DNA Trojan Horses: Self‐Assembled Floxuridine‐Containing DNA Polyhedra for Cancer Therapy

DNA Droplets: Intelligent, Dynamic Fluid

Breathtaking advances in DNA nanotechnology have established DNA as a promising biomaterial for the fabrication of programmable higher-order nano/microstructures. In the context of developing artificial cells and tissues, DNA droplets have emerged as a powerful platform for creating intelligent, dynamic cell-like machinery. DNA droplets are a microscale membrane-free coacervate of DNA formed through phase separation. This new type of DNA system couples dynamic fluid-like property with long-established DNA programmability. This hybrid nature offers an advantageous route to facile and robust control over the structures, functions, and behaviors of DNA droplets. This review begins by describing programmable DNA condensation, commenting on the physical properties and fabrication strategies of DNA hydrogels and droplets. By presenting an overview of the development pathways leading to DNA droplets, it is shown that DNA technology has evolved from static, rigid systems to soft, dynamic systems. Next, the basic characteristics of DNA droplets are described as intelligent, dynamic fluid by showcasing the latest examples highlighting their distinctive features related to sequence-specific interactions and programmable mechanical properties. Finally, this review discusses the potential and challenges of numerical modeling able to connect a robust link between individual sequences and macroscopic mechanical properties of DNA droplets.

Virus Mimetic Framework DNA as a Non-LNP Gene Carrier for Modulated Cell Endocytosis and Apoptosis

Mimicking the size and shape of spherical viruses, we constructed a soccer-ball shaped virus-inspired DNA origami (ViDO) framework as a programmable non-LNP (lipid nanoparticle) gene carrier. The DNA framework was decorated with precisely controlled recognition molecules outside and loaded with adequate genetic molecules inside. Five variants were constructed to systematically investigate their cell uptake and modulated gene silencing efficiency. Cellular uptake was enhanced with an increasing number of aptamers, while with a median number of aptamer supply, dispersed distribution performed better than the clustered pattern. Intriguingly, the transfection efficiency was maximized using the ViDO with clustered five aptamers, which exhibited a competitive RNA silencing effect induced by Lipo2000 with low cytotoxicity. Our results revealed the effects of aptamer distribution patterns on endocytosis and transfection, thus providing a programmable platform for meticulous optimization of the gene delivery system.

Boosted Productivity in Single-Tile-Based DNA Polyhedra Assembly by Simple Cation Replacement

Cations such as divalent magnesium ion (Mg²⁺ ) play an essential role in DNA self-assembly. However, the strong electrostatic shielding effect of Mg²⁺ would be disadvantageous in some situations that require relatively weak interactions to allow a highly reversible error-correcting mechanism in the process of assembly. Herein, by substituting the conventional divalent Mg²⁺ with monovalent sodium ion (Na⁺ ), we have achieved one-pot high-yield assembly of tile-based DNA polyhedra at micromolar concentration of tiles, at least 10 times higher than the DNA concentrations reported previously. This strategy takes advantage of coexisting counterions and is expected to surmount the major obstacle to potential applications of such DNA nanostructures: large-scale production.

Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers

Oligonucleotides containing cleavable linkers have emerged as versatile tools to achieve stimulus-responsive and site-specific cleavage of DNA. However, the limitations of previously reported cleavable linkers including photolabile and disulfide linkers have restricted their applications in vivo. Inspired by the cathepsin B-sensitive dipeptide linkers in antibody-drug conjugates (ADCs) such as Adcetris, we have developed Val-Ala-02 and Val-Ala-Chalcone phosphoramidites for the automated synthesis of enzyme-cleavable oligonucleotides. Cathepsin B digests Val-Ala-02 and Val-Ala-Chalcone linkers efficiently, enabling cleavage of oligonucleotides into two components or release of small-molecule payloads. Based on the prior success of dipeptide linkers in ADCs, we believe that these dipeptide linker phosphoramidites will promote new clinical applications of therapeutic oligonucleotides.

Engineering Enzyme-Cleavable Oligonucleotides by Automated Solid-Phase Incorporation of Cathepsin B Sensitive Dipeptide Linkers

Oligonucleotides containing cleavable linkers have emerged as versatile tools to achieve stimulus-responsive and site-specific cleavage of DNA. However, the limitations of previously reported cleavable linkers including photolabile and disulfide linkers have restricted their applications in vivo. Inspired by the cathepsin B-sensitive dipeptide linkers in antibody-drug conjugates (ADCs) such as Adcetris, we have developed Val-Ala-02 and Val-Ala-Chalcone phosphoramidites for the automated synthesis of enzyme-cleavable oligonucleotides. Cathepsin B digests Val-Ala-02 and Val-Ala-Chalcone linkers efficiently, enabling cleavage of oligonucleotides into two components or release of small-molecule payloads. Based on the prior success of dipeptide linkers in ADCs, we believe that these dipeptide linker phosphoramidites will promote new clinical applications of therapeutic oligonucleotides.

Functional Nucleic Acid Nanomaterials: Development, Properties, and Applications

Functional nucleic acid (FNA) nanotechnology is an interdisciplinary field between nucleic acid biochemistry and nanotechnology that focuses on the study of interactions between FNAs and nanomaterials and explores the particular advantages and applications of FNA nanomaterials. With the goal of building the next-generation biomaterials that combine the advantages of FNAs and nanomaterials, the interactions between FNAs and nanomaterials as well as FNA self-assembly technologies have established themselves as hot research areas, where the target recognition, response, and self-assembly ability, combined with the plasmon properties, stability, stimuli-response, and delivery potential of various nanomaterials can give rise to a variety of novel fascinating applications. As research on the structural and functional group features of FNAs and nanomaterials rapidly develops, many laboratories have reported numerous methods to construct FNA nanomaterials. In this Review, we first introduce some widely used FNAs and nanomaterials along with their classification, structure, and application features. Then we discuss the most successful methods employing FNAs and nanomaterials as elements for creating advanced FNA nanomaterials. Finally, we review the extensive applications of FNA nanomaterials in bioimaging, biosensing, biomedicine, and other important fields, with their own advantages and drawbacks, and provide our perspective about the issues and developing trends in FNA nanotechnology.

Parallel G-quadruplex Structures Increase Cellular Uptake and Cytotoxicity of 5-Fluoro-2'-deoxyuridine Oligomers in 5-Fluorouracil Resistant Cells

Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs have been considered first-line chemotherapy agents for the treatment of colorectal cancer. However, poor specificity and tumor cell resistance remain major limiting bottlenecks. G-quadruplexes, have been suggested as preferred nanostructures for enhancing cellular uptake mediated by G-quadruplex binding proteins which are abundant at the membranes of some tumor cells. In the current study, we propose a new strategy to deliver 5-fluoro-2′-deoxyuridine (5-FdU) monophosphate, the main active drug from 5-FU derivatives that may circumvent the cellular mechanisms of FU-resistant cancer cells. Two G-quadruplexes delivery systems containing four and six G-tetrads ((TG₄T) and (TG₆T)) linked to a FdU oligonucleotide were synthesized. Biophysical studies show that the G-quadruplex parallel structures are not affected by the incorporation of the 5 units of FdU at the 5’-end. Internalization studies confirmed the ability of such G-quadruplex nanostructures to facilitate the transport of the FdU pentamer and increase its cytotoxic effect relative to conventional FU drug in FU-resistant colorectal cancer cells. These results suggest that FdU oligomers linked to G-quadruplex parallel sequences may be a promising strategy to deliver fluoropyrimidines to cancer cells.

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.

A Tubular DNA Nanodevice as a siRNA/Chemo-Drug Co-delivery Vehicle for Combined Cancer Therapy

Using the DNA origami technique, we constructed a DNA nanodevice functionalized with small interfering RNA (siRNA) within its inner cavity and the chemotherapeutic drug doxorubicin (DOX), intercalated in the DNA duplexes. The incorporation of disulfide bonds allows the triggered mechanical opening and release of siRNA in response to intracellular glutathione (GSH) in tumors to knockdown genes key to cancer progression. Combining RNA interference and chemotherapy, the nanodevice induced potent cytotoxicity and tumor growth inhibition, without observable systematic toxicity. Given its autonomous behavior, exceptional designability, potent antitumor activity and marked biocompatibility, this DNA nanodevice represents a promising strategy for precise drug design for cancer therapy.

Branched Antisense and siRNA Co-Assembled Nanoplatform for Combined Gene Silencing and Tumor Therapy

Chemically modified DNA has been widely developed to fabricate various nucleic acid nanostructures for biomedical applications. Herein, we report a facile strategy for construction of branched antisense DNA and small interfering RNA (siRNA) co-assembled nanoplatform for combined gene silencing in vitro and in vivo. In our design, the branched antisense can efficiently capture siRNA with 3' overhangs through DNA-RNA hybridization. After being equipped with an active targeting group and an endosomal escape peptide by host-guest interaction, the tailored nucleic acid nanostructure functions efficiently as both delivery carrier and therapeutic cargo, which is released by endogenous RNase H digestion. The multifunctional nucleic acid nanosystem elicits an efficient inhibition of tumor growth based on the combined gene silencing of the tumor-associated gene polo-like kinase 1 (PLK1). This biocompatible nucleic acid nanoplatform presents a new strategy for the development of gene therapy.

The applications of functionalized DNA nanostructures in bioimaging and cancer therapy

Deoxyribonucleic acid (DNA) is a molecular carrier of genetic information that can be fabricated into functional nanomaterials in biochemistry and engineering fields. Those DNA nanostructures, synthesized via Watson-Crick base pairing, show a wide range of attributes along with excellent applicability, precise programmability, and extremely low cytotoxicity in vitro and in vivo. In this review, the applications of functionalized DNA nanostructures in bioimaging and tumor therapy are summarized. We focused on approaches involving DNA origami nanostructures due to their widespread use in previous and current reports. Non-DNA origami nanostructures such as DNA tetrahedrons are also covered. Finally, the remaining challenges and perspectives regarding DNA nanostructures in the biomedical arena are discussed.

pH-Responsive and Gemcitabine-Containing DNA Nanogel To Facilitate the Chemodrug Delivery

Herein, we construct a structure-switchable gemcitabine (Ge)-containing DNA nanogel that can respond to the intracellular acidic environment, subsequently facilitating the chemodrug release inside the cells. Based on the structural similarity between Ge and deoxycytidine (dC), dC nucleotides in the component DNA strands used for nanogel assembly are fully replaced by Ge during their synthesis. By changing the designed sequences, two Ge-containing Y-shaped motifs with different sticky ends are first assembled and then associated together to form nanogel by sticky-end hybridizations. In particular, one of the sticky-end sequences is arbitrarily designed to be rich of Ge and the other is designed to be partially complementary to the first Ge-rich sticky end. At the neutral or basic condition, the Ge-rich sticky ends hybridize with the partially complementary sticky ends on the second Y motifs, keeping the assembled nanogel stable. Upon being exposed to the acidic condition, Ge-rich sticky ends intend to form intramolecular i-motif-like quadruplex structures, resulting in the disassembly of the nanogel. On the one hand, the nanosized feature enables the Ge-containing nanogel with rapid cellular uptake behavior. On the other hand, the pH-responsive feature endows the rapid disassembly of the nanogel to facilitate the enzymatic drug release inside the cell, resulting in the enhanced anticancer activity of the DNA-based drug delivery system.

A non-cationic nucleic acid nanogel for the delivery of the CRISPR/Cas9 gene editing tool

Herein, we report a non-cationic DNA-crosslinked nanogel for intracellular delivery of a Cas9 and single guide RNA (Cas9/sgRNA) complex. A DNA-grafted polycaprolactone brush (DNA-g-PCL) is first loaded with the Cas9/sgRNA complex and then crosslinked by DNA linkers via nucleic acid hybridization to form a nanosized hydrogel, in which the gene editing tools are embedded and protected inside. With compact architecture, the Cas9/sgRNA complex-containing nanogel exhibited excellent physiological stability against nuclease digestion and enhanced cellular uptake efficiency, making the delivery system a promising tool for target genome editing.

Stimuli-Responsive DNA Self-Assembly: From Principles to Applications

Stimuli-responsive DNA self-assembly shares the advantages of both designed stimuli-responsiveness and the molecular programmability of DNA structures, offering great opportunities for basic and applied research in dynamic DNA nanotechnology. In this minireview, we summarize the most recent progress in this rapidly developing field. The trigger mechanisms of the responsive DNA systems are first divided into six categories, which are then explained with illustrative examples following this classification. Subsequently, proof-of-concept applications in terms of biosensing, in vivo pH-mapping, drug delivery, and therapy are discussed. Finally, we provide some remarks on the challenges and opportunities of this highly promising research direction in DNA nanotechnology.

Targeted Delivery of Rab26 siRNA with Precisely Tailored DNA Prism for Lung Cancer Therapy

Programmable DNA nanostructures are a new class of biocompatible, nontoxic nanomaterials. Nevertheless, their application in the field of biomedical research is still in its infancy, especially as drug delivery vehicles for gene therapy. In this study, a GTPase Rab26 was investigated as a new potential therapeutic target using a precisely tailored DNA nanoprism for targeted lung cancer therapy. Specifically, a DNA nanoprism platform with tunable targeting and siRNA loading capability is designed and synthesized. The as-prepared DNA prisms were decorated with two functional units: a Rab26 siRNA as the drug and MUC-1 aptamers as a targeting moiety for non-small cell lung cancer. The number and position of both siRNA and MUC-1 aptamers can be readily tuned by switching two short, single-stranded DNA. Native polyacrylamide gel electrophoresis (PAGE) and dynamic light scattering technique (DLS) demonstrate that all nanoprisms with different functionalities are self-assembled with high yield. It is also found that the cellular uptake of DNA prisms is proportional to the aptamer number on each nanoprism, and the as-prepared DNA nanoprism show excellent anti-cancer activities and targeting capability. This study suggests that by careful design, self-assembled DNA nanostructures are highly promising, customizable, multifunctional nanoplatforms for potential biomedical applications, such as personalized precision therapy.

Overview of DNA Self-Assembling: Progresses in Biomedical Applications

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

Floxuridine Homomeric Oligonucleotides "Hitchhike" with Albumin In Situ for Cancer Chemotherapy

Automated attachment of chemotherapeutic drugs to oligonucleotides through phosphoramidite chemistry and DNA synthesis has emerged as a powerful technology in constructing structure-defined and payload-tunable oligonucleotide-drug conjugates. In practice, however, in vivo delivery of these oligonucleotides remains a challenge. Inspired by the systemic transport of hydrophobic payloads by serum albumin in nature, we report the development of a lipid-conjugated floxuridine homomeric oligonucleotide (LFU20) that "hitchhikes" with endogenous serum albumin for cancer chemotherapy. Upon intravenous injection, LFU20 immediately inserts into the hydrophobic cave of albumin to form an LFU20/albumin complex, which accumulates in the tumor by the enhanced permeability and retention (EPR) effect and internalizes into the lysosomes of cancer cells. After degradation, cytotoxic floxuridine monophosphate is released to inhibit cell proliferation.

Floxuridine-containing nucleic acid nanogels for anticancer drug delivery

Herein, we report the self-assemblies of floxuridine-containing DNA and RNA nanogels with a precise drug loading ratio as effective drug delivery systems. Based on the structural similarity between the nucleoside analogue floxuridine (F) and the natural nucleoside thymidine (T), F can be incorporated into nucleic acid strands via either solid-phase synthesis or enzyme-mediated transcription. With the retained property of molecular recognition, the synthesized F-integrated DNA or RNA strands can be used as building units and further assembled into nucleic acid based spherical nanogels, which can be efficiently taken up by cancer cells and then release the therapeutic agents. As such, the drug-containing nucleic acid nanogels exhibit excellent inhibitory activity against cancer cells.

Translatable High Drug Loading Drug Delivery Systems Based on Biocompatible Polymer Nanocarriers

Most nanocarriers possess low drug loading, resulting in frequently repeated administration and thereby high cost and increased side effects. Furthermore, the characteristics of nanocarrier materials, especially the drug loading capacity, plays a vital role in the drug delivery efficacy. In this review, we focus on the readily translatable polymeric drug delivery systems with high drug loading, which are comprised of biocompatible polymers such as poly(ethylene glycol), poly( N-vinylpyrrolidone), polyoxazoline, natural proteins like albumin and casein, non-natural proteins such as recombinant elastin-like polypeptides, as well as nucleic acids. At the end of this review, applications of these polymeric nanocarriers on the delivery of proteins and gene drugs are also briefly discussed.