PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Nanostructures”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

18 recordsLinked to original sources
PubMed2025

DNA Nanostructure Self-Assembly in an Aqueous Ionic Liquid Solution with Enhanced Stability and Target Binding Affinity.

DNA nanostructure-enabled functional constructs have shown potential to improve healthcare outcomes by offering advanced disease diagnostic and therapeutic strategies. Translating this potential of DNA nanostructure-based constructs to real life applications relies on maintaining and enhancing the structural integrity and functions of the surface-anchored moieties. In this study, we explored the possibility of utilizing choline dihydrogen phosphate (CDHP) solution, an aqueous solution of ionic liquid, to assemble DNA nanostructures of different sizes and complexities with enhanced biostability and ligand binding affinity. We show successful formation of the DNA nanostructures in aqueous CDHP solution using gel electrophoresis, atomic force microscopy (AFM), and circular dichroism (CD). Biostability assays reveal that the aqueous CDHP solution may provide passive protection to DNA nanostructures against DNase I and human serum for up to 48 h. We also demonstrate that this enhanced biostability arises both from the structural conformation imparted during CDHP-mediated folding and from the presence of free CDHP ions in the solution. Notably, removal of free ions reduced the passive protection effect, but did not eliminate it, indicating the contribution of both folding and surrounding free ions. Using flow cytometry and surface plasmon resonance assays, we show that the presence of aqueous CDHP solution can enhance the binding of aptamer-functionalized DNA nanostructures to specific receptors on acute myeloid leukemia (AML) cells. Our strategy of using ionic liquid solution for one-pot preparation with enhanced stability and functionality offers a robust, simpler and faster alternative for DNA nanostructure-based constructs.

Ionic Liquids↗
PubMed1987

Some nanostructural features in ceramics.

Nanostructural features in some ceramics have been discussed and reviewed. Based on our research results and recent published investigations, many topics, such as grain, grain boundary, interface film, grain boundary engineering, microcrack, microdomain, nanodomain, domain boundary, and phase transformation, etc., have been dealt with; and many materials, such as Si3N4, beta''-Al2O3, MgO, SiC, (Hg, Cd) Te, BNN, ZrO2, PLZT, CdSe, Ca10(PO4)6, (OH)2, etc., have been involved. The results are important to understand the relation between the structure and property of materials and to improve the materials' technology.

Ceramics↗
PubMed2026

Insertion of CG repeats and 3' terminus overhangs drive B-to-Z transition: A case study with NF-κB bearing DNA nanostructures.

Z-DNA, a non-canonical helical structure of DNA plays a vital role in various biological processes, including transcription and genomic stability. Though low concentration of trivalent cations is known to induce B-Z transition, the effect of short CG repeats, overhangs sequences, loop length and order of nucleotides on Z-DNA formation in larger DNA is utterly unknown. Earlier, a series of self-assembled branched DNA (bDNA) nanostructures having 5T in the loop are reported to be resistant to B-to-Z DNA transition irrespective of the overhang sequences. Since the presence of alternative purine/pyrimidine sequences and direction of oligonucleotides play a vital role during replication and transcription, we hypothesize that the insertion of a small number of CG repeats, or a change in direction of overhang sequences may influence the B-to-Z DNA transition. Here, we show that Z-DNA formation was induced by inserting CG repeats into bDNA structures that were previously resistant to B-Z transition. Moreover, B-Z transition was also observed when overhangs were introduced at the 3' terminus. The generality of the approach of B-Z transition was demonstrated in a series of bDNA structures including the bDNA having NF-kβ sequences. Different dye binding experiments suggest the formation of Z-DNA in bDNA having overhangs at the 3' terminus against the control of bDNA with 5' overhangs. Interestingly, the melting temperature (Tm) was substantially reduced to 55 °C in the Z-DNA as compared to the LaCl3-induced condensed DNA having Tm of 77 °C. Fluorescence study also supports the presence of minor groove in Z-DNA which binds Hoechst. ITC indicates an entropy- and enthalpy-driven favorable binding between lanthanide cations and bDNA. Thus, the present study establishes a synthetic bDNA nanotechnology platform for systematically investigating how local sequence architecture, including the insertion of CG repeats, loop length, and overhang orientation influences B-to-Z conformational switching under controlled experimental conditions.

B-Z transition↗
PubMed1991

Molecular self-assembly and nanochemistry: a chemical strategy for the synthesis of nanostructures.

Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

Biotechnology↗
PubMed2026

The multilayered cuticle underlying structural coloration in red algae shares features with the metazoan extracellular matrix.

Structural coloration, a physical phenomenon observed in many living organisms, may arise from the interference of light with highly organized surface nanostructures. In some seaweeds, these nanostructures consist of cuticular lamellae in the outer part of the extracellular matrix (ECM) of the epidermis. However, the chemical composition of seaweed cuticles is poorly understood and the molecular components of lamellae remain unidentified. Here, we use integrated genomic, transcriptomic, proteomic, and metabolomic approaches together with analytical profiling of carbohydrates to determine the composition of the multilayered cuticle in the red alga Chondrus crispus and assess its evolutionary conservation. The structural assembly reveals common features with the ECM of animals. The carbohydrate fraction includes a complex mixture of carrageenans and glycosaminoglycan-like compositions. A major von Willebrand factor A domain protein, Lamellae Cohesive Protein, plays a critical role in protein-protein interactions and binding to sulfated polysaccharides. We have further identified the major proteins of the algal cuticle, providing a framework for addressing the evolutionary origins of the cuticle and raising important questions regarding its role, particularly across the red algal life cycle marked by major structural differences in its ECM.

Extracellular Matrix↗
PubMed2026

Morphology-engineered NiFe@C nanocages boosting electrochemical quantification of ractopamine in meat samples.

It is essential to acquire efficient electrocatalysts to develop ractopamine (RAC) electrochemical sensors. Herein, we report the synthesis of a series of carbon coated NiFe alloy nanostructures (e.g., NiFe@C nanoparticles, nanocubes and nanocages) using NiFe Prussian blue analogue (PBA) as the precursor. The NiFe@C nanocages exhibited the best electrocatalytic performance for RAC sensing. This is attributed to the embedded NiFe alloy nanoparticles that provide abundant active sites, and the unique nanocage structure facilitates electron transfer pathways while offering a high specific surface area. The resulting sensor achieves a low detection limit (LOD) of 54 nM (S/N = 3) within a linear range of 0.2-12 μM. Moreover, the sensor demonstrates good reproducibility, stability, and excellent long-term stability. Practical applicability was confirmed in meat samples, yielding satisfactory recovery rates ranging from 98% to 108%. A feasible strategy was introduced herein for rational design of metal@carbon electrocatalysts.

Phenethylamines↗
PubMed2025

Single-Molecule Nanopore Detection of Non-Canonical Thymine-Melamine Hydrogen Bonding Base Pair in DNA Abasic Site.

The binding of small molecules to DNA may represent a mutagenic process capable of inducing genomic structural alterations and functional impairment. Melamine (MA), a toxic small molecule, exhibits a hydrogen-bonding interface structurally analogous to adenine, enabling to form non-canonical thymine-melamine (T-MA) base pairs like Watson-Crick pairing. This property allows MA to program DNA nanostructure formation. Given MA's documented biological consequences, such as kidney disease, reproductive toxicity, and central nervous system dysfunction, sensitive detection of MA-DNA interactions has become critically important. However, such subtle structural changes remain challenging to identify because of the paucity of effective detection approaches in a high-resolution manner. To overcome this limitation, nanopore measurement is employed to identify T-MA hydrogen bonding base pairing in DNA. Results demonstrate that nanopore enables unambiguous identification of T-MA hydrogen bonding via mechanically unzipping thymine-melamine-thymine (T-MA-T) triplets in DNA structures. The approach achieves single-base-pair resolution, as evidenced by nucleotide substitutions flanking the abasic site in complex DNA structures. In addition, nanopore-based kinetic analysis reveals an enhanced intramolecular stability in MA-binding DNA compared to those consisting of complete canonical DNA pairs. This research establishes a powerful platform for high-resolution interrogation of DNA-small molecule interactions and quantitative biophysical characterization of mutagenic modifications at the nanoscale.

Single Molecule Imaging↗
PubMed2026

Integrating structure and experimental data annotations with computational modeling framework for predicting micro-nanoplastics toxicities.

The wide use of plastic materials leads to increased emissions of micro-nanoplastics (MNPs) into the environment, raising significant concerns about their impact on human health. Traditional experimental approaches for assessing MNPs toxicity are costly, time-consuming, and there are no experimental protocols that are universally acceptable. Computational modeling using machine learning (ML) approaches provides an efficient alternative to MNP toxicity assessment. However, most modeling studies of MNPs are limited due to the lack of high-quality data and there are few previous modeling studies considering complex structures of MNPs for model training. To address this challenge, we constructed three MNP datasets with popular toxicity endpoints from various resources and used nanostructure annotation techniques to create virtual MNPs (vMNPs) for all MNP structures. The MNP structures were digitalized from annotated vMNPs, and geometrical descriptors were calculated using the Delaunay Tessellation approach. Moreover, important experimental information, such as concentrations and cell lines, were transformed into extra training variables. Partial least squares regression (PLSR) models were built using both experimental and geometrical descriptors and validated through a leave-one-out cross validation procedure. The resulting models showed reasonable performance in predicting toxicity potentials of MNPs for the three endpoints in the present datasets. Moreover, an additional library of vMNPs with their predicted properties and bioactivities was constructed, directing further research of new MNPs. This study provides three novel ML models for MNPs by integrating geometrical and experimental descriptors, which have the potential to assess new MNPs for their toxicity. The modeling strategy developed in this study can be easily expanded to model other MNP toxicity endpoints and create promising new models for MNP toxicity assessments.

Data annotation↗
PubMed2026

Multivalent cations stabilize DNA duplexes beyond charge neutralization.

Multivalent cations are abundant in cells and play essential roles in DNA duplex stability, genome packaging, and DNA-protein interactions. They can also condense DNA, making it challenging to determine their influence on DNA duplex stability. To overcome this challenge, we studied DNA unpeeling at equilibrium under high tension using magnetic tweezers, thereby preventing condensation. Experiments show that DNA duplex stability first increases and then decreases as cation concentration increases and the maximum DNA duplex stability increases with cation valence. The maximum free energy change of DNA was 3.33 k B T/bp for Na+ and increased to 3.98 k B T/bp for protamine, which is a small arginine-rich protein with a highly positive charge (≈21 for salmon sperm), corresponding to a relative increase of 19.5%. Consistently, all-atom molecular dynamics simulations show that higher-valent cations preferentially embed in the minor groove of DNA and clamp the minor groove, in contrast to the major-groove clamping reported for RNA, thereby stabilizing the helix more efficiently. These findings establish a single-molecule framework for quantifying DNA thermodynamics in complex ionic environments, which contributes to understanding ionic control of genome stability and to designing ion-tunable DNA-based nanostructures and delivery systems.

Journal Article↗
PubMed1995

Molecular organization of histidine-tagged biomolecules at self-assembled lipid interfaces using a novel class of chelator lipids.

In molecular biology, the expression of fusion proteins is a very useful and well-established technique for the identification and one-step purification of gene products. Even a short fused sequence of five or six histidines enables proteins to bind to an immobilized metal ion chelate complex. By synthesis of a class of chelator lipids, we have transferred this approach to the concept of self-assembly. The specific interaction and lateral organization of a fluorescent fusion molecule containing a C-terminal oligohistidine sequence was studied by film balance techniques in combination with epifluorescence microscopy. Due to the phase behavior of the various lipid mixtures used, the chelator lipids can be laterally structured, generating two-dimensional arrays of histidine-tagged biomolecules. Because of the large variety of fusion proteins already available, this concept represents a powerful technique for orientation and organization of proteins at lipid interfaces with applications in biosensing, biofunctionalization of nanostructured interfaces, two-dimensional crystallization, and studies of lipid-anchored proteins.

Amines↗
PubMed2025

Stepping out of the dark: how metabolomics shed light on fungal biology.

Metabolomics, a critical tool for analyzing small-molecule metabolites, integrates with genomics, transcriptomics, and proteomics to provide a systems-level understanding of fungal biology. By mapping metabolic networks, it elucidates regulatory mechanisms driving physiological and ecological adaptations. In fungal pathogenesis, metabolomics reveals host-pathogen dynamics, identifying virulence factors like gliotoxin in Aspergillus fumigatus and metabolic shifts, such as glyoxylate cycle upregulation in Candida albicans. Ecologically, it highlights fungal responses to abiotic stressors, including osmolyte production like trehalose, enhancing survival in extreme environments. These insights highlight metabolomics' role in decoding fungal persistence and niche colonization. In drug discovery, it aids target identification by profiling biosynthetic pathways, supporting novel antifungal and nanostructured therapy development. Combined with multi-omics, metabolomics advances insights into fungal pathogenesis, ecological interactions, and therapeutic innovation, offering translational potential for addressing antifungal resistance and improving treatment outcomes for fungal infections. Its progress shed light on complex fungal molecular profiles, advancing discovery and innovation in fungal biology.

Metabolomics↗
PubMed2026

Selective and sensitive colorimetric sensing of carbosulfan based on BiO2-x/Bi2O2.75 nanosheets with excellent haloperoxidase-like activity.

The development of colorimetric methods based on directly inhibiting nanozyme activity for pesticide detection has attracted considerable attention. In this study, we report a novel colorimetric sensing strategy utilizing BiO2-x/Bi2O2.75 nanosheets (BiO2-x/Bi2O2.75 NSs) with haloperoxidase (HPO)-like activity for the rapid and sensitive detection of carbosulfan (CBS) in foods. Oxygen-vacancy-rich BiO2-x/Bi2O2.75 NSs with HPO-like activity were rationally constructed. Kinetic studies revealed a remarkable Michaelis-Menten constant (Km) of 0.014 mM for I-, indicating a higher affinity for iodide ions than other reported HPO-like nanozymes, as evidenced by its lower Km. Under acidic conditions, CBS tends to be hydrolyzed to produce reductive sulfide species, which directly inhibit the iodoperoxidase-like activity of BiO2-x/Bi2O2.75 NSs, enabling selective detection with a limit of detection (LOD) of 0.18 μg/mL and a linear range of 0.20-100 μg/mL. When the concentration of interfering pesticides and substances was 5 times that of CBS, the sensor remained unaffected, exhibiting excellent stability and specificity. This work contributes to the detection of CBS in complex food matrices, bridging the application gap of HPO-like nanozymes in pesticide detection and providing a promising method for food safety detection.

Colorimetry↗
PubMed2026

A STORM-based protocol for nanoscale imaging and quantitative analysis of protein-associated and phospholipid-associated structures in natural rubber.

Stochastic Optical Reconstruction Microscopy (STORM) enables nanoscale mapping of molecular components beyond the diffraction limit; however, its reproducible implementation in hydrophobic polymer matrices remains challenging because fluorescence-labeling specificity, fluorophore photoswitching, three-dimensional localization, chromatic registration, and quantitative image analysis must be carefully controlled. This protocol presents a standardized experimental workflow for dual-color labeling, astigmatism-based three-dimensional STORM acquisition, and quantitative analysis of protein-associated and phospholipid-associated structures in natural rubber (NR). The workflow covers sample pretreatment, Cy5 NHS ester labeling of protein-associated primary amines, DiI labeling of phospholipid-rich domains, STORM imaging-buffer preparation, three-dimensional single-molecule localization, dual-channel registration, generation of standardized xy projections, aggregate-size analysis, and projected lateral spatial correlation assessment. Reproducibility is supported by defined acquisition and localization criteria, three independent sample preparations with at least five fields of view analyzed per condition, and unlabeled, single-color, dye-only matrix, and processing-associated Cy5 controls. Mean lateral localization precisions of 11.8 ± 2.3 nm for Cy5 and 13.5 ± 2.9 nm for DiI were obtained, while two-dimensional Fourier ring correlation analysis of the xy projections yielded effective lateral image resolutions of approximately 25 and 28 nm, respectively. Image-based particle segmentation and localization-coordinate-based density-based spatial clustering of applications with noise (DBSCAN) were applied to standardized xy projections as complementary quantitative approaches. Application of the protocol to untreated, centrifuged, and protease-treated NR samples demonstrated treatment-associated changes in the detected abundance and projected size distributions of protein- and phospholipid-associated aggregates, together with a non-monotonic change in their projected lateral spatial correlation. These observations describe alterations in nanoscale organization but do not, by themselves, establish stable protein-phospholipid complex formation. Unlike previous studies that primarily demonstrated the feasibility of STORM imaging in rubber materials, the principal contribution of this work is an end-to-end, step-by-step protocol incorporating defined controls, three-dimensional localization, image-quality metrics, chromatic-registration procedures, and complementary quantitative-analysis pipelines for non-expert users. The workflow may be adaptable to other hydrophobic polymers and soft-material systems after appropriate optimization and validation.

Rubber↗
PubMed2026

HoT auto-blinking probes enable real-time, super-resolution chromatin imaging in live cells and tissues.

Single-molecule localization microscopy (SMLM) enables visualization of chromatin architecture at nanoscale resolution. However, high-performance DNA probes suitable for SMLM in both live cells and tissues remain limited. We developed Hoechst-6-Carboxytetramethylrhodamine (6-TAMRA) derivative (HoT) probes-rhodamine-based derivatives conjugated to a Hoechst moiety-through structural fine-tuning of rhodamine spirocyclization. HoTs are self-assembling, auto-blinking probes with excellent photostability and high temporal resolution. They permeate live cells, enabling long-term, real-time nanoscopic chromatin imaging in live and fixed cells and in tissue sections. In live cells, we identified nanoscale features in the 3D organization of chromatin and quantified DNA fiber kinetics at high resolution. We quantified DNA compaction in single cells within retinal and colon cancer sections. OligoSTORM (stochastic optical reconstruction microscopy)-labeled gene loci can be visualized and measured within their HoT-labeled chromatin footprints. Our work provides powerful tools for investigating chromatin structure and functions in living cells and tissues, with applications ranging from cancer diagnosis to retinal regeneration.

Chromatin↗
PubMed2026

Volumetric DNA microscopy for mapping spatial transcriptomes in three dimensions.

The architecture and function of biological systems are inherently three-dimensional, yet most existing spatial transcriptomic technologies remain restricted to thin tissue sections, limiting their capacity to resolve cellular organization and microenvironments within intact tissue volumes. To address this limitation, we developed volumetric DNA microscopy, a scalable, optics-free approach for spatial transcriptome profiling directly within intact biological specimens. The method encodes spatial information into DNA molecules that form a dense intermolecular network in situ, enabling the reconstruction of three-dimensional spatial relationships through short-read sequencing and computational analysis. Here we detail the complete workflow including in situ cDNA synthesis, spatial encoding through DNA nanoball formation, dual-scale proximity bridging between neighboring nanoballs and spatial reconstruction via geodesic spectral embedding. Sequencing libraries can be generated within 7-8 d by a competent graduate-level molecular biologist, followed by standardized downstream computational analysis. Because the workflow requires only routine molecular biology reagents and a benchtop sequencer, volumetric DNA microscopy provides a versatile platform for exploring genetic and morphological features in intact tissues.

Spatial Transcriptomics↗
PubMed2016

A synergistic approach to the design, fabrication and evaluation of 3D printed micro and nano featured scaffolds for vascularized bone tissue repair.

3D bioprinting has begun to show great promise in advancing the development of functional tissue/organ replacements. However, to realize the true potential of 3D bioprinted tissues for clinical use requires the fabrication of an interconnected and effective vascular network. Solving this challenge is critical, as human tissue relies on an adequate network of blood vessels to transport oxygen, nutrients, other chemicals, biological factors and waste, in and out of the tissue. Here, we have successfully designed and printed a series of novel 3D bone scaffolds with both bone formation supporting structures and highly interconnected 3D microvascular mimicking channels, for efficient and enhanced osteogenic bone regeneration as well as vascular cell growth. Using a chemical functionalization process, we have conjugated our samples with nano hydroxyapatite (nHA), for the creation of novel micro and nano featured devices for vascularized bone growth. We evaluated our scaffolds with mechanical testing, hydrodynamic measurements and in vitro human mesenchymal stem cell (hMSC) adhesion (4 h), proliferation (1, 3 and 5 d) and osteogenic differentiation (1, 2 and 3 weeks). These tests confirmed bone-like physical properties and vascular-like flow profiles, as well as demonstrated enhanced hMSC adhesion, proliferation and osteogenic differentiation. Additional in vitro experiments with human umbilical vein endothelial cells also demonstrated improved vascular cell growth, migration and organization on micro-nano featured scaffolds.

Bone Regeneration↗
PubMed2026

Metal-Organic Framework-Based and Metal-Organic Framework-Derived Nanomaterials for Cancer Theranostics and Antibacterial Applications: Advances, Challenges, and Perspectives.

Metal-organic frameworks (MOFs), constructed through coordination-driven self-assembly of metal ions/clusters and organic linkers, have emerged as a uniquely versatile class of porous nanomaterials with broad biomedical potential. Despite substantial clinical progress, both oncological treatment and antimicrobial intervention remain constrained by inadequate tumor-targeting selectivity, multidrug resistance, immunosuppressive tumor microenvironments, and the global proliferation of antibiotic-resistant pathogens, limitations that conventional nanocarrier platforms have addressed only in part. MOF-based and MOF-derived nanomaterials, distinguished by tunable pore architecture, structurally and compositionally adaptable metal nodes, high surface areas, and stimulus-responsive degradability, offer a rational framework for overcoming these barriers. This review systematically examines the synthetic strategies underlying MOF-based and MOF-derived nanomaterials, including pyrolysis, chemical etching, composite modification, and functional group introduction, and their structural determinants of performance. In cancer theranostics, we critically evaluate their roles as multimodal imaging contrast agents, stimulus-responsive drug delivery carriers, and platforms for combination therapies encompassing photodynamic, photothermal, chemodynamic, and immunomodulatory modalities. In antibacterial applications, we analyze the mechanistic basis of MOF-based and MOF-derived activity, including physical membrane disruption, reactive oxygen species-mediated oxidative stress, and sustained metal ion release, alongside strategies targeting biofilm formation and antibiotic resistance. Multifunctional platforms that concurrently integrate cancer theranostic and antibacterial capabilities are further discussed. This review also addresses the principal barriers to clinical translation, encompassing large-scale manufacturing, long-term biosafety, and regulatory approval, and proposes future directions incorporating artificial intelligence-assisted design and materials genomics, underscoring the transformative potential of MOF-based and MOF-derived nanomaterials as next-generation precision nanomedicines. This review establishes a unified mechanistic framework grounded in the intrinsic physicochemical properties of MOF-derived nanomaterials, systematically integrating their applications in cancer theranostics and antibacterial therapy. Critically, it bridges fundamental advances with translational reality by incorporating a rigorous assessment of regulatory pathways, scalable manufacturing constraints, and clinical implementation barriers, and offers a comprehensive, practice-oriented reference for the rational design and responsible translation of MOF-based and MOF-derived nanomaterials.

Theranostic Nanomedicine↗