DNA damage by low-energy ions

Ion-beam irradiation provides a promising treatment for some types of cancer. This promise is due mainly to the selective deposition of energy into a relatively small volume (the Bragg peak), thus reducing damage to healthy tissue. Recent observations that electrons with energies below the ionization potential of DNA can cause covalent damage to the bases and backbone have led to investigations into the ability of low-energy (

Misonidazole binding in murine liver tissue: a marker for cellular hypoxia in vivo

The hepatic microcirculation is believed to cause variable cellular oxygenation within the organ. In this study a marker of cellular hypoxia was used to demonstrate liver oxygen tension gradients in vivo. Covalent binding of misonidazole adducts to cellular macromolecules is enhanced by hypoxia. Autoradiographs of liver from mice treated with radiolabeled misonidazole demonstrated enhanced binding of adducts within hepatocytes surrounding hepatic veins. Livers from both hypoxic and normal mice had characteristic autoradiographic grain patterns reflecting regional oxygen tension variation in vivo. Differential binding of misonidazole adducts formed in hypoxic cells could have an application in studies of liver physiology and biochemistry.

Characterisation of the active/de-active transition of mitochondrial complex I

Oxidation of NADH in the mitochondrial matrix of aerobic cells is catalysed by mitochondrial complex I. The regulation of this mitochondrial enzyme is not completely understood. An interesting characteristic of complex I from some organisms is the ability to adopt two distinct states: the so-called catalytically active (A) and the de-active, dormant state (D). The A-form in situ can undergo de-activation when the activity of the respiratory chain is limited (i.e. in the absence of oxygen). The mechanisms and driving force behind the A/D transition of the enzyme are currently unknown, but several subunits are most likely involved in the conformational rearrangements: the accessory subunit 39 kDa (NDUFA9) and the mitochondrially encoded subunits, ND3 and ND1. These three subunits are located in the region of the quinone binding site. The A/D transition could represent an intrinsic mechanism which provides a fast response of the mitochondrial respiratory chain to oxygen deprivation. The physiological role of the accumulation of the D-form in anoxia is most probably to protect mitochondria from ROS generation due to the rapid burst of respiration following reoxygenation. The de-activation rate varies in different tissues and can be modulated by the temperature, the presence of free fatty acids and divalent cations, the NAD/NADH ratio in the matrix, the presence of nitric oxide and oxygen availability. Cysteine-39 of the ND3 subunit, exposed in the D-form, is susceptible to covalent modification by nitrosothiols, ROS and RNS. The D-form in situ could react with natural effectors in mitochondria or with pharmacological agents. Therefore the modulation of the re-activation rate of complex I could be a way to ameliorate the ischaemia/reperfusion damage. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference. Guest Editors: Manuela Pereira and Miguel Teixeira.

Enantioselective Assembly of a Ruthenium(II) Polypyridyl Complex into a Double Helix

Evolution can increase the complexity of matter by self-organization into helical architectures, the best example being the DNA double helix. One common aspect, apparently shared by most of these architectures, is the presence of covalent bonds within the helix backbone. Here, we report the unprecedented crystal structures of a metal complex that self-organizes into a continuous double helical structure, assembled by non-covalent building blocks. Built up solely by weak stacking interactions, this alternating tread stairs-like double helical assembly mimics the DNA double helix structure. Starting from a racemic mixture in aqueous solution, the ruthenium(II) polypyridyl complex forms two polymorphic structures of a left-handed double helical assembly of only the Λ-enantiomer. The stacking of the helices is different in both polymorphs: a crossed woodpile structure versus a parallel columnar stacking.

Graphene Nanoribbons as a Drug Delivery Agent for Lucanthone Mediated Therapy of Glioblastoma Multiforme

We report use of PEG-DSPE coated oxidized graphene nanoribbons (O-GNR-PEG-DSPE) as agent for delivery of anti-tumor drug Lucanthone (Luc) into Glioblastoma Multiformae (GBM) cells targeting base excision repair enzyme APE-1 (Apurinic endonuclease-1). Lucanthone, an endonuclease inhibitor of APE-1, was loaded onto O-GNR-PEG-DSPEs using a simple non-covalent method. We found its uptake by GBM cell line U251 exceeding 67% and 60% in APE-1-overexpressing U251, post 24 h. However, their uptake was ~ 38% and 29% by MCF-7 and rat glial progenitor cells (CG-4), respectively. TEM analysis of U251 showed large aggregates of O-GNR-PEG-DSPE in vesicles. Luc-O-GNR-PEG-DSPE was significantly toxic to U251 but showed little/no toxicity when exposed to MCF-7/CG-4 cells. This differential uptake effect can be exploited to use O-GNR-PEG-DSPEs as a vehicle for Luc delivery to GBM, while reducing nonspecific cytotoxicity to the surrounding healthy tissue. Cell death in U251 was necrotic, probably due to oxidative degradation of APE-1.

Graphical abstract

We used O-GNR-PEG-DSPE as a reliable, non-toxic vehicle for delivery of APE-1 inhibiting Lucanthone into GBM tumor cell lines. LUC-O-GNR-PEG-DSPE particles showed 60% or more uptake by CMV/U251 and A1-5/CMV/U251 where as the uptake by MCF7 and normal CG4 glial cells was much lower (38% and 29% respectively). Different concentrations of Luc (5–80 μM) loaded onto O-GNR-PEG-DSPE showed lower toxicity in the exposed cells compared to the free drug, due to possible slow release of the drug from this particle, which ensures minimum non-specific release of the drug from the particle once it is injected in vivo.
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Chaotropic and hydrophobic stress mechanisms of antifungal substances

Growth and metabolism of fungi can be curtailed by chaotropic solutes and hydrophobic substances, both of which can weaken or inhibit non-covalent interactions within and between macromolecular systems. Here we explore the potential to utilize the fungistatic and fungicidal activities of such stressors as the basis for commercial formulations. A method was developed for the quantification of chaotropicity, which can be used for chemically diverse substances, in order elucidate roles of chaotropicity and hydrophobicity in microbial ecology (both of which are sufficiently potent to limit the Earth’s microbial biosphere). A large number of naturally occurring substances act as chaotropic or hydrophobic stressors including aliphatic alcohols, salts such as MgCl2, aromatics such as phenol, and hydrocarbons such as hexane and octene. We suggest that these stress parameters provide the (hitherto unidentified) modes-of-action for some extant antifungal products. The findings are discussed in relation to the development of a new generation of antifungals.

Self-assembly using dendritic building blocks - towards controllable nanomaterials

Dendritic molecules have well defined, three-dimensional branched architectures, and constitute a unique nanoscale toolkit. This review focuses on examples in which individual dendritic molecules are assembled into more complex arrays via non-covalent interactions. In particular, it illustrates how the structural information programmed into the dendritic architecture controls the assembly process, and as a consequence, the properties of the supramolecular structures which are generated. Furthermore, the review emphasises how the use of non-covalent (supramolecular) interactions, provides the assembly process with reversibility, and hence a high degree of control. The review also illustrates how self-assembly offers an ideal approach for amplifying the branching of small, synthetically accessible, relatively inexpensive dendritic systems (e.g. dendrons), into highly branched complex nanoscale assemblies.

The review begins by considering the assembly of dendritic molecules to generate discrete, well-defined supramolecular assemblies. The variety of possible assembled structures is illustrated, and the ability of an assembled structure to encapsulate a templating unit is described. The ability of both organic and inorganic building blocks to direct the assembly process is discussed. The review then describes larger discrete assemblies of dendritic molecules, which do not exist as a single well-defined species, but instead exist as statistical distributions. For example, assembly around nanoparticles, the assembly of amphiphilic dendrons and the assembly of dendritic systems in the presence of DNA will all be discussed. Finally, the review examines dendritic molecules, which assemble or order themselves into extended arrays. Such systems extend beyond the nanoscale into the microscale or even the macroscale domain, exhibiting a wide range of different architectures. The ability of these assemblies to act as gel-phase or liquid crystalline materials will be considered.

Taken as a whole, this review emphasises the control and tunability that underpins the assembly of nanomaterials using dendritic building blocks, and furthermore highlights the potential future applications of these assemblies at the interfaces between chemistry, biology and materials science. 

Modeling study of woody biomass:Interactions of cellulose, hemicellulose, and lignin

Lignocellulosic biomass pretreatment and the subsequent thermal conversion processes to produce solid, liquid, and gas biofuels are attractive solutions for today's energy challenges. The structural study of the main components in biomass and their macromolecular complexes is an active and ongoing research topic worldwide. The interactions among the three main components, cellulose, hemicellulose, and lignin, are studied in this paper using electronic structure methods, and the study includes examining the hydrogen bond network of cellulose-hemicellulose systems and the covalent bond linkages of hemicellulose-lignin systems. Several methods (semiempirical, Hartree-Fock, and density functional theory) using different basis sets were evaluated. It was shown that theoretical calculations can be used to simulate small model structures representing wood components. By comparing calculation results with experimental data, it was concluded that B3LYP/6-31G is the most suitable basis set to describe the hydrogen bond system and B3LYP/6-31G(d,p) is the most suitable basis set to describe the covalent system of woody biomass. The choice of unit model has a much larger effect on hydrogen bonding within cellulose-hemicellulose system, whereas the model choice has a minimal effect on the covalent linkage in the hemicellulose-lignin system. © 2011 American Chemical Society.

Oligo switches: photoresponsive oligonucleotide conjugates by solid-supported click chemistry

Photoresponsive oligonucleotides (ONs) incorporating isoxazole-linked azobenzene (AB) moieties were prepared by resin-supported nitrile oxide-alkyne cycloaddition (NOAC) chemistry. The thermal and photochromic properties of the modified ONs were significantly influenced by the extent of pi-conjugation between the isoxazole and the AB modules.

FRENKEL-KONTOROVA DOMAIN-WALL PHASE-TRANSITIONS IN AN ADSORBED LAYER - POTASSIUM ON CO(10(1)OVER-BAR-0)

As the potassium fractional coverage of a cobalt {1010BAR} surface is increased over the range 0.2 to 0.6 monolayer the adlayer passes through a series of phase transitions. A commensurate phase is formed at exactly 0.5 monolayer, and corresponds to adatoms bonded in high-symmetry hollow sites on the unreconstructed cobalt surface, with an effective adatom radius lying between the ionic and covalent radii of potassium. A detailed structural study shows that the structural transitions can be characterised within a one-dimensional Frenkel-Kontorova model, with small lateral displacements of adatoms away from hollow sites in the low and high coverage phases. The low coverage phases progress from a distributed vacancy structure to a low density domain-wall structure; while the high coverage phase formed above half a monolayer is a high density asymmetric domain-wall structure.

THE SURFACE-STRUCTURE OF A C(2 X-2) POTASSIUM OVERLAYER ON CO(1010)

The surface structure of the clean Co{1010BAR} surface and a c(2 x 2) potassium overlayer have been determined by quantitative low energy electron diffraction. The Co{1010BAR} sample has been shown to be laterally unreconstructed with the surface being uniquely terminated by an outermost closely packed double layer (dz12 = 0.68 angstrom). A damped oscillatory relaxation of the outermost three atomic layers occurs, with relaxations DELTA-dz12 = -6.5 +/- 2% and DELTA-dz23 = +1.0 +/- 2%.

The c(2 x 2) overlayer formed at a coverage of 0.5 ML was subjected to a full I-V analysis. A range of adsorption sites were tested including fourfold hollow, on-top, and both long and short bridge sites in combination with both "long" and "short" cobalt interlayer terminations. A clear preference was found for adsorption in the maximal coordination fourfold hollow site. No switching of surface termination occurs. The potassium adatoms reside in the [1210BAR] surface channels directly above second layer cobalt atoms with a potassium to outermost cobalt interlayer separation of 2.44 +/- 0.05 angstrom. Potassium-cobalt bond lengths of 3.40 +/- 0.05 and 3.12 +/- 0.05 angstrom between the four (one) outermost (second) layer nearest-neighbour substrate atoms suggests a potassium effective radius of 1.87 +/- 0.05 angstrom, somewhat smaller than the Pauling covalent radius and considerably larger than the ionic radius (1.38 angstrom). The alkali-surface bonding is thus predominantly "covalent"/"metallic".

Direct oxidation of amines to nitriles in the presence of ruthenium-terpyridyl complex immobilized on ILs/SILP

The immobilization of a ruthenium complex (Ru2Cl4(az-tpy)2) within a range of supported ionic liquids ([C4C1im]Cl, [C4C1im][NTf2], [C6C1im]Cl, [C4C1pyrr]Br, [C4C1im]Br, [C4C1pyrr]Cl) dispersed silica (SILP) operates as an efficient heterogeneous catalyst in oxidation of long chain linear primary amines to corresponding nitriles. This reaction follows a “green” route using a cheap and easy to handles oxidant (oxygen or air). The conversion was found to be strongly influenced by the alkyl chain length of the amine substrate and the choice of oxidant. No condensation reaction was observed between the starting amines and the selectivity to nitrile is 100%. Moving from a composition of 20 atm N2/5 atm O2 to 5 atm N2/20 atm O2 led to enhancements in the conversion (n-alkylamines) and selectivity (benzonitrile) which have been correlated with an increase of the solubilized oxygen. This was further supported by using different inert gas (nitrogen, helium, argon)/oxygen mixtures indicating that the O2 solubility in the SILP system, has an important effect on conversions and TON in this reaction using SILP catalysts. Experiments performed in the presence of CO2 led to a different behaviour due to the formation of amine-CO2 adducts. The application of the Weisz–Prater criterion confirmed the absence of any diffusional constraints.

Bacteria microarrays as sensitive tools for exploring pathogen surface epitopes and recognition by host receptors

We describe a protocol for the generation and validation of bacteria microarrays and their application to the study of specific features of the pathogen's surface and interactions with host receptors. Bacteria were directly printed on nitrocellulose-coated glass slides, using either manual or robotic arrayers, and printing quality, immobilization efficiency and stability of the arrays were rigorously controlled by incorporating a fluorescent dye into the bacteria. A panel of wild type and mutant strains of the human pathogen Klebsiella pneumoniae, responsible for nosocomial and community-acquired infections, was selected as model bacteria, and SYTO-13 was used as dye. Fluorescence signals of the printed bacteria were found to exhibit a linear concentration-dependence in the range of 1 x 10(8) to 1 x 10(9) bacteria per ml. Similar results were obtained with Pseudomonas aeruginosa and Acinetobacter baumannii, two other human pathogens. Successful validation of the quality and applicability of the established microarrays was accomplished by testing the capacity of the bacteria array to detect recognition by anti-Klebsiella antibodies and by the complement subcomponent C1q, which binds K. pneumoniae in an antibody-independent manner. The biotin/AlexaFluor-647-streptavidin system was used for monitoring binding, yielding strain-and dose-dependent signals, distinctive for each protein. Furthermore, the potential of the bacteria microarray for investigating specific features, e.g. glycosylation patterns, of the cell surface was confirmed by examining the binding behaviour of a panel of plant lectins with diverse carbohydrate-binding specificities. This and other possible applications of the newly developed arrays, as e.g. screening/evaluation of compounds to identify inhibitors of host-pathogen interactions, make bacteria microarrays a useful and sensitive tool for both basic and applied research in microbiology, biomedicine and biotechnology.

Regenerated cellulose matrix-encapsulated active substances and method therefor.

The process involves encapsulation or immobilization of the active solid substance in a cellulose framework by regenerating cellulose dissolved in an ionic liq. solvent in a regenerating soln. The active substance can be initially present in the ionic liq. or in the regenerating solvent either as a soln. or dispersion. The invention is applicable to mol. encapsulation and to entrapping of larger particles including enzymes, nanoparticles and macroscopic components, and to the formation of bulk materials with a wide range of morphol. forms. Thus, carbamoylmethylphosphine oxide (I) encapsulated in a cellulose matrix was realized by adding I to a 10% soln. of cellulose in 1-butyl-3-methylimidazolium chloride (ionic liq.) under vigorous stirring and then removing the ionic liq. with water. [on SciFinder(R)]

Active site labeling of cysteine cathepsins by a straightforward diazomethylketone probe derived from the N-terminus of human cystatin C

We designed a straightforward biotinylated probe using the N-terminal substrate-like region of the inhibitory site of human cystatin C as a scaffold, linked to the thiol-specific reagent diazomethylketone group as a covalent warhead (i.e. Biot-(PEG)2-Ahx-LeuValGly-DMK). The irreversible activity-based probe bound readily to cysteine cathepsins B, L, S and K. Moreover affinity labeling is sensitive since active cathepsins were detected in the nM range using an ExtrAvidin®-peroxidase conjugate for disclosure. Biot-(PEG)2-Ahx-LeuValGly-DMK allowed a slightly more pronounced labeling for cathepsin S with a compelling second-order rate constant for association (kass = 2,320,000 M−1 s−1). Labeling of the active site is dose-dependent as observed using 6-cyclohexylamine-4-piperazinyl-1,3,5-triazine-2-carbonitrile, as competitive inhibitor of cathepsins. Finally we showed that Biot-(PEG)2-Ahx-LeuValGly-DMK may be a simple and convenient tool to label secreted and intracellular active cathepsins using a myelomonocytic cell line (THP-1 cells) as model.