNAs also allows for flexible modifications with nucleic acids, aptamers, peptides, antibodies, low-molecular-weight drugs, and so on, thus further strengthening the targeting and therapeutic ability. This review focuses on the ROS-scavenging potential of three representative FNAs, including tetrahedral framework nucleic acids (tFNAs), DNA origami, and DNA hydrogels, to summarize the recent advances in their anti-inflammatory therapy applications. Although FNAs exhibit great potential in treating inflammatory diseases as promising ROS scavengers, massive efforts still need to be made to overcome the emerging challenges in their clinical translation.

Natural Biopolymer-Based Delivery of CRISPR/Cas9 for Cancer Treatment

Over the last decade, the clustered, regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become the most promising gene editing tool and is broadly utilized to manipulate the gene for disease treatment, especially for cancer, which involves multiple genetic alterations. Typically, CRISPR/Cas9 machinery is delivered in one of three forms: DNA, mRNA, or ribonucleoprotein. However, the lack of efficient delivery systems for these macromolecules confined the clinical breakthrough of this technique. Therefore, a variety of nanomaterials have been fabricated to improve the stability and delivery efficiency of the CRISPR/Cas9 system. In this context, the natural biopolymer-based carrier is a particularly promising platform for CRISPR/Cas9 delivery due to its great stability, low toxicity, excellent biocompatibility, and biodegradability. Here, we focus on the advances of natural biopolymer-based materials for CRISPR/Cas9 delivery in the cancer field and discuss the challenges for their clinical translation.

Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts

Human transcriptome can undergo RNA mis-splicing due to spliceopathies contributing to the increasing number of genetic diseases including muscular dystrophy (MD), Alzheimer disease (AD), Huntington disease (HD), myelodysplastic syndromes (MDS). Intron retention (IR) is a major inducer of spliceopathies where two or more introns remain in the final mature mRNA and account for many intronic expansion diseases. Potential removal of such introns for therapeutic purposes can be feasible when utilizing bioinformatics, catalytic RNAs, and nano-drug delivery systems. Overcoming delivery challenges of catalytic RNAs was discussed in this review as a future perspective highlighting the significance of utilizing synthetic biology in addition to high throughput deep sequencing and computational approaches for the treatment of mis-spliced transcripts.

Peptide nanostructures-based delivery of DNA nanomaterial therapeutics for regulating gene expression

Self-assembled branched DNA (bDNA) nanomaterials have exhibited their functionality in various biomedical and diagnostic applications. However, the anionic cellular membrane has restricted the movement of bDNA nanostructures. Recently, amphiphilic peptides have been investigated as cationic delivery agents for nucleic acids. Herein, we demonstrate a strategy for delivering functional bDNA nanomaterials into mammalian cells using self-assembled linear peptides. In this study, antisense oligonucleotides of vascular endothelial growth factor (VEGF) were inserted in the overhangs of bDNAs. Novel linear peptides have been synthesized and the peptide-bound bDNA complex formation was examined using various biophysical experiments. Interestingly, the W4R4-bound bDNAs were found to be exceptionally stable against DNase I compared to other complexes. The delivery of fluorescent-labeled bDNAs into the mammalian cells confirmed the potential of peptide transporters. Furthermore, the functional efficacy of the peptide-bound bDNAs has been examined through RT-PCR and western blot analysis. The observed results revealed that W4R4 peptides exhibited excellent internalization of antisense bDNAs and significantly suppressed (3- to 4-fold) the transcripts and translated product of VEGF compared to the control. In summary, the results highlight the potential use of peptide-based nanocarrier for delivering bDNA nanostructures to regulate the gene expression in cell lines.

Programming Aggregate States of DNA Nanorods with Sub-10 nm Hydrophobic Patterns for Tunable Cell Entry

The intracellular application of DNA nanodevices is challenged by their inadequate cellular entry efficiency, which may be addressed by the development of amphiphilic DNA nanostructures. However, the impact of the spatial distribution of hydrophobicity in cell entry has not been fully explored. Here, we program a spectrum of amphiphilic DNA nanostructures displaying diverse sub-10 nm patterns of cholesterol, which result in distinct aggregate states in the aqueous solution and thus varied cell entry efficiencies. We find that the hydrophobic patterns can lead to discrete aggregate states, from monomers to low-number oligomers (n = 1-6). We demonstrate that the monomers or oligomers with moderate hydrophobic density are preferred for cell entry, with up to ∼174-fold improvement relative to unmodified ones. Our study provides a new clue for the rational design of amphiphilic DNA nanostructures for intracellular applications.

An Infectious Virus-like Particle Built on a Programmable Icosahedral DNA Framework

Viral genomes can be compressed into a near-spherical nanochamber to form infectious particles. In order to mimic the virus morphology and packaging behavior, we invented a programmable icosahedral DNA nanoframe with enhanced rigidity and encapsulated the phiX174 bacteriophage genome. The packaging efficiency could be modulated through specific anchoring strands adjustment, and the trapped phage genome remained accessible for enzymatic operations. Moreover, the packed complex could infect Escherichia coli (E. coli) cells through bacterial uptake to produce plaques. This rigid icosahedral DNA architecture demonstrated a versatile platform to develop virus mimetic particles for convenient functional nucleic acid entrapment, manipulation and delivery.

Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis

RNAs are involved in the crucial processes of disease progression and have emerged as powerful therapeutic targets and diagnostic biomarkers. However, efficient delivery of therapeutic RNA to the targeted location and precise detection of RNA markers remains challenging. Recently, more and more attention has been paid to applying nucleic acid nanoassemblies in diagnosing and treating. Due to the flexibility and deformability of nucleic acids, the nanoassemblies could be fabricated with different shapes and structures. With hybridization, nucleic acid nanoassemblies, including DNA and RNA nanostructures, can be applied to enhance RNA therapeutics and diagnosis. This review briefly introduces the construction and properties of different nucleic acid nanoassemblies and their applications for RNA therapy and diagnosis and makes further prospects for their development.

Recent advances in aptamer-based targeted drug delivery systems for cancer therapy

The past decade has become an important strategy in precision medicine for the targeted therapy of many diseases, expecially various types of cancer. As a promising targeted element, nucleic acid aptamers are single-stranded functional oligonucleotides which have specific abilities to bind with various target molecules ranging from small molecules to entire organisms. They are often named ‘chemical antibody’ and have aroused extensive interest in diverse clinical studies on account of their advantages, such as considerable biostability, versatile chemical modification, low immunogenicity and quick tissue penetration. Thus, aptamer-embedded drug delivery systems offer an unprecedented opportunity in bioanalysis and biomedicine. In this short review, we endeavor to discuss the recent advances in aptamer-based targeted drug delivery platforms for cancer therapy. Some perspectives on the advantages, challenges and opportunities are also presented.

A Tetrahedral Framework DNA-Based Bioswitchable miRNA Inhibitor Delivery System: Application to Skin Anti-Aging

MicroRNA (miR)-based therapy shows strong potential; however, structural limitations pose a challenge in fully exploiting its biomedical functionality. Tetrahedral framework DNA (tFNA) has proven to be an ideal vehicle for miR therapy. Inspired by the ancient Chinese myth "Sun and Immortal Birds," a novel bioswitchable miR inhibitor delivery system (BiRDS) is designed with three miR inhibitors (the three immortal birds) and a nucleic acid core (the central sun). The BiRDS fuses miR inhibitors within the framework, maximizing their loading capacity, while allowing the system to retain the characteristics of small-sized tFNA and avoiding uncertainty associated with RNA exposure in traditional loading protocols. The RNase H-responsive sequence at the tail of each "immortal bird" enables the BiRDS to transform from a 3D to a 2D structure upon entering cells, promoting the delivery of miR inhibitors. To confirm the application potential, the BiRDS is used to deliver the miR-31 inhibitor, with antiaging effects on hair follicle stem cells, into a skin aging model. Superior skin penetration ability and RNA delivery are observed with significant anti-aging effects. These findings demonstrate the capability and editability of the BiRDS to improve the stability and delivery efficacy of miRs for future innovations.

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.

A Lysosome-Activated Tetrahedral Nanobox for Encapsulated siRNA Delivery

Tetrahedral framework nucleic acids (tFNAs) have attracted extensive attention as drug nanocarriers because of their excellent cellular uptake. However, for oligonucleotide cargos, tFNA mainly acts as a static delivery platform generated via sticky-ended ligation. Here, inspired by the original stable space inside the tetrahedral scaffold, a dynamic lysosome-activated tFNA nanobox is fabricated for completely encapsulating a short interfering RNA (siRNA) of interest. The closed tetrahedral structure endows cargo siRNA with greater resistance against RNase and serum and enables solid integration with the vehicle during delivery. Moreover, the pH-responsive switch of nanobox allows the controlled release of siRNA upon entry into lysosomes at cell culture temperature. Based on protective loading and active unloading, an excellent silencing effect on the target tumor necrosis factor alpha (TNFα) gene is achieved in in vitro and in vivo experiments. Conclusively, the nanobox offers a dynamic pH-sensitive confinement delivery system for siRNA and can be an extendable strategy for other small RNA.

Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering

Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Macrophages in atherosclerotic lesions promote plaque progression and are an attractive therapeutic target in cardiovascular research. Here we present a protocol for synthesis of small interfering RNA (siRNA) nanoparticles (NP) that target lesional macrophages as a potential treatment for atherosclerosis. Ca²⁺/calmodulin-dependent protein kinase γ (CaMKIIγ) activity in macrophages of advanced human and mouse atherosclerotic plaques drives necrosis by downregulating the expression of the efferocytosis receptor MerTK. Therefore, selective inhibition of CaMKIIγ in lesional macrophages holds great promise for the treatment of advanced atherosclerosis. We recently developed a siRNA NP platform that can selectively silence CaMKIIγ in macrophages, resulting in increased plaque stability. We provide a detailed protocol for the synthesis of NP components, the preparation and characterization (physicochemical and in vitro) of siRNA NPs, and the evaluation of in vivo therapeutic effects of siRNA NPs and their biocompatibility in atherosclerotic mice. Our siRNA-loaded polymer-lipid hybrid NPs are constructed via a robust self-assembly method, exhibiting excellent in vivo features for systemic siRNA delivery. Following this protocol, it takes 3-5 d to prepare the siRNA NPs, 8-10 d to characterize the NPs and 4-5 weeks to evaluate their therapeutic effects in established atherosclerotic mice. By changing the RNA molecules loaded in the NPs, lesional macrophages can be targeted for the exploration and validation of new targets/pathways in atherosclerosis.

RNA Drug Delivery Using Biogenic Nanovehicles for Cancer Therapy

RNA-based therapies have been promising method for treating all kinds of diseases, and four siRNA-based drugs and two mRNA-based drugs have been approved and are on the market now. However, none of them is applied for cancer treatment. This is not only because of the complexity of the tumor microenvironment, but also due to the intrinsic obstacles of RNAs. Until now, all kinds of strategies have been developed to improve the performance of RNAs for cancer therapy, especially the nanoparticle-based ones using biogenic materials. They are much more compatible with less toxicity compared to the ones using synthetic polymers, and the most widely studied biogenic materials are oligonucleotides, exosomes, and cell membranes. Particular characteristics make them show different capacities in internalization and endosomal escape as well as specific targeting. In this paper, we systematically summarize the RNA-based nano-delivery systems using biogenic materials for cancer therapy, and we believe this review will provide a valuable reference for researchers involved in the field of biogenic delivery and RNA-based therapies for cancer treatment.

An autophagy-inhibitory MOF nanoreactor for tumor-targeted synergistic therapy

An autophagy-inhibitory metal-organic framework (MOF) nanoreactor was developed for tumor-targeted synergistic therapy. The nanoreactor could inhibit autophagy to enhance the glucose oxidase (GOx)-mediated starvation therapy. And the H2O2 generated in...

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.

Intercalation-Driven Formation of siRNA Nanogels for Cancer Therapy

RNA interference (RNAi) is a powerful approach in the treatment of various diseases including cancers. The clinical translation of small interfering RNA (siRNA)-based therapy requires safe and efficient delivery vehicles. Here, we report a siRNA nanogels (NG)-based delivery vehicle, which is driven directly by the intercalation between nucleic acid bis-intercalator and siRNA molecules. The intercalation-based siRNA NG exhibits good physiological stability and can enter cells efficiently via different endocytosis pathways. Furthermore, the siRNA NG can not only silence the target genes in vitro but also significantly inhibit the tumor growth in vivo. Therefore, this study provides an intercalation-based strategy for the development of a siRNA delivery platform for cancer therapy. To the best of our knowledge, this is the first report of the intercalation-driven siRNA NG.

Lipids and Lipid Derivatives for RNA Delivery

RNA-based therapeutics have shown great promise in treating a broad spectrum of diseases through various mechanisms including knockdown of pathological genes, expression of therapeutic proteins, and programmed gene editing. Due to the inherent instability and negative-charges of RNA molecules, RNA-based therapeutics can make the most use of delivery systems to overcome biological barriers and to release the RNA payload into the cytosol. Among different types of delivery systems, lipid-based RNA delivery systems, particularly lipid nanoparticles (LNPs), have been extensively studied due to their unique properties, such as simple chemical synthesis of lipid components, scalable manufacturing processes of LNPs, and wide packaging capability. LNPs represent the most widely used delivery systems for RNA-based therapeutics, as evidenced by the clinical approvals of three LNP-RNA formulations, patisiran, BNT162b2, and mRNA-1273. This review covers recent advances of lipids, lipid derivatives, and lipid-derived macromolecules used in RNA delivery over the past several decades. We focus mainly on their chemical structures, synthetic routes, characterization, formulation methods, and structure-activity relationships. We also briefly describe the current status of representative preclinical studies and clinical trials and highlight future opportunities and challenges.

Synchronous conjugation of i-motif DNA and therapeutic siRNA on the vertexes of tetrahedral DNA nanocages for efficient gene silence

The functionality of DNA biomacromolecules has been widely excavated, as therapeutic drugs, carriers, and functionalized modification derivatives. In this study, we developed a series of DNA tetrahedron nanocages (Td), via synchronous conjugating different numbers of i-(X) and therapeutic siRNA on four vertexes of tetrahedral DNA nanocage (aX-Td@bsiRNA, a+b = 4). This i-motif-conjugated Td exhibited good endosomal escape behaviours in A549 tumor cells, and the escape efficiency was affected by the number of i-motif. Furthermore, the downregulating mRNA and protein expression level of epidermal growth factor receptor (EGFR) caused by this siRNA embedded Td were verified in A549 cells. The tumor growth inhibition efficiency of the 2X-Td@2siRNA treated group in tumor-bearing mice was significantly higher than that of non-i-motif-conjugated Td@2siRNA (3.14-fold) and free siRNA (3.63-fold). These results demonstrate a general strategy for endowing DNA nanostructures with endosomal escape behaviours to achieve effective in vivo gene delivery and therapy.

DNA Based and Stimuli-Responsive Smart Nanocarrier for Diagnosis and Treatment of Cancer: Applications and Challenges

The rapid development of multidrug co-delivery and nano-medicines has made spontaneous progress in tumor treatment and diagnosis. DNA is a unique biological molecule that can be tailored and molded into various nanostructures. The addition of ligands or stimuli-responsive elements enables DNA nanostructures to mediate highly targeted drug delivery to the cancer cells. Smart DNA nanostructures, owing to their various shapes, sizes, geometry, sequences, and characteristics, have various modes of cellular internalization and final disposition. On the other hand, functionalized DNA nanocarriers have specific receptor-mediated uptake, and most of these ligand anchored nanostructures able to escape lysosomal degradation. DNA-based and stimuli responsive nano-carrier systems are the latest advancement in cancer targeting. The data exploration from various studies demonstrated that the DNA nanostructure and stimuli responsive drug delivery systems are perfect tools to overcome the problems existing in the cancer treatment including toxicity and compromised drug efficacy. In this light, the review summarized the insights about various types of DNA nanostructures and stimuli responsive nanocarrier systems applications for diagnosis and treatment of cancer.

DNA Nanodevices with Selective Immune Cell Interaction and Function

DNA nanotechnology produces precision nanostructures of defined chemistry. Expanding their use in biomedicine requires designed biomolecular interaction and function. Of topical interest are DNA nanostructures that function as vaccines with potential advantages over nonstructured nucleic acids in terms of serum stability and selective interaction with human immune cells. Here, we describe how compact DNA nanobarrels bind with a 400-fold selectivity via membrane anchors to white blood immune cells over erythrocytes, without affecting cell viability. The selectivity is based on the preference of the cholesterol lipid anchor for the more fluid immune cell membranes compared to the lower membrane fluidity of erythrocytes. Compacting DNA into the nanostructures gives rise to increased serum stability. The DNA barrels furthermore functionally modulate white blood cells by suppressing the immune response to pro-inflammatory endotoxin lipopolysaccharide. This is likely due to electrostatic or steric blocking of toll-like receptors on white blood cells. Our findings on immune cell-specific DNA nanostructures may be applied for vaccine development, immunomodulatory therapy to suppress septic shock, or the targeting of bioactive substances to immune cells.

Functional Aptamer-Embedded Nanomaterials for Diagnostics and Therapeutics

In the past decades, various nanomaterials with unique properties have been explored for bioapplications. Meanwhile, aptamers, generated from the systematic evolution of ligands by exponential enrichment technology, are becoming an indispensable element in the design of functional nanomaterials because of their small size, high stability, and convenient modification, especially endowing nanomaterials with recognition capability to specific targets. Therefore, the incorporation of aptamers into nanomaterials offers an unprecedented opportunity in the research fields of diagnostics and therapeutics. Here, we focus on recent advances in aptamer-embedded nanomaterials for bioapplications. First, we briefly introduce the properties of nanomaterials that can be functionalized with aptamers. Then, the applications of aptamer-embedded nanomaterials in cellular analysis, imaging, targeted drug delivery, gene editing, and cancer diagnosis/therapy are discussed. Finally, we provide some perspectives on the challenges and opportunities that have arisen from this promising area.

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.

Template-Mediated Assembly of DNA into Microcapsules for Immunological Modulation

There is a need for effective vaccine delivery systems and vaccine adjuvants without extraneous excipients that can compromise or minimize their efficacy. Vaccine adjuvants cytosine-phosphate-guanosine oligodeoxynucleotides (CpG ODNs) can effectively activate immune responses to secrete cytokines. However, CpG ODNs are not stable in serum due to enzymatic cleavage and are difficult to transport through cell membranes. Herein, DNA microcapsules made of CpG ODNs arranged into 3D nanostructures are developed to improve the serum stability and immunostimulatory effect of CpG. The DNA microcapsules allow encapsulation and co-delivery of cargoes, including glycogen. The DNA capsules, with >4 million copies of CpG motifs per capsule, are internalized in cells and accumulate in endosomes, where the Toll-like receptor 9 is engaged by CpG. The capsules induce up to 10-fold and 20-fold increases in tumor necrosis factor (TNF)-α and interleukin (IL)-6 secretion, respectively, in RAW264.7 cells compared with CpG ODNs. Furthermore, the microcapsules stimulate TNF-α and IL-6 secretion in a concentration- and time-dependent manner. The immunostimulatory activity of the capsules correlates to their intracellular trafficking, endosomal confinement, and degradation, assessed by confocal and super-resolution microscopy. These DNA capsules can serve as both adjuvants to stimulate an immune reaction and vehicles to encapsulate vaccine peptides/genes to achieve synergistic immune effects.

Smart Nanocarriers for the Delivery of Nucleic Acid-Based Therapeutics: A Comprehensive Review

Nucleic acid-based therapies are promising therapeutics for the treatment of several systemic disorders, and they offer an exciting opportunity to address emerging biological challenges. The scope of nucleic acid-based therapeutics in the treatment of multiple disease states including cancers has been widened by recent progress in Ribonucleic acids (RNA) biology. However, cascades of systemic and intracellular barriers, including rapid degradation, renal clearance, and poor cellular uptake, hinder the clinical effectiveness of nucleic acid-based therapies. These barriers can be circumvented by utilizing advanced smart nanocarriers that efficiently deliver and release the encapsulated nucleic acids into the target tissues. This review describes the current status of clinical trials on nucleic acid-based therapeutics and highlights representative examples that provide an overview on the current and emerging trends in nucleic acid-based therapies. A better understanding of the design of advanced nanocarriers is essential to promote the translation of therapeutic nucleic acids into a clinical reality.

Multi-targeted Antisense Oligonucleotide Delivery by a Framework Nucleic Acid for Inhibiting Biofilm Formation and Virulence

A framework nucleic acid delivery system was developed through self-assembly, which can deliver antisense oligonucleotides against multiple targets in bacterial cells.

The ASOs-tFNAs (750 nM) was found to simultaneously inhibit the expression of gtfBCD, gbpB, and ftf, and significantly reduce the extracellular polysaccharide synthesis and biofilm thickness.

Biofilm formation is responsible for numerous chronic infections and represents a serious health challenge. Bacteria and the extracellular polysaccharides (EPS) cause biofilms to become adherent, toxic, resistant to antibiotics, and ultimately difficult to remove. Inhibition of EPS synthesis can prevent the formation of bacterial biofilms, reduce their robustness, and promote removal. Here, we have developed a framework nucleic acid delivery system with a tetrahedral configuration. It can easily access bacterial cells and functions by delivering antisense oligonucleotides that target specific genes. We designed antisense oligonucleotide sequences with multiple targets based on conserved regions of the VicK protein-binding site. Once delivered to bacterial cells, they significantly decreased EPS synthesis and biofilm thickness. Compared to existing approaches, this system is highly efficacious because it simultaneously reduces the expression of all targeted genes (gtfBCD, gbpB, ftf). We demonstrate a novel nucleic acid-based nanomaterial with multi-targeted inhibition that has great potential for the treatment of chronic infections caused by biofilms.

Well-Defined DNA-Polymer Miktoarm Stars for Enzyme-Resistant Nanoflares and Carrier-Free Gene Regulation

Herein, we report a star-architectured poly(ethylene glycol) (PEG)-oligonucleotide nanoconjugate of a well-defined molecular structure. Based upon fullerene C₆₀ cores, each star bears precisely 1 DNA strand and 11 polymer chains. The elevated PEG density provides the DNA with steric selectivity: the DNA is significantly more resistant to nuclease digestion while remaining able to hybridize with a complementary sequence. The degree of resistance increases as the centers of mass for the DNA and fullerene are closer together. Such steric selectivity reduces protein-related background signals of the nanoflares synthesized from these miktoarm star polymers. Importantly, the stars improve cellular uptake and regulate gene expression as a non-cytotoxic, single-entity antisense agent without the need for a transfection carrier.

Engineered DNA nanodrugs alleviate inflammation in inflammatory arthritis

Rheumatoid arthritis (RA) is an autoimmune disease featured with chronic joint inflammation. Suppression of inflammation is critical to RA treatment and joint protection. In this study, DNA nanodrugs are prepared via the conjugation of NF-κB decoy oligodeoxynucleotides (dODNs) and VCAM-1 targeted peptides (P) onto self-assembled DNA tetrahedrons (TDs). Physicochemical properties of DNA nanodrugs are characterized using atomic force microscopy (AFM), gel electrophoresis and Fourier Transform Infrared Spectrometer (FTIR). Cytotoxicity, cellular uptake and anti-inflammatory efficacy of DNA nanodrugs are evaluated in vitro. Clinical arthritis index, inflammatory proteins in serum and joint pathophysiology are also investigated in vivo. TD-P-dODN possesses one dODN and one P and exhibits faster and higher cellular uptake by inflammatory cells compared with free dODNs. TD-P-dODN also significantly reduce inflammatory proteins in cells and adjuvant induced arthritis (AIA) mice. Reduced clinical arthritis index and improved joint rehabilitation are also achieved by TD-P-dODN treatment. This study demonstrates that an engineered DNA nanodrug (TD-P-dODN) enhances the efficacy of nucleic acid drugs and represents a promising strategy for RA treatment.

Engineering Lipid Membranes with Programmable DNA Nanostructures

Lipid and DNA are abundant biomolecules with critical functions in cells. The water-insoluble, amphipathic lipid molecules are best known for their roles in energy storage (e.g. as triglyceride), signaling (e.g. as sphingolipid), and compartmentalization (e.g. by forming membrane-enclosed bodies). The soluble, highly negatively charged DNA, which stores cells' genetic information, has proven to be an excellent material for constructing programmable nanostructures in vitro thanks to its self-assembling capabilities. These two seemingly distant molecules make contact within cell nuclei, often via lipidated proteins, with proposed functions of modulating chromatin structures. Carefully formulated lipid/DNA complexes are promising reagents for gene therapy. The past few years saw an emerging research field of interfacing DNA nanostructures with lipid membranes, with an overarching goal of generating DNA/lipid hybrid materials that possess novel and controllable structure, dynamics, and function. An arsenal of DNA-based tools has been created to coat, mold, deform, and penetrate lipid bilayers, affording us the ability to manipulate membranes with nanoscopic precision. These membrane engineering methods not only enable quantitative biophysical studies, but also open new opportunities in synthetic biology (e.g. artificial cells) and therapeutics (e.g. drug delivery).

An enzymatically self-assembled DNA patch for enhanced blood coagulation

The assembly of a DNA patch combining enzymatically fabricated DNA film and aptamer-based thrombin binding for enhanced blood coagulation is demonstrated.

Nanoparticles-based drug delivery and gene therapy for breast cancer: Recent advancements and future challenges

Breast cancer (BC) is amongst the most lethal cancer among females and conventional treatment methods like surgery, radiotherapy and chemotherapy are not effective enough as expected and suffer concerns of low bioavailability, low cellular uptake, emerging resistance, and adverse toxicities. Gene therapy using free nucleic acids has potential to deal with key candidate genes of BC, but their effect is retarded due to poor cell uptake and instability in circulation. The rapidly evolving field of nanomedicine aiming targeted drug/gene delivery curtailing BC promises to overcome the limitations of conventional therapies. Nanoparticles can be game changer for BC gene therapy as they can be effective carrier of specific drug/gene by improving the circulation time, enhancing bioavailability, reducing the immune system based recognition chances, and delivering the gene regulator accurately. Herein, we discuss the mechanism of nanoparticles targeted drug delivery, recent advancement of therapeutic strategies of nanoparticles based carriers for small interfering RNA, and microRNA, and gene augmentation therapies in BC. We also discuss the future prospect and challenges of nanoparticle-based therapies for BC.

Opportunities and Challenges in DNA-Hybrid Nanomaterials

Nature has inspired the development of many life-like materials. Although still simplistic, key biological functionalities have been incorporated, enabling a wide variety of applications. DNA-based systems, in particular, show high promise due to their ability to merge specific Watson-Crick base pairing with unique properties that are also programmable, scalable, or dynamic. By combining the fields of DNA-based covalent polymers, DNA origami, and DNA-functionalized supramolecular polymers, new frontiers in next-generation DNA-based hybrid materials that can outperform current bioartificial systems will be realized. Many challenges must still be overcome before this emerging technology can be materialized.

A minimalist's approach for DNA nanoconstructions

Structural DNA nanotechnology takes DNA, a biopolymer, far beyond being the molecule that stores and transmits genetic information in biological systems. DNA has been employed as building blocks for the assembly of designed, nanoscaled, supramolecular DNA architectures for applications in biophysics, structure determination, synthetic biology, diagnostics, and drug delivery. Herein, we review a symmetric approach of tile-based DNA self-assembly. This approach allows the construction of DNA nanostructures from minimal numbers of different types of DNA strands based on sequence and structural symmetries. Some examples of the applications of this approach in siRNA delivery are discussed as well.

At the Intersection of Biomaterials and Gene Therapy: Progress in Non-viral Delivery of Nucleic Acids

Biomaterials play a critical role in technologies intended to deliver therapeutic agents in clinical settings. Recent explosion of our understanding of how cells utilize nucleic acids has garnered excitement to develop a range of older (e.g., antisense oligonucleotides, plasmid DNA and transposons) and emerging (e.g., short interfering RNA, messenger RNA and non-coding RNAs) nucleic acid agents for therapy of a wide range of diseases. This review will summarize biomaterials-centered advances to undertake effective utilization of nucleic acids for therapeutic purposes. We first review various types of nucleic acids and their unique abilities to deliver a range of clinical outcomes. Using recent advances in T-cell based therapy as a case in point, we summarize various possibilities for utilizing biomaterials to make an impact in this exciting therapeutic intervention technology, with the belief that this modality will serve as a therapeutic paradigm for other types of cellular therapies in the near future. We subsequently focus on contributions of biomaterials in emerging nucleic acid technologies, specifically focusing on the design of intelligent nanoparticles, deployment of mRNA as an alternative to plasmid DNA, long-acting (integrating) expression systems, and in vitro/in vivo expansion of engineered T-cells. We articulate the role of biomaterials in these emerging nucleic acid technologies in order to enhance the clinical impact of nucleic acids in the near future.

Targeted Transmembrane Delivery of Ca2+ via FA-Nanogel for Synergistically Enhanced Chemotherapy

Metal ion synergistically enhanced chemotherapy is a promising strategy for cancer treatment. However, targeting delivery of ions toward cancer cells remains challenging for decades. Herein, we developed a novel folic acid-nanogel (termed as FA-nanogel) with alkane chains as diffusion barriers for targeted transmembrane delivery of calcium ions into cancer cells. With the aid of hydrophobic diffusion barriers, the FA-nanogel showed a reduced and sustained speed for release of calcium ions, significantly prolonging the ion effect. Moreover, a pH-sensitive injectable hydrogel-loaded FA-nanogel and chemotherapeutic drug 5-fluorouracil (5-Fu) was synthesized for investigating the synergistic effect of nanogel on chemotherapy. Both in vitro and in vivo experiments confirmed that the intracellular calcium ions were continuously increased because of the targeted delivery ability and ion sustained release ability of the smart FA-nanogel, and the tumor growth was effectively inhibited by the ion synergistic chemotherapy. This study not only provides a powerful nanoplatform for sustained transmembrane delivery of ions into malignant cells but also creates better conditions for improving the therapeutic efficacy of chemotherapy.

Molecular Engineering of Functional Nucleic Acid Nanomaterials toward In Vivo Applications

Recent advances in nanotechnology and engineering have generated many nanomaterials with unique physical and chemical properties. Over the past decade, numerous nanomaterials are introduced into many research areas, such as sensors for environmental monitoring, food safety, point-of-care diagnostics, and as transducers for solar energy transfer. Meanwhile, functional nucleic acids (FNAs), including nucleic acid enzymes, aptamers, and aptazymes, have attracted major attention from the biomedical community due to their unique target recognition and catalytic properties. Benefiting from the recent progress of molecular engineering strategies, the physicochemical properties of nanomaterials are endowed by the target recognition and catalytic activity of FNAs in the presence of a target analyte, resulting in numerous smart nanoprobes for diverse applications including intracellular imaging, drug delivery, in vivo imaging, and tumor therapy. This progress report focuses on the recent advances in designing and engineering FNA-based nanomaterials, highlighting the functional outcomes toward in vivo applications. The challenges and opportunities for the future translation of FNA-based nanomaterials into clinical applications are also discussed.