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29 pages, 1351 KB  
Review
Molecular Targets for Pharmacotherapy of Head and Neck Squamous Cell Carcinomas
by Robert Sarna, Robert Kubina, Marlena Paździor-Heiske, Adrianna Halama, Patryk Chudy, Paulina Wala, Kamil Krzykawski and Ilona Nowak
Curr. Issues Mol. Biol. 2025, 47(8), 609; https://doi.org/10.3390/cimb47080609 - 1 Aug 2025
Viewed by 426
Abstract
Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of tumors with a complex molecular profile. Despite therapeutic advances, patient prognosis remains poor, emphasizing the need for more effective treatment strategies. Traditional chemotherapy, with cisplatin and 5-fluorouracil (5-FU), remains the gold [...] Read more.
Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of tumors with a complex molecular profile. Despite therapeutic advances, patient prognosis remains poor, emphasizing the need for more effective treatment strategies. Traditional chemotherapy, with cisplatin and 5-fluorouracil (5-FU), remains the gold standard but is limited by toxicity and tumor resistance. Immunotherapy, particularly immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) and its ligand (PD-L1), has improved overall survival, especially in patients with high PD-L1 expression. In parallel, targeted therapies such as poly (ADP-ribose) polymerase 1 (PARP1) inhibitors—which impair DNA repair and increase replication stress—have shown promising activity in HNSCC. Cyclin-dependent kinase (CDK) inhibitors are also under investigation due to their potential to correct dysregulated cell cycle control, a hallmark of HNSCC. This review aims to summarize current and emerging pharmacotherapies for HNSCC, focusing on chemotherapy, immunotherapy, and PARP and CDK inhibitors. It also discusses the evolving role of targeted therapies in improving clinical outcomes. Future research directions include combination therapies, nanotechnology-based delivery systems to enhance treatment specificity, and the development of diagnostic tools such as PARP1-targeted imaging to better guide personalized treatment approaches. Full article
(This article belongs to the Special Issue Future Challenges of Targeted Therapy of Cancers: 2nd Edition)
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33 pages, 2309 KB  
Review
Recent Progress of Nanomedicine for the Synergetic Treatment of Radiotherapy (RT) and Photothermal Treatment (PTT)
by Maria-Eleni Zachou, Ellas Spyratou, Nefeli Lagopati, Kalliopi Platoni and Efstathios P. Efstathopoulos
Cancers 2025, 17(14), 2295; https://doi.org/10.3390/cancers17142295 - 10 Jul 2025
Cited by 1 | Viewed by 687
Abstract
Nanotechnology has significantly advanced cancer therapy, particularly through the development of multifunctional nanoparticles (NPs) capable of acting as both therapeutic and diagnostic agents. This review focuses on the synergistic integration of radiotherapy (RT) and photothermal therapy (PTT) mediated by engineered NPs—a rapidly evolving [...] Read more.
Nanotechnology has significantly advanced cancer therapy, particularly through the development of multifunctional nanoparticles (NPs) capable of acting as both therapeutic and diagnostic agents. This review focuses on the synergistic integration of radiotherapy (RT) and photothermal therapy (PTT) mediated by engineered NPs—a rapidly evolving strategy that enhances tumor specificity, minimizes healthy tissue damage, and enables real-time imaging. By analyzing the recent literature, we highlight the dual role of NPs in amplifying radiation-induced DNA damage and converting near-infrared (NIR) light into localized thermal energy. The review classifies various metal-based and composite nanomaterials (e.g., Au, Pt, Bi, Cu, and Fe) and evaluates their performance in preclinical RT–PTT settings. We also discuss the physicochemical properties, targeting strategies, and theragnostic applications that contribute to treatment efficiency. Unlike conventional combinatorial therapies, NP-mediated RT–PTT enables high spatial–temporal control, immunogenic potential, and integration with multimodal imaging. We conclude with the current challenges, translational barriers, and outlooks for clinical implementation. This work provides a comprehensive, up-to-date synthesis of NP-assisted RT–PTT as a powerful approach within the emerging field of nano-oncology. Full article
(This article belongs to the Special Issue Nanomedicine’s Role in Oncology)
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25 pages, 1263 KB  
Review
Nanoneedle-Based Transdermal Gene Delivery: A Minimally Invasive Strategy for Gene Therapy
by Fatma Julide Akbuğa, Muhammet Davut Arpa and Emine Şalva
Int. J. Mol. Sci. 2025, 26(13), 6235; https://doi.org/10.3390/ijms26136235 - 27 Jun 2025
Cited by 1 | Viewed by 660
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Nanomedicine in Gene Therapy and Immunotherapy)
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18 pages, 5972 KB  
Review
Single-Molecule Detection of Optical Signals Using DNA-Based Plasmonic Nanostructures
by Renjie Niu, Jintian Shao, Mingnan Wu, Chang Liu and Jie Chao
Biosensors 2025, 15(7), 398; https://doi.org/10.3390/bios15070398 - 20 Jun 2025
Viewed by 1096
Abstract
Single-molecule optical signal detection provides high sensitivity and specificity for the detection of biomolecules and chemical substances, which is of significant importance in fields such as biomedicine, environmental monitoring, and materials science. In recent years, DNA-based plasmonic nanostructures have emerged as powerful tools [...] Read more.
Single-molecule optical signal detection provides high sensitivity and specificity for the detection of biomolecules and chemical substances, which is of significant importance in fields such as biomedicine, environmental monitoring, and materials science. In recent years, DNA-based plasmonic nanostructures have emerged as powerful tools for achieving single-molecule optical signal detection due to their unique self-assembly properties and excellent optical performance. In particular, DNA origami technology enables the precise construction of metallic nanostructures with specific shapes and functions, which can effectively enhance the interaction between light and matter, thereby significantly increasing signal intensity and detection sensitivity. Furthermore, the programmability of DNA not only simplifies the implementation of single-molecule operations but also allows researchers to design and optimize nanostructures according to specific detection requirements. This review will explore the applications of DNA-based plasmonic nanostructures in single-molecule optical signal detection, including surface-enhanced Raman spectroscopy and enhanced fluorescence for single-molecule signal detection. We will analyze their working principles, advantages, current research progress, and future research directions. By summarizing the work in this field, we hope to provide references and insights for researchers, contributing to the advancement of biomedicine and environmental monitoring. Full article
(This article belongs to the Special Issue Advanced Optical Methods for Biosensing)
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33 pages, 2401 KB  
Review
Recent Advances in Enzyme Immobilization: The Role of Artificial Intelligence, Novel Nanomaterials, and Dynamic Carrier Systems
by Melesse Tadesse and Yun Liu
Catalysts 2025, 15(6), 571; https://doi.org/10.3390/catal15060571 - 9 Jun 2025
Cited by 2 | Viewed by 5233
Abstract
Enzymes, as nature’s precision biocatalysts, hold transformative potential across industrial, environmental, and biomedical sectors. However, their instability, solvent sensitivity, and limited reusability in their free form necessitate advanced immobilization strategies to enhance their robustness and scalability. This review critically examines cutting-edge advancements in [...] Read more.
Enzymes, as nature’s precision biocatalysts, hold transformative potential across industrial, environmental, and biomedical sectors. However, their instability, solvent sensitivity, and limited reusability in their free form necessitate advanced immobilization strategies to enhance their robustness and scalability. This review critically examines cutting-edge advancements in enzyme immobilization, focusing on the integration of artificial intelligence (AI), novel nanomaterials, and dynamic carrier systems to overcome the traditional limitations of mass transfer, enzyme leakage, and cost inefficiency. Key innovations such as metal–organic frameworks (MOFs), magnetic nanoparticles, self-healing hydrogels, and 3D-printed scaffolds are highlighted for their ability to optimize enzyme orientation, stability, and catalytic efficiency under extreme conditions. Moreover, AI-driven predictive modeling and machine learning emerge as pivotal tools for rationalizing nanomaterial synthesis, multi-enzyme cascade design, and toxicity assessment, while microfluidic systems enable precise biocatalyst fabrication. This review also explores emerging carrier-free strategies, including cross-linked enzyme aggregates (CLEAs) and DNA-directed immobilization, which minimize diffusion barriers and enhance substrate affinity. Despite progress, challenges persist in regards to eco-friendly nanomaterial production, industrial scalability, and real-world application viability. Future directions emphasize sustainable hybrid material design, AI-aided lifecycle assessments, and interdisciplinary synergies between synthetic biology, nanotechnology, and data analytics. By connecting laboratory innovation with industrial needs, this work provides a forward-thinking framework to harness immobilized enzymes for achieving global sustainability goals, particularly in bioremediation, bioenergy, and precision medicine. Full article
(This article belongs to the Section Biocatalysis)
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26 pages, 2250 KB  
Review
Sustainable Nanotechnology Strategies for Modulating the Human Gut Microbiota
by Gréta Törős, Gabriella Gulyás, Hassan El-Ramady, Walaa Alibrahem, Arjun Muthu, Prasad Gangakhedkar, Reina Atieh and József Prokisch
Int. J. Mol. Sci. 2025, 26(12), 5433; https://doi.org/10.3390/ijms26125433 - 6 Jun 2025
Cited by 1 | Viewed by 933
Abstract
Antibiotic resistance remains a pressing global health concern, necessitating the development of sustainable and innovative antimicrobial strategies. Plant-based nanomaterials, particularly those synthesized from agricultural byproducts, such as mango seeds, tomato skins, and orange peels, have emerged as promising candidates due to their potent [...] Read more.
Antibiotic resistance remains a pressing global health concern, necessitating the development of sustainable and innovative antimicrobial strategies. Plant-based nanomaterials, particularly those synthesized from agricultural byproducts, such as mango seeds, tomato skins, and orange peels, have emerged as promising candidates due to their potent antimicrobial activity and reduced likelihood of resistance development. These nanomaterials exert their effects through diverse mechanisms, including the generation of reactive oxygen species, the disruption of microbial membranes, and interference with critical cellular functions, such as DNA replication. Beyond their antimicrobial properties, recent studies have demonstrated their ability to modulate gut microbiota composition—promoting beneficial genera such as, Lactobacillus and Bifidobacterium, while inhibiting pathogenic species like Staphylococcus spp. This dual functionality positions them as attractive agents for prebiotic interventions and targeted dietary strategies. The convergence of plant-derived nanotechnology and personalized nutrition, guided by individual microbiota profiles, offers a novel paradigm for enhancing host health and preventing infection-related disorders. This review provides a comprehensive overview of the sustainable production of nanomaterials from agricultural and food industry waste, their antimicrobial and prebiotic applications, and their potential in regulating gut microbiota. Furthermore, we discuss emerging nanoenabled strategies to combat infectious diseases and highlight future directions for mechanistic studies, safety assessments, and clinical translation in pharmaceutical, nutraceutical, and functional food contexts. Full article
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31 pages, 4568 KB  
Review
Stimuli-Responsive DNA Hydrogel Design Strategies for Biomedical Applications
by Minhyuk Lee, Minjae Lee, Sungjee Kim and Nokyoung Park
Biosensors 2025, 15(6), 355; https://doi.org/10.3390/bios15060355 - 4 Jun 2025
Cited by 1 | Viewed by 1437
Abstract
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 [...] Read more.
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
(This article belongs to the Special Issue Hydrogel-Based Biosensors: From Design to Applications)
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32 pages, 1404 KB  
Review
Next-Generation Vaccine Platforms: Integrating Synthetic Biology, Nanotechnology, and Systems Immunology for Improved Immunogenicity
by Majid Eslami, Bahram Fadaee Dowlat, Shayan Yaghmayee, Anoosha Habibian, Saeedeh Keshavarzi, Valentyn Oksenych and Ramtin Naderian
Vaccines 2025, 13(6), 588; https://doi.org/10.3390/vaccines13060588 - 30 May 2025
Cited by 1 | Viewed by 1993
Abstract
The emergence of complex and rapidly evolving pathogens necessitates innovative vaccine platforms that move beyond traditional methods. This review explores the transformative potential of next-generation vaccine technologies, focusing on the combined use of synthetic biology, nanotechnology, and systems immunology. Synthetic biology provides modular [...] Read more.
The emergence of complex and rapidly evolving pathogens necessitates innovative vaccine platforms that move beyond traditional methods. This review explores the transformative potential of next-generation vaccine technologies, focusing on the combined use of synthetic biology, nanotechnology, and systems immunology. Synthetic biology provides modular tools for designing antigenic components with improved immunogenicity, as seen in mRNA, DNA, and peptide-based platforms featuring codon optimization and self-amplifying constructs. At the same time, nanotechnology enables precise antigen delivery and controlled immune activation through engineered nanoparticles such as lipid-based carriers, virus-like particles, and polymeric systems to improve stability, targeting, and dose efficiency. Systems immunology aids these advancements by analyzing immune responses through multi-omics data and computational modeling, which assists in antigen selection, immune profiling, and adjuvant optimization. This approach enhances both humoral and cellular immunity, solving challenges like antigen presentation, response durability, and vaccine personalization. Case studies on SARS-CoV-2, Epstein–Barr virus, and Mycobacterium tuberculosis highlight the practical application of these platforms. Despite promising progress, challenges include scalability, safety evaluation, and ethical concerns with data-driven vaccine designs. Ongoing interdisciplinary collaboration is crucial to fully develop these technologies for strong, adaptable, globally accessible vaccines. This review emphasizes next-generation vaccines as foundational for future immunoprophylaxis, especially against emerging infectious diseases and cancer immunotherapy. Full article
(This article belongs to the Special Issue Vaccine Development and Global Health)
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20 pages, 1329 KB  
Review
Mitochondrial Dysfunction: The Silent Catalyst of Kidney Disease Progression
by Nikola Pavlović, Marinela Križanac, Marko Kumrić, Katarina Vukojević and Joško Božić
Cells 2025, 14(11), 794; https://doi.org/10.3390/cells14110794 - 28 May 2025
Cited by 2 | Viewed by 3581
Abstract
Mitochondrial dysfunction is a pivotal driver in the pathogenesis of acute kidney injury (AKI), chronic kidney disease (CKD), and congenital anomalies of the kidney and urinary tract (CAKUT). The kidneys, second only to the heart in mitochondrial density, rely on oxidative phosphorylation to [...] Read more.
Mitochondrial dysfunction is a pivotal driver in the pathogenesis of acute kidney injury (AKI), chronic kidney disease (CKD), and congenital anomalies of the kidney and urinary tract (CAKUT). The kidneys, second only to the heart in mitochondrial density, rely on oxidative phosphorylation to meet the high ATP demands of solute reabsorption and filtration. Disrupted mitochondrial dynamics, such as excessive fission mediated by Drp1, exacerbate tubular apoptosis and inflammation in AKI models like ischemia–reperfusion injury. In CKD, persistent mitochondrial dysfunction drives oxidative stress, fibrosis, and metabolic reprogramming, with epigenetic mechanisms (DNA methylation, histone modifications, non-coding RNAs) regulating genes critical for mitochondrial homeostasis, such as PMPCB and TFAM. Epigenetic dysregulation also impacts mitochondrial–ER crosstalk, influencing calcium signaling and autophagy in renal pathology. Mitophagy, the selective clearance of damaged mitochondria, plays a dual role in kidney disease. While PINK1/Parkin-mediated mitophagy protects against cisplatin-induced AKI by preventing mitochondrial fragmentation and apoptosis, its dysregulation contributes to fibrosis and CKD progression. For instance, macrophage-specific loss of mitophagy regulators like MFN2 amplifies ROS production and fibrotic responses. Conversely, BNIP3/NIX-dependent mitophagy attenuates contrast-induced AKI by suppressing NLRP3 inflammasome activation. In diabetic nephropathy, impaired mitophagy correlates with declining eGFR and interstitial fibrosis, highlighting its diagnostic and therapeutic potential. Emerging therapeutic strategies target mitochondrial dysfunction through antioxidants (e.g., MitoQ, SS-31), mitophagy inducers (e.g., COPT nanoparticles), and mitochondrial transplantation, which mitigates AKI by restoring bioenergetics and modulating inflammatory pathways. Nanotechnology-enhanced drug delivery systems, such as curcumin-loaded nanoparticles, improve renal targeting and reduce oxidative stress. Epigenetic interventions, including PPAR-α agonists and KLF4 modulators, show promise in reversing metabolic reprogramming and fibrosis. These advances underscore mitochondria as central hubs in renal pathophysiology. Tailored interventions—ranging from Drp1 inhibition to mitochondrial transplantation—hold transformative potential to mitigate kidney injury and improve clinical outcomes. Additionally, dietary interventions and novel regulators such as adenogens are emerging as promising strategies to modulate mitochondrial function and attenuate kidney disease progression. Future research should address the gaps in understanding the role of mitophagy in CAKUT and optimize targeted delivery systems for precision therapies. Full article
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27 pages, 6361 KB  
Article
Antineoplastic Activity of Podophyllotoxin and Juniper Extracts Encapsulated in MPEG-b-PLA Diblock Copolymer Micelles in Cutaneous Squamous Carcinoma Cells
by Radostina G. Kalinova, Ivaylo V. Dimitrov, Yana Ilieva, Dimitar B. Iliev, George A. Miloshev, Dessislava N. Staneva, Maya M. Zaharieva, Aleksandrina Nesheva, Galya Staneva, Diana I. Ivanova, George Angelov and Hristo M. Najdenski
Int. J. Mol. Sci. 2025, 26(11), 5167; https://doi.org/10.3390/ijms26115167 - 28 May 2025
Viewed by 613
Abstract
Nanotechnology offers alternative approaches to the discovery of anticancer drugs. Hydrophobic bioactive components can be included in the cores of amphiphilic nanocarriers, which leads to the formation of a water-dispersible product with improved bioavailability, facilitated excretion, and reduced systemic toxicity in the treated [...] Read more.
Nanotechnology offers alternative approaches to the discovery of anticancer drugs. Hydrophobic bioactive components can be included in the cores of amphiphilic nanocarriers, which leads to the formation of a water-dispersible product with improved bioavailability, facilitated excretion, and reduced systemic toxicity in the treated organisms. This study was aimed at the formation of polymer nanocarriers, loaded with anticancer drug precursor podophylotoxin (PPT) or PPT-containing juniper leaf extracts, seeking to study their antineoplastic activity in A-431 epidermoid carcinoma cells and HaCaT normal keratinocytes. The amphiphilic, biodegradable, and biocompatible MPEG-b-PLA diblock copolymer was self-assembled in aqueous media into nanosized particles, whose physicochemical characteristics were studied by dynamic light scattering, transmission electron microscopy, and other methods. High encapsulation efficiency was determined for the PPT component-loaded micelles. DNA fragmentation, cell cycle arrest, nuclear condensation, membrane lipid order assessment, reactive oxygen species, and apoptosis induction by the loaded nanocarriers in A-431 or HaCaT cells were analyzed by the comet assay, FACS, Hoechst DNA staining, Laurdan generalized polarization, and other methods. As a result of various cellular processes induced by the PPT component-loaded nanoparticles, effector caspase-3 and caspase-7 activation showed selectivity towards tumor cells compared to the normal cells. The newly obtained PPT-containing nanoparticles have applications as potential drugs in the prospective nanomedicine. Full article
(This article belongs to the Special Issue Recent Discovery and Mechanisms of Potential Anticancer Drugs)
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20 pages, 2819 KB  
Review
Research Progress on Nanotechnology-Driven Enzyme Biosensors for Electrochemical Detection of Biological Pollution and Food Contaminants
by Liang Qu, Xue Zhang, Yanhong Chu, Yuyang Zhang, Zhiyuan Lin, Fanzhuo Kong, Xing Ni, Yani Zhao, Qiongya Lu and Bin Zou
Foods 2025, 14(7), 1254; https://doi.org/10.3390/foods14071254 - 3 Apr 2025
Viewed by 996
Abstract
Electrochemical biosensors have attracted widespread attention from researchers due to their simple and rapid operation. Recent advancements in nanobiotechnology have further enhanced their performance, with nanomaterials like graphene, carbon nanotubes, and metal nanoparticles being widely used as carriers for immobilizing enzymes, cells, and [...] Read more.
Electrochemical biosensors have attracted widespread attention from researchers due to their simple and rapid operation. Recent advancements in nanobiotechnology have further enhanced their performance, with nanomaterials like graphene, carbon nanotubes, and metal nanoparticles being widely used as carriers for immobilizing enzymes, cells, and DNA molecules. These materials improve stability, sensitivity, and selectivity, making biosensors more effective. This article reviews the introduction, principles, and classification of enzyme-based electrode sensors, as well as their research and application progress in the detection of food risk factors (including foodborne pathogens, biotoxins, drug residues, food additives, allergens, etc.). It also explores future prospects, including advancements in nanotechnology and enzyme immobilization techniques, highlighting their potential in food safety and beyond. Full article
(This article belongs to the Special Issue Food Grade Immobilisation Systems for Enzymes)
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10 pages, 5208 KB  
Communication
A DNA-Based Plasmonic Nano-Ruler
by Aura Cencini, Mary Bortoluzzi, Graziano Rilievo, Federica Tonolo, Fabio Vianello, Massimiliano Magro and Alessandro Cecconello
Int. J. Mol. Sci. 2025, 26(6), 2557; https://doi.org/10.3390/ijms26062557 - 12 Mar 2025
Viewed by 954
Abstract
DNA is an exceptional building block for the fabrication of dynamic supramolecular systems with switchable geometries. Here, a self-assembled, tunable plasmonic–fluorescent nanostructure was developed. A precise sliding motion mechanism was operated through the control of strand displacement reactions, shifting two single-strand DNA (ssDNA) [...] Read more.
DNA is an exceptional building block for the fabrication of dynamic supramolecular systems with switchable geometries. Here, a self-assembled, tunable plasmonic–fluorescent nanostructure was developed. A precise sliding motion mechanism was operated through the control of strand displacement reactions, shifting two single-strand DNA (ssDNA) rails connected by a ssDNA quasi-ring structure. The system was reconfigured as a nano-mechanical structure, generating six discrete configurations, and setting specific distances between a tethered gold nanoparticle (AuNP) and a fluorophore, Sulfo-Cyanine3 (Cy3). Each configuration produced a distinct fluorescence emission intensity via plasmonic quenching/enhancement effects, and therefore the structure behaved as a nano-ruler. To optimize the system, the reversible distance-dependent fluorescence quenching or enhancement phenomena were investigated by testing AuNPs with diameters of 5, 10, and 15 nm, yielding the best performances with 10 nm AuNPs. Furthermore, a geometric model of the system was produced, confirming the observed results. The fluorophore–plasmonic surface positioning, conferred by the DNA ruler, led to a finite state nano-machine with six alternative signal outputs. This mechanism, working as a fluorescent reporter, could find application in a multiple-responsive detection system of single-strand nucleic acids, such as viruses or microRNAs. Full article
(This article belongs to the Section Molecular Biophysics)
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19 pages, 1438 KB  
Review
Progress in Plant Nitric Oxide Studies: Implications for Phytopathology and Plant Protection
by Michaela Sedlářová, Tereza Jedelská, Aleš Lebeda and Marek Petřivalský
Int. J. Mol. Sci. 2025, 26(5), 2087; https://doi.org/10.3390/ijms26052087 - 27 Feb 2025
Cited by 2 | Viewed by 1156
Abstract
Nitric oxide (NO) is a gaseous free radical known to modulate plant metabolism through crosstalk with phytohormones (especially ABA, SA, JA, and ethylene) and other signaling molecules (ROS, H2S, melatonin), and to regulate gene expression (by influencing DNA methylation and histone [...] Read more.
Nitric oxide (NO) is a gaseous free radical known to modulate plant metabolism through crosstalk with phytohormones (especially ABA, SA, JA, and ethylene) and other signaling molecules (ROS, H2S, melatonin), and to regulate gene expression (by influencing DNA methylation and histone acetylation) as well as protein function through post-translational modifications (cysteine S-nitrosation, metal nitrosation, tyrosine nitration, nitroalkylation). Recently, NO has gained attention as a molecule promoting crop resistance to stress conditions. Herein, we review innovations from the NO field and nanotechnology on an up-to-date phytopathological background. Full article
(This article belongs to the Special Issue Phytohormones: From Physiological Response to Application)
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14 pages, 3867 KB  
Article
A Localized Scalable DNA Logic Circuit System Based on the DNA Origami Surface
by Zhen Tang, Shiyin Li, Chunlin Chen, Zhaohua Zhou and Zhixiang Yin
Int. J. Mol. Sci. 2025, 26(5), 2043; https://doi.org/10.3390/ijms26052043 - 26 Feb 2025
Viewed by 1387
Abstract
DNA (Deoxyribonucleic Acid) logic circuit systems provide a powerful arithmetic architecture for the development of molecular computations. DNA nanotechnology, particularly DNA origami, provides a nanoscale addressable surface for DNA logic circuit systems. Although molecular computations based on DNA origami surfaces have received significant [...] Read more.
DNA (Deoxyribonucleic Acid) logic circuit systems provide a powerful arithmetic architecture for the development of molecular computations. DNA nanotechnology, particularly DNA origami, provides a nanoscale addressable surface for DNA logic circuit systems. Although molecular computations based on DNA origami surfaces have received significant attention in research, there are still obstacles to constructing localized scalable DNA logic circuit systems. Here, we developed elementary DNA logic circuits on a DNA origami surface by employing the strand displacement reaction (SDR) to realize the localized scalable DNA logic circuit systems. We showed that the constructed elementary logic circuits can be scaled up to the localized DNA logic circuit systems that perform arbitrary digital computing tasks, including square root functions, full adder and full subtractor. We used a 50% reduction in the number of localized DNA logic components, compared to localized logic systems based on the threshold strategy. We further demonstrated that the localized DNA logic circuit systems for three-satisfiability (3-SAT) problem solving and disease classification can be implemented using the constructed elementary DNA logic circuits. We expect our approach to provide a new design paradigm for the development of molecular computations and their applications in complex mathematical problem solving and disease diagnosis. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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44 pages, 11801 KB  
Review
Layer-by-Layer Nanoarchitectonics: A Method for Everything in Layered Structures
by Katsuhiko Ariga
Materials 2025, 18(3), 654; https://doi.org/10.3390/ma18030654 - 1 Feb 2025
Cited by 9 | Viewed by 1835
Abstract
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 [...] Read more.
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
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