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PubMed2026

Spatially confined electrochemical strategy with DNA-assembled nanogaps for SNP detection.

Accurate detection of low-abundance single nucleotide polymorphisms (SNPs) against a large excess of homologous wild-type sequences requires both selective molecular recognition and effective transduction of small sequence differences into measurable signals. Here, we report a spatially confined electrochemical strategy that couples sequence-selective recognition with size-dependent mass-transport gating. DNA-hybridization-driven self-assembly of gold nanoparticles (AuNPs) forms a three-dimensional self-assembled electrode (3D-SAE) with a DNA-defined interparticle architecture. Competitive probes (SP/WP) convert single-base recognition into distinct molecular-size states: the SNP-associated pathway preferentially triggers a hybridization chain reaction (HCR), generating bulky AuNP-anchored HCR/methylene blue complexes (Au@HCR/MB) with reduced electrochemical accessibility through the porous 3D-SAE, whereas the wild-type pathway does not trigger HCR and maintains a high-current response from more readily accessible MB-containing species. Thus, sequence recognition is translated into a molecular-size difference and subsequently into an electrochemical signal through differential mass transport. Under buffer conditions, the platform achieved a statistically estimated detection limit of ∼0.47 fM and a quantitative range of 1 fM-100 pM. It discriminated a 0.1% mutant abundance in a fragmented genomic-DNA background. The downstream signal-transduction chemistry is enzyme-free and isothermal. This work establishes a mechanistical recognition-size-conversion-mass-transport-gating architecture for electrochemical nucleic acid analysis.

Polymorphism, Single Nucleotide↗
PubMed2026

RADA16 as a novel hemostatic and regenerative agent in urology: European Association of Urology endourology up-to-date overview.

PURPOSE OF REVIEW: Self-assembling peptide (SAP) hydrogels represent a novel class of synthetic biomaterials with growing relevance in surgery. Among them, the ion-complementary peptide RADA16 has gained attention as an athermal, transparent, and biocompatible hemostatic agent. While its use is increasingly reported in multiple surgical specialties, evidence specific to urology remains fragmented. This review aims to summarize the physicochemical properties, mechanisms of action, and current clinical evidence for RADA16-based hydrogels, with a particular focus on urological applications. RECENT FINDINGS: RADA16 rapidly self-assembles into a transparent, extracellular-matrix-like nanofibrillar hydrogel upon exposure to physiological fluids, providing effective local hemostasis without reliance on the coagulation cascade. Preclinical and clinical data from other surgical fields demonstrate rapid bleeding control, favorable safety, and potential regenerative effects. Emerging urological evidence suggests that RADA16 is effective in managing hemorrhagic cystitis, radiation-induced hematuria, and bleeding during prostate surgery, including robot-assisted radical prostatectomy and benign prostate surgery. Beyond hemostasis, RADA16 may support wound healing and promotion of re-epithelialization. However, the current evidence base is limited by small sample sizes, lack of comparative studies, heterogeneous methodologies, and short follow-up. SUMMARY: RADA16-based hydrogels represent a promising adjunctive hemostatic option in urology, offering technical advantages such as transparency, absence of thermal injury, minimal swelling, and applicability in confined or high-risk settings. Robust prospective, comparative, and cost-effectiveness studies are required to define its definitive role in routine urological practice.

Humans↗
PubMed1979

Nocodazole action on tubulin assembly, axonal ultrastructure and fast axoplasmic transport.

The action of a synthetic antitubulin agent, nocodazole, on tubulin self-assembly, preformed microtubules, fast axoplasmic transport and axonal ultrastructure was studied. Nocodazole completely blocks the self-assembly of tubulin containing or lacking associated proteins. This inhibition is readily reversible. At similar concentrations, nocodazole also depolymerizes preformed microtubules in vitro. Fast axoplasmic transport in cat vagus nerve is disrupted by bathing the nerve fivers in a medium containing 10 micrometer nocodazole for periods of 2.5 hr or longer. A 4-hr exposure results in extensive inhibition. The nocodazole action on fast axoplasmic transport appears to be reversible but with a high degree of variability. After 2.5 hr of exposure to 10 micrometers nocodazole, there is a slight decrease in axonal microtubules and an increase in 10 nm neurofilaments. A 4 hr exposure results in a marked reduction in microtubules. These results suggest that nocodazole has a mode of action similar to other antimicrotubule agents.

Animals↗
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↗
PubMed1979

Sporogenesis of a myxosporidan with motile spores.

Three types of cells comprise each Fabespora vermicola sporoblast: valvogenic (VAV), capsulogenic (CAP), and germinative (GEM). Walls, polar caps, and sutures are the main assemblages produced by the VAV cells. The unique polar cap organelle extends over the aperture region of the polar capsule component of the CAP cell. The VAV cell also assembles a wall located on the cytoplasmic side of the plasma membrane facing the sporoblast exterior. Bundles of 7 nm microfilaments develop within the extracellular space between the VAV and interior cells of the sporoblast. These microfilaments assemble late in sporogenesis when the spore acquires the capacity for locomotion. Polar filament construction takes place exclusively within the polar capsule primordium (PCP) by apparent self-assembly prior to the PCP being enveloped by membranes. The CAP and GEM cells accumulate considerable glycogen during sporogenesis. The first identifiable GEM cell is single, but has two unpaired nuclei. These GEM cell nuclei later form a paired structure which is sustained into the spore stage.

Animals↗
PubMed1975

The nature of the attachment of a regularly arranged surface protein to the outer membrane of an Acinetobacter sp.

Acinetobacter 199A carries on the outer surface of its outer membrane a layer of regularly arranged protein subunits. The isolated surface protein assembles into the same regular array even in the absence of the underlying outer membrane. Cl- minus is required for this self-assembly. Evidence is presented that the interaction of the surface protein with the outer membrane involves the linking of a carboxyl group in the surface protein to a negatively charged group in the outer membrane protein, via a divalent cation. The surface protein could be detached from the outer membrane by the protein perturbant urea, by the chelating agent EDTA and by replacing Mg-2+ with Na+. It could not be detached by treatment with phospholipases A anc D or the detergents Tween 80 and sodium deoxycholate. The conditions favourable for reattachment of surface protein to the cell wall were the presence of divalent cations and a pH of 3-5. Conversion of carboxyl groups in the surface protein to amine with carbodiimide and ethylene diamine interfered with reattachment. The surface protein did not attach to isolated cell wall lipid or lipopolysaccharide.

Acinetobacter↗
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

The TUBG meshwork is associated with centromere dynamics and micronuclear organization.

This study investigates how γ-tubulin and the centrosome contribute to interphase centromere dynamics and nuclear organization. Although classically associated with mitotic microtubule nucleation, here we show that γ-tubulin associates with chromatin and is enriched within centromere-defined volumes. Using live-cell imaging, immunofluorescence, and chromatin immunoprecipitation sequencing, we detect γ-tubulin-associated signal at satellite-rich, centromere-proximal chromatin. Reduced γ-tubulin levels are associated with increased centromere fluorescence intensity and reduced mobility, linking the γ-tubulin network to centromere organization. Under acute cisplatin-induced stress, centromere mobility increases, whereas centromere clustering is observed in separate fixed-cell analyses. Ser131 phosphorylation is associated with γ-tubulin self-assembly and centromere-related dynamics. Additionally, γ-tubulin accumulates in micronuclei, coinciding with increased replication-associated signal and DNA fluorescence. In primary clear cell renal cell carcinoma cells, stress is associated with higher γ-tubulin fluorescence intensity within centromere-defined volumes. Together, these findings support an association between the γ-tubulin meshwork and centromere organization, chromatin compartmentalization, and responses to genomic stress.

Centromere↗
PubMed2026

A proteomic analysis of the PHF-forming tau fragment (tau297-391) following uptake into differentiated human neuronal SHSY5Y cells.

Tau self-assembly and intracellular deposition are associated with a group of neurodegenerative diseases called tauopathies, which include Alzheimer's disease (AD) and Pick's disease. Here, we measured the proteome response in human neuronal cells (differentiated SH-SY5Y) following the addition of a spontaneously amyloidogenic region of tau known as dGAE (tau297-391), which forms AD-like paired helical filaments in vitro, and proteomic analysis showed increased endogenous tau expression. Further interactome analysis uncovered increased association between tau and proteins associated with nuclear chromatin, the nucleolus, and the spliceosome, as well as the thiol-peroxidase, PRDX6, alongside an increase in reactive oxygen species. The present work highlights a method to identify proteome pathways that may play an important role in the development of tau pathology and reveals an oxidative stress response to dGAE.

Humans↗
PubMed1976

A molecular concept of the properdin pathway.

The sequential events of the properdin system were analyzed. Properdin-depleted serum allows the formation of a Factor B- and D-dependent C3 convertase. This enzyme, called the properdin-receptor-forming enzyme, was shown to utilize a novel serum component, the initiating factor. The protein is a beta-globulin in precursor form and is distinct from immunoglobulins. The function of the enzyme is to deposit C3b on the surface of activator particles. Apparently doublets of C3b are required for the formation of the properdin-activating principle. It consists of a complex containing surface-bound C3b and activated Factor B. properdin precursor is activated by binding to this complex without detectable change in molecular weight. The transition of properdin precursor to activated properdin is probably caused by a conformational change. The complex, consisting of bound C3b, properdin, and activated Factor B, represents the enzyme that acts on C5, thereby initiating self-assembly of the membrane attack system. Native C3 is not needed for the function of the enzyme. It is disassembled by soluble C3 or C3b and its formation is under the control of the properdin-receptor-destroying enzyme, which may be identical with the C3b inactivator.

Beta-Globulins↗
PubMed1976

The microsporidian spore invasion tube. The ultrastructure, isolation, and characterization of the protein comprising the tube.

The extrusion apparatus of the microsporidian parasitic protozoan Nosema michaelis discharges an invasion (or polar) tube with a velocity suitalbe for piercing cells and injecting infective sporoplasm. The tube is composed of a polar tube protein (PTP) which consists of a single, low molecular weight polypeptide slightly smaller than chymotrypsinogen-A. Assembled PTP tubes resist dissociation in sodium dodecyl sulfate and brief exposures in media at extreme ends of the pH range; however, the tubes are reduced by mercaptoethanol and dithiothreitol. When acidified, mercaptoethanol-reduced PTP self-assembles into plastic, two-dimensional monolayers. Dithiothreitol-reduced PTP will not reassemble when acidified. Evidence is presented which indicates that PTP is assembled as a tube within the spore; that the ejected tube has plasticity during sporoplasm passage; and, finally, that the subunits within the tube polymer are bound together, in part, by interprotein disulfide linkages.

Amino Acids↗
PubMed1979

Chick brain actin and myosin. Isolation and characterization.

Brain actin extracted from an acetone powder of chick brains was purified by a cycle of polymerization-depolymerization followed by molecular sieve chromatography. The brain actin had a subunit molecular weight of 42,000 daltons as determined by co-electrophoresis with muscle actin. It underwent salt-dependent g to f transformation to form double helical actin filaments which could be "decorated" by muscle myosin subfragment 1. A critical concentration for polymerization of 1.3 microM was determined by measuring either the change in viscosity or absorbance at 232 nm. Brain actin was also capable of stimulating the ATPase activity of muscle myosin. Brain myosin was isolated from whole chick brain by a procedure involving high salt extraction, ammonium sulfate fractionation and molecular sieve chromatography. The purified myosin was composed of a 200,000-dalton heavy chain and three lower molecular weight light chains. In 0.6 M KCl the brain myosin had ATPase activity which was inhibited by Mg++, stimulated by Ca++, and maximally activated by EDTA. When dialyzed against 0.1 M KCl, the brain myosin self-assembled into short bipolar filaments. The bipolar filaments associated with each other to form long concatamers, and this association was enhanced by high concentrations of Mg++ ion. The brain myosin did not interact with chicken skeletal muscle myosin to form hybrid filaments. Furthermore, antibody recognition studies demonstrated that myosins from chicken brain, skeletal muscle, and smooth muscle were unique.

Actins↗
PubMed2025

Transcriptome-wide analysis reveals sequence selection to avoid mRNA aggregation in E. coli.

The stability of RNA base pairing and its limited four-letter code create an intrinsic potential for promiscuous RNA-RNA interactions. In vitro, such interactions drive RNA to self-assemble into aggregates. This raises a fundamental unanswered question: within a confined cellular volume at physiological mRNA abundances, how much aggregation would arise from sequence-encoded chemistry alone? Here, we establish this baseline with large-scale kinetic simulations of the E. coli transcriptome. Our simulations reveal that sequence-encoded base-pairing energetics is sufficient to generate a dynamic network of large aggregates, organized by long, multivalent mRNA hubs. Strikingly, evolutionary analysis shows that native E. coli sequences exhibit clear signatures of selection to counteract this propensity: they fold more stably, minimize unstructured regions, and form weaker intermolecular contacts than dinucleotide-preserving controls. These findings demonstrate that maintaining transcriptome solubility has been a significant, previously unrecognized constraint shaping genome evolution, and provide a new lens to interpret cellular RNA management.

Biological Sciences (Biophysics and Computational ↗
PubMed1977

Purification of protected syntheic peptides by preparative high performance liquid chromatography on silica gel 60.

A simple preparative system is described for rapid and efficient purification of protected synthetic peptides on a gram scale by high performance liquid chromatography on prepacked silica gel 60 columns. A variety of protected peptides up to tetradecapeptides have been chromatographed at pressures of 50 to 150 psi and obtained in analytically pure from within 2 to 4 h. With such commonly used protecting groups as N-benzyloxycarbonyl (Z), N-2-(p-biphenylyl)-2-propyloxycarbonyl (Bpoc), N-t-butyloxycarbonyl (Boc), O- and S-t-butyl (But), and S-acetamidomethyl (Acm), compounds were sufficiently soluble in chloroform, alcohols, acetic acid, or mixtures of these solvents for column loading. Dimethylformamide was also used as a solvent for loading. Solvent systems for column elution in isocratic, stepwise, or gradient modes were composed of chloroform, isopropanol, ethanol, or methanol and acetic acid in ratios that differed for each protected peptide depending on Rf values on t.l.c. plates. A simple chromatography is described which was self-assembled using standard instruments commonly in use in most laboratories. A shut-off valve was designed to prevent loss of material between fractions.

Chromatography, Liquid↗
PubMed2025

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.

The Immunoglobulin fold (Ig-fold) is found in proteins from all domains of life and represents the most populous fold in the human genome, with current estimates ranging from 2 to 3% of protein coding regions. That proportion is much higher in the surfaceome where Ig and Ig-like domains orchestrate cell-cell recognition, adhesion and signaling. The ability of Ig-domains to reliably fold and self-assemble through highly specific interfaces represents a remarkable property of these domains, making them key elements of molecular interaction systems: the immune system, the nervous system, the vascular system and the muscular system. We define a universal residue numbering scheme, common to all domains sharing the Ig-fold in order to study the wide spectrum of Ig-domain variants constituting the Ig-proteome and Ig-Ig interactomes at the heart of these systems. The "IgStrand numbering scheme" enables the identification of Ig structural proteomes and interactomes in and between any species, and comparative structural, functional, and evolutionary analyses. We review how Ig-domains are classified today as topological and structural variants and highlight the "Ig-fold irreducible structural signature" shared by all of them. The IgStrand numbering scheme lays the foundation for the systematic annotation of structural proteomes by detecting and accurately labeling Ig-, Ig-like and Ig-extended domains in proteins, which are poorly annotated in current databases and opens the door to accurate machine learning. Importantly, it sheds light on the robust Ig protein folding algorithm used by nature to form beta sandwich supersecondary structures. The numbering scheme powers an algorithm implemented in the interactive structural analysis software iCn3D to systematically recognize Ig-domains, annotate them and perform detailed analyses comparing any domain sharing the Ig-fold in sequence, topology and structure, regardless of their diverse topologies or origin. The scheme provides a robust fold detection and labeling mechanism that reveals unsuspected structural homologies among protein structures beyond currently identified Ig- and Ig-like domain variants. Indeed, multiple folds classified independently contain a common structural signature, in particular jelly-rolls. Examples of folds that harbor an "Ig-extended" architecture are given. Applications in protein engineering around the Ig-architecture are straightforward based on the universal numbering.

Humans↗
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↗
PubMedDate not supplied

[Role of phospholipids in the generation of membrane potentials by proteoliposomes].

Closed protein-phospholipid particles (proteoliposomes), obtained by self-assembly method, are capable to generate and to maintain the membrane potential in the case if their protein complex is represented by: a) a complex of mitochondrial ATPase; b) a complex of cytochrome oxidase and cytochrome c and c) bacteriorhodopsin from Halobacterium halobium; and their phospholipid component is represented by phosphatidylethanolamine or by a mixture of mitochondrial phospholipids. Only cytochromoxidase and bacteriorhodopsin (but not ATPase) proteoliposomes with phosphatidylserine are active. Cardiolipin also is not active in experiments with ATPase. Phosphatidylcholine produces in all the cases proteoliposomes incapable of maintaining the membrane potential. It is concluded that the inefficiency of phosphatidylcholine in the formation of proteoliposomes, generating the membrane potential, is due to the impossibility of obtaining closed membrane forms with a high electric resistance. The inefficiency of phosphatidylserine and cardiolipine, in the case of ATPase protein component of proteoliposomes, may be due to a specific requirement of this generator of the membrane potential in phosphatidylethanolamine.

Adenosine Triphosphatases↗
PubMedDate not supplied

[Cooperative interaction of serum albumin with quaternized poly-4-vinyl pyridine and structure of the complexes].

Interaction of bovine serum albumin (BSA) with quaternized poly-4-vinyl pyridine (PE) in aqueous solutions at pH 7 was studied. It was shown that in a wide range of the ratios of the components (nBSA/nPE) soluble stable cooperative complexes were formed. At the same time a certain critical content of the protein exists at which the system loses its homogeneity. Complex formation is not accompanied by protein denaturation. At smaller nBSA/nPE ratios non-homogeneous distribution of protein globulas among polyelectrolite macromolecules was found; this corresponded to the "all or none" principle. Using ultracentrifugation technique viscosimetric measurements and electron microscopy it was shown that the soluble complexes exist in the form of rode-like particles consisting of protein globules stabilized by polycation chains. Such particle can be considered as a model of nucleoprotein complex. At certain crytical nBSA/nPE rations the rod-like particles aggregate with additional number of BSA-molecules and form more complicate soluble and insoluble cooperative complexes. Possible structural models of the complexes described were suggested and the thermodinamic and kinetic cryteria of their self-assembly were discussed.

Drug Stability↗