Search Results (86)

Transdermal drug delivery systems have recently been explored as an alternative to oral systems, which have many challenges. Due to the limitations of first-generation transdermal systems, second- and third-generation systems have been developed, among which microneedles have been the most remarkable products. Building on the advancements of nanotechnology, nanoneedles have recently been developed. Gene therapy molecules—such as DNA, RNA, siRNA, miRNA, and other nucleic acids—are typically delivered using viral or chemical carriers, but these methods face several challenges. In this context, nanoneedles offer a promising and efficient solution for delivering these large molecules. Nanoneedles are a biocompatible and reliable physical method for gene delivery, enabling transdermal administration by penetrating the skin barrier and delivering nucleic acids directly into cells. Their ability to penetrate cellular barriers with minimal invasiveness makes them advantageous for delivering genetic materials. This review will focus on the potential applications of nanoneedles in pharmaceutical contexts, especially in gene therapy. In addition, information on the properties, structure, and fabrication of nanoneedles is also provided. Full article

Hydrogels are three-dimensional network structures composed of hydrophilic polymers that can swell in water and are very similar to soft tissues such as connective tissue or the extracellular matrix. DNA hydrogels are particularly notable for biomedical applications due to their high biocompatibility, physiological stability, molecular recognition, biodegradability, easy functionalization, and low immunogenicity. Based on these advantages, stimuli-responsive DNA hydrogels that have the property of reversibly changing their structure in response to various microenvironments or molecules are attracting attention as smart nanomaterials that can be applied to biosensing and material transfer, such as in the case of cells and drugs. As DNA nanotechnology advances, DNA can be hybridized with a variety of nanomaterials, from inorganic nanomaterials such as gold nanoparticles (AuNPs) and quantum dots (QDs) to synthetic polymers such as polyacrylamide (PAAm) and poly(N-isopropylacrylamide) (pNIPAM). These hybrid structures exhibit various optical and chemical properties. This review discusses recent advances and remaining challenges in biomedical applications of stimuli-responsive smart DNA hydrogel-based systems. It also highlights various types of hybridized DNA hydrogel, explores various response mechanism strategies of stimuli-responsive DNA hydrogel, and provides insights and prospects for biomedical applications such as biosensing and drug delivery. Full article

The development of functional materials and the use of nanotechnology are ongoing projects. These fields are closely linked, but there is a need to combine them more actively. Nanoarchitectonics, a concept that comes after nanotechnology, is ready to do this. Among the related research efforts, research into creating functional materials through the formation of thin layers on surfaces, molecular membranes, and multilayer structures of these materials have a lot of implications. Layered structures are especially important as a key part of nanoarchitectonics. The diversity of the components and materials used in layer-by-layer (LbL) assemblies is a notable feature. Examples of LbL assemblies introduced in this review article include quantum dots, nanoparticles, nanocrystals, nanowires, nanotubes, g-C₃N₄, graphene oxide, MXene, nanosheets, zeolites, nanoporous materials, sol–gel materials, layered double hydroxides, metal–organic frameworks, covalent organic frameworks, conducting polymers, dyes, DNAs, polysaccharides, nanocelluloses, peptides, proteins, lipid bilayers, photosystems, viruses, living cells, and tissues. These examples of LbL assembly show how useful and versatile it is. Finally, this review will consider future challenges in layer-by-layer nanoarchitectonics. Full article

In the field of chemical biology, DNA origami has been actively researched. This technique, which involves folding DNA strands like origami to assemble them into desired shapes, has made it possible to create complex nanometer-sized structures, marking a major breakthrough in nanotechnology. On the other hand, controlling the folding mechanisms and folded structures of proteins or shorter peptides has been challenging. However, recent advances in techniques such as protein origami, peptide origami, and de novo design peptides have made it possible to construct various nanoscale structures and create functional molecules. These approaches suggest the emergence of new molecular design principles, which can be termed “molecular origami”. In this review, we provide an overview of recent research trends in protein/peptide origami and DNA/RNA origami and explore potential future applications of molecular origami technologies in electrochemical biosensors. Full article

The development of new convenient tools for the design of multicomponent nucleic acid (NA) complexes is one of the challenges in biomedicine and NA nanotechnology. In this paper, we analyzed the formation of hybrid RNA/DNA concatemers and self-limited complexes by a pair of oligonucleotides using UV melting, circular dichroism spectroscopy, and a gel shift assay. Effects of the size of the linker between duplex-forming segments of the oligonucleotides on complexes’ shape and number of subunits were compared and systematized for RNA/DNA, DNA/DNA, and RNA/RNA assemblies. The data on complex types summarized here as heat maps offer a convenient tool for the design of NA constructs. General rules found for RNA/DNA, DNA/DNA, and RNA/RNA complexes allow not only designing complexes with desired structures but also purposefully transforming their geometry. The A-form of the double helix of the studied RNA/DNA complexes was confirmed by circular dichroism analysis. Moreover, we show for the first time efficient degradation of RNA in hybrid self-limited complexes by RNase H and imidazole. The results open up new prospects for the design of supramolecular complexes as tools for nanotechnology, nanomachinery, and biomedical applications. Full article

Molecular assembly is promising in the construction of advanced materials, obtaining structures with specific functions. In-depth investigation of the relationships between the formation, dynamics, structure, and functionality of the specific molecular assemblies is one of the greatest challenges in nanotechnology and chemistry, which is essential in the rational design and development of functional materials for a variety of applications. Super-resolution microscopy (SRM) has been used as a versatile tool for investigating and elucidating the structures of individual molecular assemblies with its nanometric resolution, multicolor ability, and minimal invasiveness, which are also complementary to conventional optical or electronic techniques that provide the direct observation. In this review, we will provide an overview of the representative studies that utilize SRM to probe molecular assemblies, mainly focusing on the imaging of biomolecular assemblies (lipid-based, peptide-based, protein-based, and DNA-based), organic–inorganic hybrid assemblies, and polymer assemblies. This review will provide guidelines for the evaluation of the dynamics of molecular assemblies, assembly and disassembly processes with distinct dynamic behaviors, and multicomponent assembly through the application of these advanced imaging techniques. We believe that this review will inspire new ideas and propel the development of structural analyses of molecular assemblies to promote the exploitation of new-generation functional materials. Full article

This article provides a comprehensive examination of non-canonical DNA structures, particularly focusing on G-quadruplexes (G4s) and i-motifs. G-quadruplexes, four-stranded structures formed by guanine-rich sequences, are stabilized by Hoogsteen hydrogen bonds and monovalent cations like potassium. These structures exhibit diverse topologies and are implicated in critical genomic regions such as telomeres and promoter regions of oncogenes, playing significant roles in gene expression regulation, genome stability, and cellular aging. I-motifs, formed by cytosine-rich sequences under acidic conditions and stabilized by hemiprotonated cytosine–cytosine (C:C+) base pairs, also contribute to gene regulation despite being less prevalent than G4s. This review highlights the factors influencing the stability and dynamics of these structures, including sequence composition, ionic conditions, and environmental pH. Molecular dynamics simulations and high-resolution structural techniques have been pivotal in advancing our understanding of their folding and unfolding mechanisms. Additionally, the article discusses the therapeutic potential of small molecules designed to selectively bind and stabilize G4s and i-motifs, with promising implications for cancer treatment. Furthermore, the structural properties of these DNA forms are explored for applications in nanotechnology and molecular devices. Despite significant progress, challenges remain in observing these structures in vivo and fully elucidating their biological functions. The review underscores the importance of continued research to uncover new insights into the genomic roles of G4s and i-motifs and their potential applications in medicine and technology. This ongoing research promises exciting developments in both basic science and applied fields, emphasizing the relevance and future prospects of these intriguing DNA structures. Full article

Structural DNA nanotechnology is an emerging field and is expected to be used for various applications in materials science. In this study, we designed a DNA tensegrity triangle to accommodate the bipyridine complexes with metal ions (Ni²⁺ and Fe²⁺) at the center of the space within the triangle. A metal–bipyridine-incorporated DNA tensegrity triangle was crystalized, and the presence of metals within it was confirmed through X-ray crystal structure analysis. A signal of the anomalous dispersion effect derived from metal was observed in the center of the DNA triangle. Full article

The efficient preparation of single-stranded DNA (ssDNA) rings, as a macromolecular construction approach with topological features, has aroused much interest due to the ssDNA rings’ numerous applications in biotechnology and DNA nanotechnology. However, an extra splint is essential for enzymatic circularization, and by-products of multimers are usually present at high concentrations. Here, we proposed a simple and robust strategy using permuted precursor (linear ssDNA) for circularization by forming an intramolecular dynamic nick using a part of the linear ssDNA substrate itself as the template. After the simulation of the secondary structure for desired circular ssDNA, the linear ssDNA substrate is designed to have its ends on the duplex part (≥5 bp). By using this permuted substrate with 5′-phosphate, the splint-free circularization is simply carried out by T4 DNA ligase. Very interestingly, formation of only several base pairs (2–4) flanking the nick is enough for ligation, although they form only instantaneously under ligation conditions. More significantly, the 5-bp intramolecular duplex part commonly exists in genomes or functional DNA, demonstrating the high generality of our approach. Our findings are also helpful for understanding the mechanism of enzymatic DNA ligation from the viewpoint of substrate binding. Full article

The rise of DNA nanotechnology has driven the development of DNA-based molecular machines, which are capable of performing specific operations and tasks at the nanoscale. Benefitting from the programmability of DNA molecules and the predictability of DNA hybridization and strand displacement, DNA-based molecular machines can be designed with various structures and dynamic behaviors and have been implemented for wide applications in the field of biosensing due to their unique advantages. This review summarizes the reported controlling mechanisms of DNA-based molecular machines and introduces biosensing applications of DNA-based molecular machines in amplified detection, multiplex detection, real-time monitoring, spatial recognition detection, and single-molecule detection of biomarkers. The challenges and future directions of DNA-based molecular machines in biosensing are also discussed. Full article

Metal-mediated base pairing of DNA has been a topic of extensive research spanning over more than four decades. Precise positioning of a single metal ion by predetermining the DNA sequence, as well as improved conductivity offered by the ions, make these structures interesting candidates in the context of using DNA in nanotechnology. Here, we report the formation and characterization of conjugates of long (kilo bases) homoguanine DNA strands with silver ions. We demonstrate using atomic force microscopy (AFM) and scanning tunneling microscope (STM) that binding of silver ions leads to folding of homoguanine DNA strands in a “hairpin” fashion to yield double-helical, left-handed molecules composed of G-G base pairs each stabilized by a silver ion. Further folding of the DNA–silver conjugate yields linear molecules in which the two halves of the double helix are twisted one against the other in a right-handed fashion. Quantum mechanical calculations on smaller molecular models support the helical twist directions obtained by the high resolution STM analysis. These long guanine-based nanostructures bearing a chain of silver ions have not been synthesized and studied before and are likely to possess conductive properties that will make them attractive candidates for nanoelectronics. Full article

Gene therapeutics are promising for treating diseases at the genetic level, with some already validated for clinical use. Recently, nanostructures have emerged for the targeted delivery of genetic material. Nanomaterials, exhibiting advantageous properties such as a high surface-to-volume ratio, biocompatibility, facile functionalization, substantial loading capacity, and tunable physicochemical characteristics, are recognized as non-viral vectors in gene therapy applications. Despite progress, current non-viral vectors exhibit notably low gene delivery efficiency. Progress in nanotechnology is essential to overcome extracellular and intracellular barriers in gene delivery. Specific nanostructures such as carbon nanotubes (CNTs), carbon quantum dots (CQDs), nanodiamonds (NDs), and similar carbon-based structures can accommodate diverse genetic materials such as plasmid DNA (pDNA), messenger RNA (mRNA), small interference RNA (siRNA), micro RNA (miRNA), and antisense oligonucleotides (AONs). To address challenges such as high toxicity and low transfection efficiency, advancements in the features of carbon-based nanostructures (CBNs) are imperative. This overview delves into three types of CBNs employed as vectors in drug/gene delivery systems, encompassing their synthesis methods, properties, and biomedical applications. Ultimately, we present insights into the opportunities and challenges within the captivating realm of gene delivery using CBNs. Full article

Nucleobase-containing molecules are compounds essential in biology due to the fundamental role of nucleic acids and, in particular, G-quadruplex DNA and RNA in life. Moreover, some molecules different from nucleic acids isolated from different vegetal sources or microorganisms show nucleobase moieties in their structure. Nucleoamino acids and peptidyl nucleosides belong to this molecular class. Closely related to the above, nucleopeptides, also known as nucleobase-bearing peptides, are chimeric derivatives of synthetic origin and more rarely isolated from plants. Herein, the self-assembly properties of a vast number of structures, belonging to the nucleic acid and nucleoamino acid/nucleopeptide family, are explored in light of the recent scientific literature. Moreover, several technologically relevant properties, such as the hydrogelation ability of some of the nucleobase-containing derivatives, are reviewed in order to make way for future experimental investigations of newly devised nucleobase-driven hydrogels. Nucleobase-containing molecules, such as mononucleosides, DNA, RNA, quadruplex (G4)-forming oligonucleotides, and nucleopeptides are paramount in gel and hydrogel formation owing to their distinctive molecular attributes and ability to self-assemble in biomolecular nanosystems with the most diverse applications in different fields of biomedicine and nanotechnology. In fact, these molecules and their gels present numerous advantages, underscoring their significance and applicability in both material science and biomedicine. Their versatility, capability for molecular recognition, responsiveness to stimuli, biocompatibility, and biodegradability collectively contribute to their prominence in modern nanotechnology and biomedicine. In this review, we emphasize the critical role of nucleobase-containing molecules of different nature in pioneering novel materials with multifaceted applications, highlighting their potential in therapy, diagnostics, and new nanomaterials fabrication as required for addressing numerous current biomedical and nanotechnological challenges. Full article

Gold nanoparticles (Au NPs) have become one of the building blocks for superior assembly and device fabrication due to the intrinsic, tunable physical properties of nanoparticles. With the development of DNA nanotechnology, gold nanoparticles are organized in a highly precise and controllable way under the mediation of DNA, achieving programmability and specificity unmatched by other ligands. The successful construction of abundant gold nanoparticle assembly structures has also given rise to the fabrication of a wide range of sensors, which has greatly contributed to the development of the sensing field. In this review, we focus on the progress in the DNA-mediated assembly of Au NPs and their application in sensing in the past five years. Firstly, we highlight the strategies used for the orderly organization of Au NPs with DNA. Then, we describe the DNA-based assembly of Au NPs for sensing applications and representative research therein. Finally, we summarize the advantages of DNA nanotechnology in assembling complex Au NPs and outline the challenges and limitations in constructing complex gold nanoparticle assembly structures with tailored functionalities. Full article

Prostate cancer (PC) is one of the major causes of death among elderly men. PC is often diagnosed later in progression due to asymptomatic early stages. Early detection of PC is thus crucial for effective PC treatment. The aim of this study is the simultaneous highly sensitive detection of a palette of PC-associated microRNAs (miRNAs) in human plasma samples. With this aim, a nanoribbon biosensor system based on “silicon-on-insulator” structures (SOI-NR biosensor) has been employed. In order to provide biospecific detection of the target miRNAs, the surface of individual nanoribbons has been sensitized with DNA oligonucleotide probes (oDNA probes) complementary to the target miRNAs. The lowest concentration of nucleic acids, detectable with our biosensor, has been found to be 1.1 × 10⁻¹⁷ M. The successful detection of target miRNAs, isolated from real plasma samples of PC patients, has also been demonstrated. We believe that the development of highly sensitive nanotechnology-based biosensors for the detection of PC markers is a step towards personalized medicine. Full article