Search Results (94)

In biological systems, DNA serves as the primary carrier of genetic information, and the stability of its structure is fundamental to cellular function. Metal ions and temperature are critical environmental factors that modulate DNA conformation and activity. However, the differential morphological effects of alkali, alkaline earth, and transition metal ions, especially when combined with thermal treatment, have not been systematically visualized and quantified. In this work, atomic force microscopy (AFM) was employed to investigate the effects of different metal ions (Na⁺, K⁺, Mg²⁺, Ca²⁺, Cu²⁺) and temperature on DNA structure. The results demonstrated that monovalent ions (Na⁺ and K⁺) neutralized the negative charges on the DNA backbone, thereby reducing intermolecular electrostatic repulsion and promoting DNA aggregation into dendritic structures. Divalent ions (Mg²⁺ and Ca²⁺) not only provided more effective charge screening but also formed ion bridges between DNA strands, leading to more compact and cross-linked networks. In contrast, Cu²⁺ ions directly coordinated with DNA bases, causing local structural distortion and strand scission. Elevated temperatures induced DNA melting, with distinct morphological transitions from extended double strands to condensed single-stranded globules observed at temperatures exceeding the melting point ($T_m$). These findings elucidate the mechanisms by which environmental factors govern DNA morphology, providing insights relevant to nanotechnology and molecular biology applications. Full article

Bacterial biofilms are structured microbial communities enclosed within a self-produced extracellular polymeric substance matrix composed of polysaccharides, proteins, extracellular DNA, and lipids. This matrix promotes adhesion, structural stability, and the development of heterogeneous microenvironments that restrict antimicrobial penetration and shield bacteria from host immune responses. As a result, biofilms are major contributors to chronic, recurrent, device-related, and difficult-to-treat infections, posing a major challenge for clinical management and antimicrobial stewardship. This review summarizes current understandings of biofilm biology, its clinical relevance, including the stages of biofilm development, the composition and protective roles of the matrix, and the physiological heterogeneity that arises during maturation. It also examines key mechanisms underlying biofilm tolerance and resistance, such as limited antibiotic diffusion, and sequestration, enzymatic inactivation, efflux pump upregulation, persister cell formation, and horizontal gene transfer. In addition, it highlights important clinical settings in which biofilms are implicated, including cystic fibrosis, chronic wounds, osteomyelitis, implant- or device-associated infections, and breast implant illness, in which persistent implant-associated biofilms and the resulting chronic inflammatory milieu have been hypothesized to contribute to local and systemic manifestations in a subset of patients. The review further discusses conventional and emerging approaches for biofilm detection alongwith real-time monitoring. Biofilm-associated infections remain difficult to eradicate because persistence is driven by multiple interconnected protective mechanisms. Effective management therefore requires integrated strategies that combine accurate detection with multifaceted therapies, including antibiotics alongside matrix-disrupting enzymes, quorum-sensing inhibitors, bacteriophages, metabolic reactivators, and nanotechnology-based delivery systems. Advances in multi-omics and system-level modeling will be essential for developing next-generation strategies to prevent, monitor, and treat biofilm-associated disease. Full article

DNA and RNA, by focusing on their unique molecular properties, have transcended their role as carriers of genetic information in life and pioneered new application fields such as molecular robotics and molecular computing. However, as these technologies advance, the limitations inherent in natural nucleic acids and their ecosystems are increasingly becoming apparent as barriers to further application. To overcome these constraints, efforts to create artificial nucleic acids using chemical synthesis are underway and are now reaching a new stage of development. This paper proposes a concept of ultimate nucleic acid, “Omega Nucleic Acids ($\mathsf{\Omega }$NA),” as a thought experiment. We discuss the specifications required for this molecule, its implementable functions and approaches, and the construction of an ecosystem centered around $\mathsf{\Omega }$NA. By working backward from the characteristics of known natural and artificial nucleic acids, while envisioning next-generation artificial systems and applications in extreme environments, we aim to explore new approaches to nucleic acid chemistry and provide guidelines for constructing innovative artificial molecular systems. Full article

DNA nanotechnology offers an unprecedented level of structural programmability for organizing metallic nanoparticles into precisely defined architectures, providing a powerful platform for plasmonic biosensing. In particular, gold and silver nanoparticles assembled on DNA nanostructures enable nanometer-scale control over interparticle distance, orientation, and spatial symmetry, which directly govern collective plasmonic behaviors and optical signal transduction. This review summarizes recent advances in DNA nanostructure-mediated assembly of metal nanoparticles, with an emphasis on design principles and assembly strategies that enable static and dynamic control of nanoparticle organization. Representative examples are discussed to illustrate how well-defined plasmonic assemblies give rise to tunable optical responses, including localized surface plasmon resonance modulation, chiroptical signals, fluorescence enhancement or quenching, and surface-enhanced Raman scattering. The role of structural programmability and stimulus-responsive reconfiguration in translating molecular recognition events into amplified optical outputs is highlighted in the context of biosensing. Finally, current challenges and future perspectives are outlined, focusing on structural robustness, signal reproducibility, and integration toward practical and multiplexed biosensing platforms. Full article

DNA nanoparticles have emerged as potent platforms for wearable and implantable biosensors owing to their molecular programmability, biocompatibility, and structural precision. This study delineates two principal categories of DNA-based sensing materials, DNA hydrogels and DNA origami, and encapsulates their fabrication methodologies, sensing mechanisms, and applications at the device level. DNA hydrogels serve as pliable, aqueous signal transduction mediums exhibiting stimulus-responsive characteristics, facilitating applications such as sweat-based cytokine detection with limits of detection as low as pg·mL⁻¹ and microneedle-integrated hydrogels for femtomolar miRNA sensing. DNA origami offers nanometer-scale spatial precision that improves electrochemical, optical, and plasmonic biosensing, as shown by origami-facilitated luminous nucleic acid detection and ultrasensitive circulating tumor DNA assays with fM-level sensitivity. Emerging integration technologies, such as flexible electronics, microfluidics, and wireless readout, are examined, alongside prospective developments in AI-assisted DNA design and materials produced from synthetic biology. This study offers a thorough and practical viewpoint on the progression of DNA nanotechnology for next-generation wearable and implantable biosensing devices. Full article

Since the introduction of the DNA origami technology by Seeman and Rothemund, the integration of functional entities (nanoparticles, quantum dots, antibodies, etc.) has been of huge interest to broaden the area of applications for this technology. The possibility of precise functionalization of the DNA origami technology gives opportunity to build up complex novel structures, opening up endless opportunities in medicine, nanotechnology, photonics and many more. The main advantage of the DNA origami technology, namely the self-assembly mechanism, can represent a challenge in the construction of complex mixed-material structures. Commonly, DNA origami structures are purified post-assembly by filtration (either spin columns or membranes) to wash away excess staple strands. However, this purification step can be critical since these functionalized DNA origami structures tend to agglomerate during purification. Therefore, custom production and purification procedures need to be applied to produce purified functionalized DNA origami structures. In this paper, we present a workflow to produce functionalized DNA origami structures, as well as a method to qualify the successful hybridization of a quantum dot to a square frame DNA origami structure. Through the utilization of a FRET fluorophore–quencher pair as well as a subsequent assembly, successful hybridization can be performed and confirmed using photoluminescence measurements. Full article

Methodological fusion of materials chemistry, which enables us to create materials, with nanotechnology, which enables us to control nanostructures, could enable us to create advanced functional materials with well controlled nanostructures. Positioned as a post-nanotechnology concept, nanoarchitectonics will enable this purpose. This review paper highlights the broad scope of applications of the new concept of nanoarchitectonics, selecting and discussing recent papers that contain the term ‘nanoarchitectonics’ in their titles. Topics include controls of dopant atoms in solid electrolytes, transforming the framework of carbon materials, single-atom catalysts, nanorobots and microrobots, functional nanoparticles, nanotubular materials, 2D-organic nanosheets and MXene nanosheets, nanosheet assemblies, nitrogen-doped carbon, nanoporous and mesoporous materials, nanozymes, polymeric materials, covalent organic frameworks, vesicle structures from synthetic polymers, chirality- and topology-controlled structures, chiral helices, Langmuir monolayers, LB films, LbL assembly, nanocellulose, DNA, peptides bacterial cell components, biomimetic nanoparticles, lipid membranes of protocells, organization of living cells, and the encapsulation of living cells with exogenous substances. Not limited to these examples selected in this review article, the concept of nanoarchitectonics is applicable to diverse materials systems. Nanoarchitectonics represents a conceptual framework for creating materials at all levels and can be likened to a method for everything in materials science. Developing technology that can universally create materials with unexpected functions could represent the final frontier of materials science. Nanoarchitectonics will play a significant part in achieving this final frontier in materials science. Full article

White Spot Syndrome Virus (WSSV) is one of the most devastating viral pathogens affecting shrimp, causing severe economic losses to the global farmed shrimp trade. The globalization of live shrimp trade and waterborne transmission have facilitated the rapid spread of WSSV across major shrimp-producing countries since its initial emergence. The present review gives an updated account of WSSV biology, pathology, transmission dynamics, and recent developments in control measures. The virus, a double-stranded DNA virus of the Nimaviridae family, utilizes advanced immune evasion strategies, resulting in severe mortality. Shrimp lack adaptive immunity and hence rely predominantly on innate immunity, which is insufficient to mount an effective response against severe infections. Traditional disease control measures such as augmented biosecurity, selective breeding, and immunostimulants have, despite extensive research, achieved only limited success. New biotechnological tools such as RNA interference, CRISPR-Cas gene editing, and nanotechnology offer tremendous potential for disease mitigation. In parallel, the development of DNA and RNA vaccines targeting WSSV structural proteins, such as VP28, holds significant promise for stimulating the shrimp immune system. This review highlights the urgent need for a convergent approach to sustainable disease management in global shrimp aquaculture, with interdisciplinarity playing a pivotal role in shaping the future of WSSV control. Full article

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