Conformational Change of Self-Assembled DNA Nanotubes Induced by Two-Photon Excitation

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.

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.

Light Responsive DNA Nanomaterials and Their Biomedical Applications

DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.

A review of DNA nanoparticles-encapsulated drug/gene/protein for advanced controlled drug release: Current status and future perspective over emerging therapy approaches

In the last ten years, the field of nanomedicine has experienced significant progress in creating novel drug delivery systems (DDSs). An effective strategy involves employing DNA nanoparticles (NPs) as carriers to encapsulate drugs, genes, or proteins, facilitating regulated drug release. This abstract examines the utilization of DNA NPs and their potential applications in strategies for controlled drug release. Researchers have utilized the distinctive characteristics of DNA molecules, including their ability to self-assemble and their compatibility with living organisms, to create NPs specifically for the purpose of delivering drugs. The DNA NPs possess numerous benefits compared to conventional drug carriers, such as exceptional stability, adjustable dimensions and structure, and convenient customization. Researchers have successfully achieved a highly efficient encapsulation of different therapeutic agents by carefully designing their structure and composition. This advancement enables precise and targeted delivery of drugs. The incorporation of drugs, genes, or proteins into DNA NPs provides notable advantages in terms of augmenting therapeutic effectiveness while reducing adverse effects. DNA NPs serve as a protective barrier for the enclosed payloads, preventing their degradation and extending their duration in the body. The protective effect is especially vital for delicate biologics, such as proteins or gene-based therapies that could otherwise be vulnerable to enzymatic degradation or quick elimination. Moreover, the surface of DNA NPs can be altered to facilitate specific targeting towards particular tissues or cells, thereby augmenting the accuracy of delivery. A significant benefit of DNA NPs is their capacity to regulate the kinetics of drug release. Through the manipulation of the DNA NPs structure, scientists can regulate the rate at which the enclosed cargo is released, enabling a prolonged and regulated dispensation of medication. This control is crucial for medications with limited therapeutic ranges or those necessitating uninterrupted administration to attain optimal therapeutic results. In addition, DNA NPs have the ability to react to external factors, including alterations in temperature, pH, or light, which can initiate the release of the payload at precise locations or moments. This feature enhances the precision of drug release control. The potential uses of DNA NPs in the controlled release of medicines are extensive. The NPs have the ability to transport various therapeutic substances, for example, drugs, peptides, NAs (NAs), and proteins. They exhibit potential for the therapeutic management of diverse ailments, including cancer, genetic disorders, and infectious diseases. In addition, DNA NPs can be employed for targeted drug delivery, traversing biological barriers, and surpassing the constraints of conventional drug administration methods.

Versatile nanodiamond-based tools for therapeutics and bioimaging

Nanodiamonds (NDs) are a remarkable class of carbon-based nanoparticles in nanomedicine which have recently become a hot topic of research due to their unique features including functionalization versatility, tunable opto-magnetic properties, chemical stability, minimal cytotoxicity, high affinity to biomolecules and biocompatibility. These attractive features make NDs versatile tools for a wide range of biologically relevant applications. In this feature article, we discuss the opto-magnetic properties of negatively charged nitrogen vacancy (NV^-) centres in NDs as fluorescence probes. We further discuss the frequently used chemical methods for surface chemistry modification of NDs which are relevant for biomedical applications. The in vitro and in vivo biocompatibility of modified NDs is also highlighted. Subsequently, we give an overview of recent state-of-the-art biomedical applications of NDs as versatile tools for bioimaging and detection, and as targeting nanocarriers for chemotherapy, photodynamic therapy, gene therapy, antimicrobial and antiviral therapy, and bone tissue engineering. Finally, we pinpoint the main challenges for NDs in biomedical applications which lie ahead and discuss perspectives on future directions in advancing the field for practical applications and clinical translations.

Wavelength-Dependent, Orthogonal Photoregulation of DNA Liberation for Logic Operations

In this study, we synthesized two phosphoramidites based on 2,7-bis-{4-nitro-8-[3-(2-propyl)-styryl]}-9,9-bis-[1-(3,6-dioxaheptyl)]-fluorene (BNSF) and 4,4'-bis-{8-[4-nitro-3-(2-propyl)-styryl]}-3,3'-di-methoxybiphenyl (BNSMB) structures as visible light-cleavable linkers for oligonucleotide conjugation. In addition to the commercial ultraviolet (UV) photocleavable (PC) linker, the BNSMB linker was further applied as a building component to construct photoregulated DNA devices as duplex structures, which are functionalized with fluorophores and quenchers. Selective cleavage of PC and BNSMB is achieved in response to ultraviolet (UV) and visible light irradiations as two inputs, respectively. This leads to controllable dissociation of pieces of DNA fragments, which is followed by changes of fluorescence emission as signal outputs of the system. By tuning the number and position of the photocleavable molecules, fluorophores, and quenchers, various DNA devices were developed, which mimic the functions of Boolean logic gates and achieve logic operations in AND, OR, NOR, and NAND gates in response to two different wavelengths of light inputs. By sequence design, the photolysis products can be precisely programmed in DNA devices and triggered to release in a selective and/or sequential manner. Thus, this photoregulated DNA device shows potential as a wavelength-dependent drug delivery system for selective control over the release of multiple individual therapeutic oligonucleotide-based drugs. We believe that our work not only enriches the library of photocleavable phosphoramidites available for bioconjugation but also paves the way for developing spatiotemporal-controlled, orthogonal-regulated DNA-based logic devices for a range of applications in materials science, polymers, chemistry, and biology.

Light responsive nucleic acid for biomedical application

Nucleic acids are widely used in biomedical applications because of their programmability and biocompatibility. The light responsive nucleic acids have attracted wide attention due to their remote control and high spatiotemporal resolution. In this review, we summarized the latest developments in biomedicine of light responsive molecules. The molecules which confer light responsive properties to nucleic acids were summarized. The binding sites of molecules to nucleic acids, the induced structural changes, and functional regulation of nucleic acids were reviewed. Then, the biomedical applications of light responsive nucleic acids were listed, such as drug delivery, biosensing, optogenetics, gene editing, etc. Finally, the challenges were discussed and possible future directions of light-responsive nucleic acids were proposed.

Nucleic Acids and Their Analogues for Biomedical Applications

Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.

Facile Construction of a Solely-DNA-Based System for Targeted Delivery of Nucleic Acids

We designed a functional drug delivery system based solely on DNA. The whole system was built with only four DNA strands. Cyclization of DNA strands excluded the formation of byproducts. DNA aptamers were equipped to endow triangular DNA nanostructures with targeting ability. The homogeneity of materials enabled not only facile construction but also convenient loading of nucleic acid-based drugs with much ease.

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

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

Dynamic DNA Assemblies in Biomedical Applications

Deoxyribonucleic acid (DNA) has been widely used to construct homogeneous structures with increasing complexity for biological and biomedical applications due to their powerful functionalities. Especially, dynamic DNA assemblies (DDAs) have demonstrated the ability to simulate molecular motions and fluctuations in bionic systems. DDAs, including DNA robots, DNA probes, DNA nanochannels, DNA templates, etc., can perform structural transformations or predictable behaviors in response to corresponding stimuli and show potential in the fields of single molecule sensing, drug delivery, molecular assembly, etc. A wave of exploration of the principles in designing and usage of DDAs has occurred, however, knowledge on these concepts is still limited. Although some previous reviews have been reported, systematic and detailed reviews are rare. To achieve a better understanding of the mechanisms in DDAs, herein, the recent progress on the fundamental principles regarding DDAs and their applications are summarized. The relative assembly principles and computer-aided software for their designing are introduced. The advantages and disadvantages of each software are discussed. The motional mechanisms of the DDAs are classified into exogenous and endogenous stimuli-triggered responses. The special dynamic behaviors of DDAs in biomedical applications are also summarized. Moreover, the current challenges and future directions of DDAs are proposed.

Photoresponsive Self-Assembled DNA Nanomaterials: Design, Working Principles, and Applications

Photoresponsive DNA nanomaterials represent a new class of remarkable functional materials. By adjusting the irradiation wavelength, light intensity, and exposure time, various photocontrolled DNA-based systems can be reversibly or irreversibly regulated in respect of their size, shape, conformation, movement, and dissociation/association. This Review introduces the most updated progress in the development of photoresponsive DNA-based system and emphasizes their advantages over other stimuli-responsive systems. Their design and mechanisms to trigger the photoresponses are shown and discussed. The potential application of these photon-responsive DNA nanomaterials in biology, biomedicine, materials science, nanophotonic and nanoelectronic are also covered and described. The challenges faced and further directions of the development of photocontrolled DNA-based systems are also highlighted.

Biomimetic DNA Nanotubes: Nanoscale Channel Design and Applications

Biomacromolecular nanotubes play important physiological roles in transmembrane ion/molecule channeling, intracellular transport, and inter-cellular communications. While genetically encoded protein nanotubes are prevalent in vivo, the in vitro construction of biomimetic DNA nanotubes has attracted intense interest with the rise of structural DNA nanotechnology. The abiotic use of DNA assembly provides a powerful bottom-up approach for the rational construction of complex materials with arbitrary size and shape at the nanoscale. More specifically, a typical DNA nanotube can be assembled either with parallel-aligned DNA duplexes or by closing DNA tile lattices. These artificial DNA nanotubes can be tailored and site-specifically modified to realize biomimetic functions including ionic or molecular channeling, bioreactors, drug delivery, and biomolecular sensing. In this Minireview, we aim to summarize recent advances in design strategies, including the characterization and applications of biomimetic DNA nanotubes.

Photo-switchable patterning of gold nanoparticles along 3D DNA nanotubes

We have developed a reversible photoswitching platform based on 3D DNA nanotubes by integrating photoisomerizable azobenzene molecules along the edges. This would allow the reversible conformational changes of the nanotubes between linear and bent features and the switchable patterning of gold nanoparticles in response to UV/Vis irradiation. This work provides a new strategy to create reversibly reconfigurable transformative nanomaterials for potential applications in the fields of renewable energy, sensing, nanorobotics and nanomedicine.

CAGE: Chromatin Analogous Gene Expression

Self-assembled nucleic acids perform biological, chemical, and mechanical work at the nanoscale. DNA-based molecular machines have been designed here to perform work by reacting with cancer-specific miRNA mimics and then regulating gene expression in vitro by tuning RNA polymerase activity. Because RNA production is topologically restrained, the machines demonstrate chromatin analogous gene expression (CAGE). With modular and tunable design features, CAGE has potential for molecular biology, synthetic biology, and personalized medicine applications.

Stimuli-Responsive Self-Assembled DNA Nanomaterials for Biomedical Applications

Stimuli-responsive DNA-based materials represent a major class of remarkable functional nanomaterials for nano-biotechnological applications. In this review, recent progress in the development of stimuli-responsive systems based on self-assembled DNA nanostructures is introduced and classified. Representative examples are presented in terms of their design, working principles and mechanisms to trigger the response of the stimuli-responsive DNA system upon expose to a large variety of stimuli including pH, metal ions, oligonucleotides, small molecules, enzymes, heat, and light. Substantial in vitro studies have clearly revealed the advantages of the use of stimuli-responsive DNA nanomaterials in different biomedical applications, particularly for biosensing, drug delivery, therapy and diagnostic purposes in addition to bio-computing. Some of the challenges faced and suggestions for further development are also highlighted.

A highly versatile platform based on geometrically well-defined 3D DNA nanostructures for selective recognition and positioning of multiplex targets

We develop a versatile recognition system based on 3D triangular-shaped DNA nanotubes by integrating three different aptamer sequences along the three edges. This would allow multiple binding activities to be combined into a single system. The versatility of this nanotube platform can also provide a framework for spatial orientation and positioning of different aptamer-binding ligands in a 'pea-pod' architecture.