Supramolecular chiral self-assembly and supercoiling behavior of carrageenans at varying salt conditions

The self-assembly of anionic kappa and iota carrageenan polysaccharides in the presence of NaCl, KCl and CaCl2 is studied by high-resolution atomic force microscopy (AFM). A hierarchical supramolecular chirality amplification over various length scales is observed upon the addition of KCl, whereas in the presence of NaCl and CaCl2 the chains undergo solely a coil-helix transition with stiff kappa carrageenan and more flexible iota carrageenan helical conformations.

Fibrillar networks of glycyrrhizic acid for hybrid nanomaterials with catalytic features

Self-assembly of the naturally occurring sweetening agent, glycyrrhizic acid (GA) in water is studied by small-angle X-ray scattering and microscopic techniques. Statistical analysis on atomic force microscopy images reveals the formation of ultralong GA fibrils with uniform thickness of 2.5 nm and right-handed twist with a pitch of 9 nm, independently of GA concentration. Transparent nematic GA hydrogels are exploited to create functional hybrid materials. Two-fold and three-fold hybrids are developed by introducing graphene oxide (GO) and in situ-synthesized gold nanoparticles (Au NPs) in the hydrogel matrix for catalysis applications. In the presence of GO, the catalytic efficiency of Au NPs in the reduction of p-nitrophenol to p-aminophenol is enhanced by 2.5 times. Gold microplate single crystals are further synthesized in the GA hydrogel, expanding the scope of these hybrids and demonstrating their versatility in materials design.

Influence of the β-sheet content on the mechanical properties of aggregates during amyloid fibrillization

Amyloid fibrils associated with neurodegenerative diseases, such as Parkinson's and Alzheimer's, consist of insoluble aggregates of α-synuclein and Aβ-42 proteins with a high β-sheet content. The aggregation of both proteins occurs by misfolding of the monomers and proceeds through the formation of intermediate oligomeric and protofibrillar species to give the final fibrillar cross-β-sheet structure. The morphological and mechanical properties of oligomers, protofibrils, and fibrils formed during the fibrillization process were investigated by thioflavin T fluorescence and circular dichroism in combination with AFM peak force quantitative nanomechanical technique. The results reveal an increase in the Young's modulus during the transformation from oligomers to mature fibrils, thus inferring that the difference in their mechanical properties is due to an internal structural change from a random coil to a structure with increased β-sheet content.

Enzyme immobilization on silicate glass through simple adsorption of dendronized polymer–enzyme conjugates for localized enzymatic cascade reactions

Conjugation of enzymes to a dendronized polymer via bis-aryl hydrazone bonds enables simple and stable enzyme immobilisation on unmodified glass.

Universal behavior in the mesoscale properties of amyloid fibrils

Amyloid fibrils are ubiquitous proteinaceous aggregates occurring in vivo and in vitro, with an invariant structural fingerprint at the molecular length scale. However, interpretation of their mesoscopic architectures is complicated by diverse observable polymorphic states. We here present a constitutive model for amyloid fibrils based on the minimization of the total energy per fibril. The model is benchmarked on real amyloid fibrils studied by atomic force microscopy. We use multistranded β-lactoglobulin amyloid fibrils as a model system exhibiting a rich polymorphism. The constitutive model quantitatively recapitulates the main mesoscopic topological features of amyloid fibrils, that is, the evolution of fibril periodicity as a function of the ionic strength of the solution and of the fibril width. A universal mesoscopic structural signature of the fibrils emerges from this picture, predicting a general, parameter-free law for the periodicity of the fibrils, that depends solely on the number of protofilaments per fibril. These predictions are validated experimentally and conclusively highlight the role of competing electrostatic and elastic contributions as the main players in the establishment of amyloid fibrils structure.

Modulating materials by orthogonally oriented β-strands: composites of amyloid and silk fibroin fibrils

Amyloid fibrils and silk fibroin (SF) fibrils are proteinaceous aggregates occurring either naturally or as artificially reconstituted fibrous systems, in which the constituent β-strands are aligned either orthogonally or parallel to the fibril main axis, conferring complementary physical properties. Here, it is shown how the combination of these two classes of protein fibrils with orthogonally oriented β-strands results in composite materials with controllable physical properties at the molecular, mesoscopic, and continuum length scales.

Unravelling secondary structure changes on individual anionic polysaccharide chains by atomic force microscopy

The structural conformations of the anionic carrageenan polysaccharides in the presence of monovalent salt close to physiological conditions are studied by atomic force microscopy. Iota-carrageenan undergoes a coil-helix transition at high ionic strength, whereas lambda-carrageenan remains in the coiled state. Polymer statistical analysis reveals an increase in persistence length from 22.6±0.2 nm in the random coil, to 26.4±0.2 nm in the ordered helical conformation, indicating an increased rigidity of the helical iota-carrageenan chains. The many decades-long debated issue on whether the ordered state can exist as single or double helix, is conclusively resolved by demonstrating the existence of a unimeric helix formed intramolecularly by a single polymer chain.

Directed Growth of Silk Nanofibrils on Graphene and Their Hybrid Nanocomposites

Combination of proteins with other nanomaterials offers a promising strategy to fabricate novel hybrids with original functions in biology, medicine, nanotechnology, and materials science. Under carefully selected experimental conditions, we show that graphene nanosheets are able to direct one-dimensional self-assembly of silk fibroin, forming an unprecedented type of nanohybrids. These silk/graphene hybrids combine physical properties of both constituents and form functional composites with well-ordered hierarchical structures. Due to the facile fabrication process and their tunable nanostructures, the resultant hybrids show promise in applications as diverse as tissue engineering, drug delivery, nanoelectronics, nanomedicine, biosensors, and functional composites.

Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA

The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.

Polymorphism complexity and handedness inversion in serum albumin amyloid fibrils

Protein-based amyloid fibrils can show a great variety of polymorphic structures within the same protein precursor, although the origins of these structural homologues remain poorly understood. In this work we investigate the fibrillation of bovine serum albumin--a model globular protein--and we follow the polymorphic evolution by a statistical analysis of high-resolution atomic force microscopy images, complemented, at larger length scales, by concepts based on polymer physics formalism. We identify six distinct classes of coexisting amyloid fibrils, including flexible left-handed twisted ribbons, rigid right-handed helical ribbons and nanotubes. We show that the rigid fibrils originate from flexible fibrils through two diverse polymorphic transitions, first, via a single-fibril transformation when the flexible left-handed twisted ribbons turn into the helical left-handed ribbons, to finally evolve into nanotube-like structures, and second, via a double-fibril transformation when two flexible left-handed twisted ribbons wind together resulting in a right-handed twisted ribbon, followed by a rigid right-handed helical ribbon polymorphic conformation. Hence, the change in handedness occurs with an increase in the level of the fibril's structural organization.

Hierarchically structured microfibers of "single stack" perylene bisimide and quaterthiophene nanowires

Organic nanowires and microfibers are excellent model systems for charge transport in organic semiconductors under nanoscopic confinement and may be relevant for future nanoelectronic devices. For this purpose, however, the preparation of well-ordered organic nanowires with uniform lateral dimensions remains a challenge to achieve. Here, we used the self-assembly of oligopeptide-substituted perylene bisimides and quaterthiophenes to obtain well-ordered nanofibrils. The individual nanofibrils were investigated by spectroscopic and imaging methods, and the preparation of hierarchically structured microfibers of aligned nanofibrils allowed for a comprehensive structural characterization on all length scales with molecular level precision. Thus, we showed that the molecular chirality resulted in supramolecular helicity, which supposedly serves to suppress lateral aggregation. We also proved that, as a result, the individual nanofibrils comprised a single stack of the π-conjugated molecules at their core. Moreover, the conformational flexibility between the hydrogen-bonded oligopeptides and the π-π stacked chromophores gave rise to synergistically enhanced strong π-π interactions and hydrogen-bonding. The result is a remarkably tight π-π stacking inside the nanofibrils, irrespective of the electronic nature of the employed chromophores, which may render them suitable nanowire models to investigate one-dimensional charge transport along defined π-π stacks of p-type or n-type semiconductors.

Structure and enzymatic properties of molecular dendronized polymer-enzyme conjugates and their entrapment inside giant vesicles

Macromolecular hybrid structures were prepared in which two types of enzymes, horseradish peroxidase (HRP) and bovine erythrocytes Cu,Zn-superoxide dismutase (SOD), were linked to a fluorescently labeled, polycationic, dendronized polymer (denpol). Two homologous denpols of first and second generation were used and compared, and the activities of HRP and SOD of the conjugates were measured in aqueous solution separately and in combination. In the latter case the efficiency of the two enzymes in catalyzing a two-step cascade reaction was evaluated. Both enzymes in the two types of conjugates were highly active and comparable to free enzymes, although the efficiency of the enzymes bound to the second-generation denpol was significantly lower (up to a factor of 2) than the efficiency of HRP and SOD linked to the first-generation denpol. Both conjugates were analyzed by atomic force microscopy (AFM), confirming the expected increase in object size compared to free denpols and demonstrating the presence of enzyme molecules localized along the denpol chains. Finally, giant phospholipid vesicles with diameters of up to about 20 μm containing in their aqueous interior pool a first-generation denpol-HRP conjugate were prepared. The HRP of the entrapped conjugate was shown to remain active toward externally added, membrane-permeable substrates, an important prerequisite for the development of vesicular multienzyme reaction systems.

Magnetic-responsive hybrids of Fe3O4 nanoparticles with β-lactoglobulin amyloid fibrils and nanoclusters

We report on the synthesis and magnetic-responsive behavior of hybrids formed by dispersing negatively charged iron oxide (Fe3O4) magnetic nanoparticles in positively charged β-lactoglobulin protein solutions at acidic pH, followed by heating at high temperatures. Depending on the pH used, different hybrid aggregates can be obtained, such as nanoparticle-modified amyloid fibrils (pH 3) and spherical nanoclusters (pH 4.5). We investigate the effect of magnetic fields of varying strengths (0-5 T) on the alignment of these Fe3O4-modified amyloid fibrils and spherical nanoclusters using a combination of scattering, birefringence and microscopic techniques and we find a strong alignment of the hybrids upon increasing the intensity of the magnetic field, which we quantify via 2D and 3D order parameters. We also demonstrate the possibility of controlling magnetically the sol-gel behavior of these hybrids: addition of salt (NaCl, 150 mM) to a solution containing nanoparticles modified with β-lactoglobulin amyloid fibrils (2 wt % fibrils modified with 0.6 wt % Fe3O4 nanoparticles) induces first the formation of a reversible gel, which can then be converted back to solution upon application of a moderate magnetic field of 1.1 T. These hybrids offer a new appealing functional colloidal system in which the aggregation, orientational order and rheological behavior can be efficiently controlled in a purely noninvasive way by external magnetic fields of weak intensity.

Tunable carbon nanotube/protein core-shell nanoparticles with NIR- and enzymatic-responsive cytotoxicity

A unique procedure is developed to capture carbon nanotubes into closed virus-like protein cages with a controllable shell. The cross-linked shell varies in thickness within ≈10(0) -10(2) nm, and can be entirely removed by enzyme degradation. The cytotoxicity is entirely suppressed, but can be promoted again by enzymes and near-infrared light. These hybrids can be decorated with functional inorganic nanoparticles or processed into nanocomposites.

Nuclear Factor I genomic binding associates with chromatin boundaries

Background

The Nuclear Factor I (NFI) family of DNA binding proteins (also called CCAAT box transcription factors or CTF) is involved in both DNA replication and gene expression regulation. Using chromatin immuno-precipitation and high throughput sequencing (ChIP-Seq), we performed a genome-wide mapping of NFI DNA binding sites in primary mouse embryonic fibroblasts.

Results

We found that in vivo and in vitro NFI DNA binding specificities are indistinguishable, as in vivo ChIP-Seq NFI binding sites matched predictions based on previously established position weight matrix models of its in vitro binding specificity. Combining ChIP-Seq with mRNA profiling data, we found that NFI preferentially associates with highly expressed genes that it up-regulates, while binding sites were under-represented at expressed but unregulated genes. Genomic binding also correlated with markers of transcribed genes such as histone modifications H3K4me3 and H3K36me3, even outside of annotated transcribed loci, implying NFI in the control of the deposition of these modifications. Positional correlation between + and - strand ChIP-Seq tags revealed that, in contrast to other transcription factors, NFI associates with a nucleosomal length of cleavage-resistant DNA, suggesting an interaction with positioned nucleosomes. In addition, NFI binding prominently occurred at boundaries displaying discontinuities in histone modifications specific of expressed and silent chromatin, such as loci submitted to parental allele-specific imprinted expression.

Conclusions

Our data thus suggest that NFI nucleosomal interaction may contribute to the partitioning of distinct chromatin domains and to epigenetic gene expression regulation.

NFI ChIP-Seq and input control DNA data were deposited at Gene Expression Omnibus (GEO) repository under accession number GSE15844. Gene expression microarray data for mouse embryonic fibroblasts are on GEO accession number GSE15871.

FM-AFM constant height imaging and force curves: high resolution study of DNA-tip interactions

Interaction of the atomic force microscopy (AFM) tip with the sample can be invasive for soft samples. Frequency Modulation (FM) AFM is gentler because it allows scanning in the non-contact regime where only attractive forces exist between the tip and the sample, and there is no sample compression. Recently, FM-AFM was used to resolve the atomic structure of single molecules of pentacene and of carbon nanotubes. We are testing similar FM-AFM-based approaches to study biological samples. We present FM-AFM experiments on dsDNA deposited on 3-aminopropyltriethoxysilane modified mica in ultra high vacuum. With flexible samples such as DNA, the substrate flatness is a sub-molecular resolution limiting factor. Non-contact topographic images of DNA show variations that have the periodicity of the right handed helix of B-form DNA - this is an unexpected result as dehydrated DNA is thought to assume the A-form structure. Frequency shift maps at constant height allow working in the non-monotonic frequency shift range, show a rich contrast that changes significantly with the tip-sample separation, and show 0.2 to 0.4 nm size details on DNA. Frequency shift versus distance curves acquired on DNA molecules and converted in force curves show that for small molecules (height < 2.5 nm), there is a contribution to the interaction force from the substrate when the tip is on top of the molecules. Our data shine a new light on dehydrated and adsorbed DNA behavior. They show a longer tip-sample interaction distance. These experiments may have an impact on nanotechnological DNA applications in non-physiological environments such as DNA based nanoelectronics and nanotemplating.