Mapping the sites for selective oxidation of guanines in DNA

The effective energy of a positive charge when it is localized at a specific guanine nucleobase in DNA was calculated using density functional theory. The results demonstrate that the efficiency of a guanine to act as a hole-trap in DNA strongly depends on the nature of the flanking nucleobases. The presence of a pyrimidine base at the 3' position adjacent to a guanine significantly increases the localization energy of the positive charge. The calculated distributions of a positive charge in sequences of two or three adjacent guanines, flanked by other nucleobases, provide an explanation for experimental literature data on the site-selective oxidation of DNA.     

Combinatorial diversity of fission yeast SCF ubiquitin ligases by homo- and heterooligomeric assemblies of the F-box proteins Pop1p and Pop2p

Background  

SCF ubiquitin ligases share the core subunits cullin 1, SKP1, and HRT1/RBX1/ROC1, which associate with different F-box proteins. F-box proteins bind substrates following their phosphorylation upon stimulation of various signaling pathways. Ubiquitin-mediated destruction of the fission yeast cyclin-dependent kinase inhibitor Rum1p depends on two heterooligomerizing F-box proteins, Pop1p and Pop2p. Both proteins interact with the cullin Pcu1p when overexpressed, but it is unknown whether this reflects their co-assembly into bona fide SCF complexes.     

Concentration and vertical distribution of plutonium and americium in Italian mosses and lichens

The plutonium and americium concentration and vertical distribution in some Italian mosses and lichens have been determined. The^239,240Pu,²³⁸Pu and²⁴¹Am concentration ranges in tree trunk lichens 0.83–1.87, 0.052–0.154 and 0.180–0.770 Bq/kg, respectively. The corresponding values in tree mosses are higher and more scattered ranging from 0.321 to 4.96, from 0.029 to 0.171 and from 0.200 to 1.93 Bq/kg. The mean²³⁸Pu/^239,240Pu and²⁴¹Am/^239,240Pu ratios are 0.088±0.037 and 0.38±0.13 in lichens and 0.091±0.072 and 0.54±0.16 in tree mosses. The Pu and Am concentrations are relatively low in terrestrial mosses. The^239,240Pu,²³⁸Pu and²⁴¹Am vertical distributions in a terrestrial moss core (Neckera Crispa) collected near Urbino (central Italy) show an exponential decrease with the height. On the contrary the²⁴¹Am vertical distribution in another terrestrial moss core (Sphagnum Compactum) collected in the Alps (northern Italy) shows an interesting peak at 16 cm which corresponds to the deposition of fallout from the nuclear weapon tests in 1960's. The²⁴¹Am movement upward and downward in the moss core is also studied. The results show once again that both mosses and lichens are very effective accumulators of Pu and Am and that they can be used as good biological indicators of the radionuclide airbome pollution from nuclear facilities and nuclear weapon tests. They can play a very impotant role in cycling naturally or artificially enhanced radionuclides in the atmosphere over long time scales.     

Far-UV laser flash photolysis in solution. A study of the chemistry of 1,1-dimethylsilene in hydrocarbon solvents

The far-UV (193 nm) laser flash photolysis of nitrogen-saturated isooctane solutions of 1,1-dimethylsiletane allows the direct detection of 1,1-dimethylsilene as a transient species, which (at low laser intensities) decays with pseudo-first-order kinetics (τ 10 μs) and exhibits a UV absorption spectrum with λ_max 255 nm. Characteristic rapid quenching is observed for the silene with methanol (k_McOH = (4.9 ± 0.2) × 10⁹ M⁻¹ s⁻¹), tert-butanol (k_BuOH = (1.8 ± 0.1) × 10⁹ M⁻¹ s⁻¹) and oxygen (k_O2 = (2.0 ± 0.5) × 10⁸ M⁻¹ s⁻¹). The Arrhenius activation parameters for the reaction with methanol have been determined to be E_a = −2.6 ± 0.6 kcal mol⁻¹ and log A = 7.7 ± 0.3.     

Poly(ethylene terephthalate) copolymers containing nitroterephthalic units. III. Methanolytic degradation

The methanolytic degradation of poly(ethylene terephthalate) (PET) copolymers containing nitroterephthalic units was investigated. Random poly(ethylene terephthalate‐co‐nitroterephthalate) copolyesters (PETNT) containing 15 and 30 mol % nitrated units were prepared from ethylene glycol and a mixture of dimethyl terephthalate and dimethyl nitroterephthalate. A detailed study of the influence of the nitro group on the methanolytic degradation rate of the nitrated bis(2‐hydroxyethyl) nitroterephthalate (BHENT) model compound in comparison with the nonnitrated bis(2‐hydroxyethyl) terephthalate (BHET) model compound was carried out. The kinetics of the methanolysis of BHENT and BHET were evaluated with high‐performance liquid chromatography and ¹H NMR spectroscopy. BHENT appeared to be much more reactive than BHET. The methanolytic degradation of PET and PETNT copolyesters at 80 °C was followed by changes in the weight and viscosity, gel permeation chromatography, differential scanning calorimetry, scanning electron microscopy, and ¹H and ¹³C NMR spectroscopy. The copolyesters degraded faster than PET, and the degradation increased with the content of nitrated units and occurred preferentially by cleavage of the ester groups placed at the meta position of the nitro group in the nitrated units. For both PET and PETNT copolyesters, an increase in crystallinity accompanied methanolysis. A surface degradation mechanism entailing solubilization of the fragmented polymer and consequent loss of mass was found to operate in the methanolysis of the copolyesters. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2276–2285, 2002     

Conjugated Azoalkenesi Part III. Synthesis of Sone Phosphorous Azoalkenes

Recently, some of us reviewed the synthes is and chemical reactions of conjugated azoalkenes.¹ Emphasis was placed on the fact that these derivatives represent at the same time interesting products and useful intermediates in organic chemistry. In fact, conjugated azoolefins undergo a wide range of 1,4-additions, (3+2)- and (4+2)-cycloadditions allowing various functionalizations of the carbon atom adjacent to the carbonyl group, and the construction of many types of interesting five - and six-membered heterocycles, such as widely substituted pyrrole and pyridazine rings. These relevant synthetic objectives appear not to be smoothly obtained by other procedures. In addition, many of the compounds produced from conjugated azoalkenes can profitably be employed in the preparation of natural, pharmaceutical, and phytopharmaceutical products.¹     

Modified Guanines as Constituents of Smart Ligands for Nucleic Acid Quadruplexes

Repetitive guanine‐rich nucleic acid sequences play a crucial role in maintaining genome stability and the cell life cycle and represent potential targets for regulatory drugs. Recently, it has been demonstrated that guanine‐based ligands with a porphyrin core can be used as markers of G‐quadruplex assemblies in cell tissues. Herein, model systems of guanine‐based ligands are explored by DFT methods. The energies of formation of modified guanine tetrads and those of modified tetrads stacked on the top of natural guanine tetrads have been calculated. The interaction energy has been decomposed into contributions from hydrogen bonding, stacking, and ion coordination and a twist–rise potential energy scan has been performed to find the individual local minima. Energy decomposition analysis reveals the impact of various substituents (F, Cl, Br, I, Me, NMe₂) on individual energy terms. In addition, cooperative reinforcement in forming the modified and stacked tetrads, as well as the frontier orbitals participating in the hydrogen‐bonding framework involving the HOMO–LUMO gap between the occupied σ_HOMO on the proton‐accepting C=O and =N? groups and unoccupied σ_LUMO on the N?H groups, has been studied. The investigated systems are demonstrated to have a potential in ligand development, mainly due to stacking enhancement compared with natural guanine, which is used as a reference.     

Biodegradable aromatic copolyesters made from bicyclic acetalized galactaric acid

Random poly(hexamethylene terephthalate‐co‐galactarate)s and poly(dodecamethylene terephthalate‐co‐galactarate)s copolyesters covering the whole range of compositions were obtained with weight‐average molecular weights of ～30,000–50,000 g mol^?1 by melt polycondensation. They were thermally stable above 300 °C, and displayed T_g in the +20 to ?20 °C range with values steadily decreasing with the content in galactarate units. All the copolyesters were semicrystalline with T_m between 50 and 150 °C and those made from dodecanediol were able to crystallize from the melt at a crystallization rate depending on composition. Copolyesters containing up to 50% of galactaric units retained the crystal structure of their respective polyterephthalate homopolyesters, whereas they adopted the structure of the respective polygalactarates when the content in Galx units reached 70%. Stress‐strain essays revealed decay in the mechanical parameters as the aromatic units were replaced by Galx. Incubation in aqueous buffer revealed that hydrolysis of the polyesters were largely enhanced by copolymerization and evidenced the capacity of the Galx unit for making aromatic polyesters susceptible to biodegradation. A detailed NMR analysis complemented by SEM observations indicated that hydrolysis took place by preferred splitting of galactarate ester bonds with releasing of alkanediol and Galx‐diacid. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

An inverse problem for infinitely divisible moving average random fields

Statistical Inference for Stochastic Processes - Given a low frequency sample of an infinitely divisible moving average random field $$\{\int _{\mathbb {R}^d} f(x-t)\varLambda (dx); \ t \in \mathbb...