DNA is Wrapped by the Nuclear Aggregates of Polyamines: The Imaging Evidence

Transduction of Amine-Phosphate Supramolecular Interactions and Biosensing of Acetylcholine through PEDOT-Polyamine Organic Electrochemical Transistors

Organic electrochemical transistors (OECTs) are important devices for the development of flexible and wearable sensors due to their flexibility, low power consumption, sensitivity, selectivity, ease of fabrication, and compatibility with other flexible materials. These features enable the creation of comfortable, versatile, and efficient portable devices that can monitor and detect a wide range of parameters for various applications. Herein, we present OECTs based on PEDOT-polyamine thin films for the selective monitoring of phosphate-containing compounds. Our findings reveal that supramolecular single phosphate-amino interaction induces higher changes in the OECT response compared to ATP-amino interactions, even at submillimolar concentrations. The steric character of binding anions plays a crucial role in OECT sensing, resulting in a smaller shift in maximum transconductance voltage and threshold voltage for bulkier binding species. The OECT response reflects not only the polymer/solution interface but also events within the conducting polymer film, where ion transport and concentration are affected by the ion size. Additionally, the investigation of enzyme immobilization reveals the influence of phosphate species on the assembly behavior of acetylcholinesterase (AchE) on PEDOT-PAH OECTs, with increasing phosphate concentrations leading to reduced enzyme anchoring. These findings contribute to the understanding of the mechanisms of OECT sensing and highlight the importance of careful design and optimization of the biosensor interface construction for diverse sensing applications.

Effectiveness of a novel gene nanotherapy based on putrescine for cancer treatment

Gene therapy has long been proposed for cancer treatment. However, the use of therapeutic nucleic acids presents several limitations such as enzymatic degradation, rapid clearance, and poor cellular uptake and efficiency. In this work we propose the use of putrescine, a precursor for higher polyamine biosynthesis for the preparation of cationic nanosystems for cancer gene therapy. We have formulated and characterized putrescine-sphingomyelin nanosystems (PSN) and studied their endocytic pathway and intracellular trafficking in cancer cells. After loading a plasmid DNA (pDNA) encoding the apoptotic Fas Ligand (FasL), we proved their therapeutic activity by measuring the cell death rate after treatment of MDA-MB-231 cells. We have also used xenografted zebrafish embryos as a first in vivo approach to demonstrate the efficacy of the proposed PSN-pDNA formulation in a more complex model. Finally, intratumoral and intraperitoneal administration to mice-bearing MDA-MB-231 xenografts resulted in a significant decrease in tumour cell growth, highlighting the potential of the developed gene therapy nanoformulation for the treatment of triple negative breast cancer.

Determination of urinary spermine using controlled dissolution of polysulfide modified gold electrode

Spermine (SPM) is considered a biomarker for prostate cancer and detecting it becomes highly challenging due to its electro- and optical-inactive nature. SPM has a tendency to interact with groups such as phosphates and sulfides to form macrocyclic arrangements known as nuclear aggregates of polyamines. Using this tendency, an electrochemical sensor has been developed using a polysulfide (PS) modified Au electrode (PS@Au electrode). PS has been synthesized from elemental sulfur by hydrothermal method and characterized using UV-Vis, fluorescence, FTIR, SEM, and XPS analyses. The PS@Au electrode was employed for electrochemical sensing of SPM. In the presence of SPM, a decrease in gold oxide reduction current was noted which is proportional to the concentration of SPM. The decrease in gold oxide reduction (0.5 V) current was attributed to the complexing nature of SPM-PS at the electrode interface. The reason for the decrease in current has been substantiated using XRF, XPS, and spectroelectrochemical studies. Under the optimized conditions, the PS@Au electrode exhibited a linear range of 1.55-250 µM with LOD of 0.511 ± 0.02 µM (3σ). The electrochemical strategy for SPM sensing exhibited better selectivity even in the presence of possible interferents. The selectivity stems from the selective interaction of SPM with PS on the Au electrode surface; the tested amino acids, and other molecules do not complex with PS and hence they could not interfere. The PS@Au electrode has been subjected to the determination of SPM in artificial urine samples and exhibited outstanding performance in the synthetic sample.

The Effect of Amino-Phosphate Interactions on the Biosensing Performance of Enzymatic Graphene Field-Effect Transistors

The interaction between polyamines and phosphate species is found in a wide range of biological and abiotic systems, yielding crucial consequences that range from the formation of supramolecular colloids to structure determination. In this work, the occurrence of phosphate-amino interactions is evidenced from changes in the electronic response of graphene field effect transistors (gFETs). First, the surface of the transistors is modified with poly(allylamine), and the effect of phosphate binding on the transfer characteristics is interpreted in terms of its impact on the surface charge density. The electronic response of the polyamine-functionalized gFETs is shown to be sensitive to the presence of different phosphate anions, such as orthophosphate, adenosine triphosphate, and tripolyphosphate, and a simple binding model is developed to explain the dependence of the shift of the Dirac point potential on the phosphate species concentration. Afterward, the impact of phosphate-amino interactions on the immobilization of enzymes to polyamine-modified graphene surfaces is investigated, and a decrease in the amount of anchored enzyme as the phosphate concentration increases is found. Finally, multilayer polyamine-urease biosensors are fabricated while increasing the phosphate concentration in the enzyme solution, and the sensing properties of the gFETs toward urea are evaluated. It is found that the presence of simple phosphate anions alters the nanoarchitecture of the polyelectrolyte-urease assemblies, with direct implications on urea sensing.

Formation and Repair of an Interstrand DNA Cross-Link Arising from a Common Endogenous Lesion

Interstrand DNA cross-links (ICLs) are cytotoxic because they block the strand separation required for read-out and replication of the genetic information in duplex DNA. The unavoidable formation of ICLs in cellular DNA may contribute to aging, neurodegeneration, and cancer. Here, we describe the formation and properties of a structurally complex ICL derived from an apurinic/apyrimidinic (AP) site, which is one of the most common endogenous lesions in cellular DNA. The results characterize a cross-link arising from aza-Michael addition of the N²-amino group of a guanine residue to the electrophilic sugar remnant generated by spermine-mediated strand cleavage at an AP site in duplex DNA. An α,β-unsaturated iminium ion is the critical intermediate involved in ICL formation. Studies employing the bacteriophage φ29 polymerase provided evidence that this ICL can block critical DNA transactions that require strand separation. The results of biochemical studies suggest that this complex strand break/ICL might be repaired by a simple mechanism in which the 3'-exonuclease action of the enzyme apurinic/apyrimidinic endonuclease (APE1) unhooks the cross-link to initiate repair via the single-strand break repair pathway.

Ablation of polyamine catabolic enzymes provokes Purkinje cell damage, neuroinflammation, and severe ataxia

BACKGROUND

Polyamine catabolism plays a key role in maintaining intracellular polyamine pools, yet its physiological significance is largely unexplored. Here, we report that the disruption of polyamine catabolism leads to severe cerebellar damage and ataxia, demonstrating the fundamental role of polyamine catabolism in the maintenance of cerebellar function and integrity.

METHODS

Mice with simultaneous deletion of the two principal polyamine catabolic enzymes, spermine oxidase and spermidine/spermine N1-acetyltransferase (Smox/Sat1-dKO), were generated by the crossbreeding of Smox-KO (Smox-/-) and Sat1-KO (Sat1-/-) animals. Development and progression of tissue injury was monitored using imaging, behavioral, and molecular analyses.

RESULTS

Smox/Sat1-dKO mice are normal at birth, but develop progressive cerebellar damage and ataxia. The cerebellar injury in Smox/Sat1-dKO mice is associated with Purkinje cell loss and gliosis, leading to neuroinflammation and white matter demyelination during the latter stages of the injury. The onset of tissue damage in Smox/Sat1-dKO mice is not solely dependent on changes in polyamine levels as cerebellar injury was highly selective. RNA-seq analysis and confirmatory studies revealed clear decreases in the expression of Purkinje cell-associated proteins and significant increases in the expression of transglutaminases and markers of neurodegenerative microgliosis and astrocytosis. Further, the α-Synuclein expression, aggregation, and polyamination levels were significantly increased in the cerebellum of Smox/Sat1-dKO mice. Finally, there were clear roles of transglutaminase-2 (TGM2) in the cerebellar pathologies manifest in Smox/Sat1-dKO mice, as pharmacological inhibition of transglutaminases reduced the severity of ataxia and cerebellar injury in Smox/Sat1-dKO mice.

CONCLUSIONS

These results indicate that the disruption of polyamine catabolism, via coordinated alterations in tissue polyamine levels, elevated transglutaminase activity and increased expression, polyamination, and aggregation of α-Synuclein, leads to severe cerebellar damage and ataxia. These studies indicate that polyamine catabolism is necessary to Purkinje cell survival, and for sustaining the functional integrity of the cerebellum.

Continuous assembly of supramolecular polyamine-phosphate networks on surfaces: preparation and permeability properties of nanofilms

Supramolecular self-assembly of molecular building blocks represents a powerful "nanoarchitectonic" tool to create new functional materials with molecular-level feature control. Here, we propose a simple method to create tunable phosphate/polyamine-based films on surfaces by successive assembly of poly(allylamine hydrochloride) (PAH)/phosphate anions (Pi) supramolecular networks. The growth of the films showed a great linearity and regularity with the number of steps. The coating thickness can be easily modulated by the bulk concentration of PAH and the deposition cycles. The PAH/Pi networks showed chemical stability between pH 4 and 10. The transport properties of the surface assemblies formed from different deposition cycles were evaluated electrochemically by using different redox probes in aqueous solution. The results revealed that either highly permeable films or efficient anion transport selectivity can be created by simply varying the concentration of PAH. This experimental evidence indicates that this new strategy of supramolecular self-assembly can be useful for the rational construction of single polyelectrolyte nanoarchitectures with multiple functionalities.

Native DNA electronics: is it a matter of nanoscale assembly?

The genomic DNA is enveloped by nanotubes formed by the nuclear aggregates of polyamines (NAPs) that induce DNA conformational changes and provide protection and increased interaction abilities for the double strands. In a physiological environment, the nanotube arrangement is initiated by spontaneous interaction among the terminal amino groups of the polyamines and the phosphate ions, with the consequent formation of cyclic monomers that hook at the DNA grooves. The polymer thus formed has the morphological features of an organic semiconductor and therefore, it can be considered to be able to conduct electric charges. Phosphate ions positioned on the NAP external surface could regulate, as in a physical electric circuit, both linear and rotational (histones) protein motion, in accordance with the basilar principles of the electronics. A model of a carrier system for protein motion along the polymer wrapping the DNA strands, based on the phosphate-phosphate complexation, is proposed.

DNA-surfactant complexes: self-assembly properties and applications

Over the last few years, DNA-surfactant complexes have gained traction as unique and powerful materials for potential applications ranging from optoelectronics to biomedicine because they self-assemble with outstanding flexibility spanning packing modes from ordered lamellar, hexagonal and cubic structures to disordered isotropic phases. These materials consist of a DNA backbone from which the surfactants protrude as non-covalently bound side chains. Their formation is electrostatically driven and they form bulk films, lyotropic as well as thermotropic liquid crystals and hydrogels. This structural versatility and their easy-to-tune properties render them ideal candidates for assembly in bulk films, for example granting directional conductivity along the DNA backbone, for dye dispersion minimizing fluorescence quenching allowing applications in lasing and nonlinear optics or as electron blocking and hole transporting layers, such as in LEDs or photovoltaic cells, owing to their extraordinary dielectric properties. However, they do not only act as host materials but also function as a chromophore itself. They can be employed within electrochromic DNA-surfactant liquid crystal displays exhibiting remarkable absorptivity in the visible range whose volatility can be controlled by the external temperature. Concomitantly, applications in the biological field based on DNA-surfactant bulk films, liquid crystals and hydrogels are rendered possible by their excellent gene and drug delivery capabilities. Beyond the mere exploitation of their material properties, DNA-surfactant complexes proved outstandingly useful for synthetic chemistry purposes when employed as scaffolds for DNA-templated reactions, nucleic acid modifications or polymerizations. These promising examples are by far not exhaustive but foreshadow their potential applications in yet unexplored fields. Here, we will give an insight into the peculiarities and perspectives of each material and are confident to inspire future developments and applications employing this emerging substance class.

A Review of Autoimmune Disease Hypotheses with Introduction of the "Nucleolus" Hypothesis

Numerous hypotheses have been proposed in order to explain the complexity of autoimmune diseases. These hypotheses provide frameworks towards understanding the relations between triggers, autoantigen development, symptoms, and demographics. However, testing and refining these hypotheses are difficult tasks since autoimmune diseases have a potentially overwhelming number of variables due to the influence on autoimmune diseases from environmental factors, genetics, and epigenetics. Typically, the hypotheses are narrow in scope, for example, explaining the diseases in terms of genetics without defining detailed roles for environmental factors or epigenetics. Here, we present a brief review of the major hypotheses of autoimmune diseases including a new one related to the consequences of abnormal nucleolar interactions with chromatin, the "nucleolus" hypothesis which was originally termed the "inactive X chromosome and nucleolus nexus" hypothesis. Indeed, the dynamic nucleolus can expand as part of a cellular stress response and potentially engulf portions of chromatin, leading to disruption of the chromatin. The inactive X chromosome (a.k.a. the Barr body) is particularly vulnerable due to its close proximity to the nucleolus. In addition, the polyamines, present at high levels in the nucleolus, are also suspected of contributing to the development of autoantigens.

DNA-HMGB1 interaction: The nuclear aggregates of polyamine mediation

Nuclear aggregates of polyamines (NAPs) are supramolecular compounds generated by the self-assembly of protonated nuclear polyamines (spermine, spermidine and putrescine) and phosphate ions. In the presence of genomic DNA, the hierarchical process of self-structuring ultimately produces nanotube-like polymers that envelop the double helix. Because of their modular nature and their aggregation-disaggregation dynamics, NAPs confer plasticity and flexibility to DNA. Through the disposition of charges, NAPs also enable a bidirectional stream of information between the genome and interacting moieties. High mobility group (HMG) B1 is a non-histone chromosomal protein that binds to DNA and that influences multiple nuclear processes. Because genomic DNA binds to either NAPs or HMGB1 protein, we explored the ability of in vitro self-assembled NAPs (ivNAPs) to mediate the DNA-HMGB1 interaction. To this end, we structured DNA-NAPs-HMGB1 and DNA-HMGB1-NAPs ternary complexes in vitro through opportune sequential incubations. Mobility shift electrophoresis and atomic force microscopy showed that the DNA-ivNAPs-HGMB1 complex had conformational assets supposedly more suitable those of the DNA-HGMB1-ivNAPs to comply with the physiological and functional requirements of DNA. Our findings indicated that ivNAPs act as mediators of the DNA-HMGB1 interaction.

Multi-tunable self-assembled morphologies of stimuli-responsive diblock polyampholyte films on solid substrates

Intelligent polymers, due to their sensitive stimuli response to changes in the environment, have gained increasing amounts of attention over recent years and have become a popular topic in polymer materials science. In this study, the aggregation behaviors and stimuli responses of the stimuli-responsive diblock polyampholyte poly(2-(dimethylamino)ethyl methacrylate)-b-poly(acrylic acid) (PDMAEMA-b-PAA) are conveniently tunable by introducing pH changes, temperature changes, salt addition and surfactant neutralization. Under different pH values, either globular or fractal self-assemblies can be observed in which the latter have crystal properties. Salts and alkalis can promote the fractal aggregation growth because their deposited crystals can act as nucleation sites for the polyampholyte chains. A combination of fluorescence spectroscopy, atom force microscopy and transmission electron microscopy revealed that the presence of anionic surfactants in the PDMAEMA-b-PAA solutions promoted the solubility of the polyampholyte, consequently leading to a more homogeneous distribution of the polymer chains on the solid substrate upon drying the mixtures. The fractal formation was suppressed for the studied Gemini surfactants, and a higher surfactant hydrophobicity results in an earlier start of the formation of the fractal pattern.

Mass spectrometric analysis of in vitro nuclear aggregates of polyamines

RATIONALE

In the nuclei of eukaryotic cells, polyamines and phosphate ions self-assemble via ionic interactions and hydrogen bonding, generating three families of supramolecular compounds that have been named large (l-), medium (m-) and small (s-) nuclear aggregates of polyamines (NAPs). In a simulated nuclear environment, polyamines and phosphate ions generate the in vitro NAPs (ivNAPs) that share strict structural and functional analogies with their cellular cognates. Mass spectrometric data are expected to provide important structural details of NAPs/ivNAPs.

METHODS

We used both electrospray ionization (ESI) and nitrocellulose (NC) matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to support a variety of analytical techniques previously addressed to structurally characterize NAPs/ivNAPs.

RESULTS

The dominant m/z values of s-ivNAP (m/z 735, 749, 761) are compatible with a defined set of cyclic or linear aggregates. On the basis of the experimental molecular mass (a cluster centred at m/z 2980), the m-ivNAP corresponds to the supramolecular assembly of four modules of s-ivNAPs. No informative mass spectra were obtained for the l-ivNAP.

CONCLUSIONS

MS data support the models of NAPs that have been inferred by using an array of analytical techniques. NC MALDI-MS contributed much more effectively than ESI-MS to the structural characterization of ivNAPs.

Nuclear aggregates of polyamines in a radiation-induced DNA damage model

Polyamines (PA) are believed to protect DNA minimizing the effect of radiation damage either by inducing DNA compaction and aggregation or acting as scavengers of free radicals. Using an in vitro pDNA double strand breakage assay based on gel electrophoretic mobility, we compared the protective capability of PA against γ-radiation with that of compounds generated by the supramolecular self-assembly of nuclear polyamines and phosphates, named Nuclear Aggregates of Polyamines (NAPs). Both unassembled PA and in vitro produced NAPs (ivNAPs) were ineffective in conferring pDNA protection at the sub-mM concentration. Single PA showed an appreciable protective effect only at high (mM) concentrations. However, concentrations of spermine (4+) within a critical range (0.481 mM) induced pDNA precipitation, an event that was not observed with NAPs-pDNA interaction. We conclude that the interaction of individual PA is ineffective to assure DNA protection, simultaneously preserving the flexibility and charge density of the double strand. Furthermore, data obtained by testing polyamine and ivNAPS with the current radiation-induced DNA damage model support the concept that PA-phosphate aggregates are the only forms through which PA interact with DNA.

Increased polyamines alter chromatin and stabilize autoantigens in autoimmune diseases

Polyamines are small cations with unique combinations of charge and length that give them many putative interactions in cells. Polyamines are essential since they are involved in replication, transcription, translation, and stabilization of macro-molecular complexes. However, polyamine synthesis competes with cellular methylation for S-adenosylmethionine, the methyl donor. Also, polyamine degradation can generate reactive molecules like acrolein. Therefore, polyamine levels are tightly controlled. This control may be compromised in autoimmune diseases since elevated polyamine levels are seen in autoimmune diseases. Here a hypothesis is presented explaining how polyamines can stabilize autoantigens. In addition, the hypothesis explains how polyamines can inappropriately activate enzymes involved in NETosis, a process in which chromatin is modified and extruded from cells as extracellular traps that bind pathogens during an immune response. This polyamine-induced enzymatic activity can lead to an increase in NETosis resulting in release of autoantigenic material and tissue damage.

DNA and nuclear aggregates of polyamines

Polyamines (PAs) are linear polycations that are involved in many biological functions. Putrescine, spermidine and spermine are highly represented in the nucleus of eukaryotic cells and have been the subject of decades of extensive research. Nevertheless, their capability to modulate the structure and functions of DNA has not been fully elucidated. We found that polyamines self-assemble with phosphate ions in the cell nucleus and generate three forms of compounds referred to as Nuclear Aggregates of Polyamines (NAPs), which interact with genomic DNA. In an in vitro setting that mimics the nuclear environment, the assembly of PAs occurs within well-defined ratios, independent of the presence of the DNA template. Strict structural and functional analogies exist between the in vitro NAPs (ivNAPs) and their cellular homologues. Atomic force microscopy showed that ivNAPs, as theoretically predicted, have a cyclic structure, and in the presence of DNA, they form a tube-like arrangement around the double helix. Features of the interaction between ivNAPs and genomic DNA provide evidence for the decisive role of "natural" NAPs in regulating important aspects of DNA physiology, such as conformation, protection and packaging, thus suggesting a new vision of the functions that PAs accomplish in the cell nucleus.

Synthesis, rapid responsive thickening, and self-assembly of brush copolymer poly(ethylene oxide)-graft-poly(N,N-dimethylaminoethyl methacrylate) in aqueous solutions

Double hydrophilic brush copolymer poly(ethylene oxide)-graft-poly(N,N-dimethylaminoethyl methacrylate) (PEO-g-PDMAEMA) was successfully prepared via atom transfer radical polymerization (ATRP). We investigated the pH/thermoresponsive behaviors of PEO-g-PDMAEMA brush-shaped copolymer concentrated aqueous solutions by rheology. The observed LCST strongly decreased with increasing pH of the solutions, which was lower than that of linear block copolymer for different pH, indicating rapid thermoresponsiveness of the brush PDMAEMA chains. An unexpected shear thickening behavior was observed and could be tuned by the pH, resulting from the mobile nature and tractive force of the densely grafted hydrophobic chains of PDMAEMA at high pH. Self-assembly of the brush copolymer in a different pH and ionic strength environment was studied by transmission electron microscopy. A wormlike cylinder structure was formed at low pH. Fractals were observed for the brush copolymer aqueous solution in the presence of NaCl. The results showed that by adjusting the pH and NaCl concentration of the dispersions fractal aggregates with different topology were obtained. The observations reported here can supply a better understanding of the molecular self-assembling nature and be used to develop responsive materials with better performance.