Dynamic behavior of DNA base pairs containing 8-oxoguanine

The process by which DNA repair enzymes recognize and selectively excise damaged bases in duplex DNA is fundamental to our mechanistic understanding of these critical biological reactions. 8-Oxoguanine (8-oxoG) is the most common form of oxidative DNA damage; unrepaired, this lesion generates a G:C-->T:A mutation. Central to the recognition and repair of DNA damage is base extrusion, a process in which the damaged base lesion or, in some cases, its partner disengages from the helix and is bound to the enzyme's active site where base excision takes place. The conformation adopted by 8-oxoG in duplex DNA is affected by the base positioned opposite this lesion; conformational changes may also take place when the damaged base binds to its cognate repair enzyme. We performed unrestrained molecular dynamics simulations for several 13-mer DNA duplexes. Oligomers containing G:C and 8oxoG:C pairs adopted Watson-Crick geometries in stable B-form duplexes; 8oxoG showed increased local and global flexibility and a reduced barrier to base extrusion. Duplexes containing the G:A mismatch showed much larger structural fluctuations and failed to adopt a well-defined structure. For the 8oxoG:A mismatch that is recognized by the DNA glycosylase MutY, the damaged nucleoside underwent spontaneous and reproducible anti-->syn transitions. The syn conformation is thermodynamically preferred. Steric hindrance and unfavorable electrostatics associated with the 8oxoG O8 atom in the anti conformation were the major driving forces for this transition. Transition events follow two qualitatively different pathways. The overall anti-->syn transition rate and relative probability of the two transition paths were dependent on local sequence context. These simulations indicate that both the dynamic and equilibrium behavior of the duplex change as a result of oxidation; these differences may provide valuable new insight into the selective action of enzymes on damaged DNA.     

Fractionation of metals and metalloids by chemical bonding from particles accumulated by electrostatic precipitation in an Argentine thermal power plant

A study was undertaken to evaluate the distribution of Al, As, Cr, Cu, Fe, Mn, Ni, Pb, Ti, V and Zn in fly ashes collected in the electrostatic precipitator of a thermal power plant in San Nicolás (Argentina). Five samples were collected during one week of operation. For the fractionation, the scheme applied consisted in extracting the elements in four fractions namely (i) soluble and exchangeable elements; (ii) carbonates, oxides and reducible elements; (iii) bound to sulfidic metals; and (iv) residual elements. Metals and metalloids at μg g^− 1 level were determined in each fraction by inductively coupled plasma optical emission spectrometry (ICP OES). For validation, a standard reference material (SRM 1633 coal fly ash) from NIST was subjected to the same chemical sequential extraction procedure that the samples. X-ray diffraction powder (XRD) analysis and scanning electron microscopy (SEM) were used to characterize the major minerals present in the matrix. Total analyte concentration (in μg g^− 1) varied from 10.6 for Pb to 17,622 for Al. Minimum and maximum concentrations (in μg g^− 1) found in individual samples in the four fractions were: Al, 92.7–9668; As, < 0.3–143; Cr, 2.0–10.4; Cu, < 0.2–35.6; Fe, < 0.3–4992; Mn, < 0.1–128; Ni, < 0.3–139; Pb, < 0.5–9.1; Ti, < 0.3–2243; V, 17.0–112.9; and Zn, < 0.1–68.2. The leachability of the 11 elements under study proved to be different. Low percentages of Al (1%), V (7%) and Cr (8%) were detected in the most bioavailable fraction. Arsenic was found to be most abundant in the non-silicate phase, represented by the second and third fractions, while Cr, Fe, Ni, Pb and Zn were mostly associated to the residual fraction.     

Trapping H- bound to the nitrogenase FeMo-cofactor active site during H2 evolution: characterization by ENDOR spectroscopy

We here show that the iron-molybdenum (FeMo)-cofactor of the nitrogenase alpha-70(Ile) molybdenum-iron (MoFe) protein variant accumulates a novel S = (1)/(2) state that can be trapped during the reduction of protons to H(2). (1,2)H-ENDOR measurements disclose the presence of two protons/hydrides (H(+/)(-)) whose hyperfine tensors have been determined from two-dimensional field-frequency (1)H ENDOR plots. The two H(+/)(-) have large isotropic hyperfine couplings, A(iso)( )() approximately 23 MHz, which shows they are bound to the cofactor. The favored analysis for these plots indicates that the two H(+/)(-) have the same principal values, which indicates that they are chemically equivalent. The tensors are further related to each other by a permutation of the tensor components, which indicates an underlying symmetry of binding relative to the cofactor. At present, no model for the structure of the iron-molybdenum (FeMo)-cofactor in the S = (1)/(2) state trapped during the reduction of H(+) can be shown unequivocally to satisfy all of the constraints generated by the ENDOR analysis. The data disfavors any model that involves protonation of sulfides, and thus suggests that the intermediate instead contains two chemically equivalent bound hydrides; it appears unlikely that these are terminal monohydrides.     

DNA LESIONS AND DNA DEGRADATION IN MOUSE LYMPHOMA L5178Y CELLS AFTER PHOTODYNAMIC TREATMENT SENSITIZED BY CHLOROALUMINUM PHTHALOCYANINE

Two closely related strains of mouse lymphoma L5178Y cells, LY-R and LY-S, have been found to differ in their sensitivity to the cytotoxic effects of photodynamic treatment (PDT) with chloroaluminum phthalocyanine (CAPC) and red light. Strain LY-R is more sensitive to photodynamic cell killing than strain LY-S. Differences in uptake of CAPC could not account for the differences in cytotoxic effects. There was no marked difference between the two strains in the induction of single-strand breaks (which includes frank single-strand breaks and alkali-labile lesions), but substantially more DNA-protein cross-links were formed in strain LY-R by CAPC and light. Repair of single-strand breaks proceeded with similar kinetics in both strains for the first 30 min post-irradiation, suggesting that these lesions are not responsible for the differential sensitivity of the two strains to the lethal effects of photodynamic treatment. Thereafter, alkaline elution revealed the presence of increasing DNA strand breakage in strain LY-R. DNA degradation, as measured by the conversion of prelabeled [14C] DNA to acid-soluble radioactivity, was more rapid and extensive in strain LY-R.     

Hydrolytically stable, diaminocarboxylic acid-based membranes buffering in the pH range from 6 to 8.5 for isoelectric trapping separations

Diaminocarboxylic acid carrier ampholytes, such as L-histidine, 2,3-diaminopropionic acid, L-ornithine, and L-lysine, were reacted with glycerol-1,3-diglycidyl ether (GDGE) and poly(vinyl alcohol) (PVA) in the presence of sodium hydroxide to produce hydrolytically and mechanically stable hydrogels, supported on a PVA substrate, for use as buffering membranes in isoelectric trapping (IET) separations. The pH values of the DACAPVA membranes were determined with the help of small-molecule pI markers and proteins and were found to be in the 6 < pH < 8.5 range. The membranes were successfully used to isoelectrically trap small ampholytes, desalt ampholyte solutions in IET mode, and effect the binary separation of chicken egg white proteins.     

Characterisation of the surface Lewis acid-base properties of poly(butylene terephthalate) by inverse gas chromatography

Two modes of high-speed counter-current chromatography (HSCCC) were applied to separate 3- and 4-sulfophthalic acid from a mixture. Conventional HSCCC was useful for the separation of up to several hundred milligram quantities of these positional isomers, while pH-zone-refining CCC was implemented successfully to separations at the multigram level. The conventional HSCCC separations were performed with a standard J-type HSCCC system that has a superior resolution but a lower level of retention of the stationary phase of the biphasic solvent system used (acidified n-butanol-water). The pH-zone-refining CCC separations were performed with an X-type HSCCC system (a cross-axis system) that has a higher capability for retention of the stationary phase. The purified positional isomers (over 99% pure as determined by HPLC) were characterized by 1H NMR and negative ion electrospray ionization mass spectrometry.     

31P{1H}-n.m.r. as a tool for identification of ruthenium isomers containing PPh3 or 1,4-bis(diphenylphosphino)butane ligands. X-ray structures of the cis-{RuCl2(PPh3)2 [4,4′-(-X)2-2,2′-bipy]} complexes [X=-H, -Me, -SMe and (-Cl, -Me)]

A series of cis-{RuCl₂(PPh₃)₂[4,4-(X)₂-2,2-bipy]} [cis-chlorines; X=-H, -Me, -SMe, and (-Cl,-Me)] complexes have had their structures determined by single crystal X-ray diffraction. The geometry of these complexes, also determined in CH₂Cl₂ solution by ³¹P{¹H}-n.m.r. spectroscopy, showed that the chemical shifts for the phosphorus atoms are slightly dependent on the pKa of the 4,4-(-X)₂-2,2-bipy ligands.     

Lanthanum chromites partially substituted by calcium,strontium and barium synthesized by urea combustion

Because of their electrical, magnetic and catalytic properties rare earth and transition metal mixed oxides are important compounds. Lanthanum chromites have been extensively used as solid oxide fuel cell (SOFC) interconnect materials. In this work, lanthanum chromites partially substituted by alkaline earth metals were synthesized by the urea combustion process. TG and DSC techniques were used to evaluate the presence of the organic material in the powder after reaction on the hot plate. The powders were calcinated at 900°C and characterized by XRD and SEM. The results show that the particles have nanometric dimensions and the perovskite structure was formed.     

Asymmetric synthesis of 2H-azirines derived from phosphine oxides using solid-supported amines. Ring opening of azirines with carboxylic acids

A simple and efficient asymmetric synthesis of 2H-azirine-2-phosphine oxides 3 is described. The key step is a solid-phase bound achiral or chiral amine-mediated Neber reaction of beta-ketoxime tosylates derived from phosphine oxides 1. Reaction of 2H-azirines 3 and 11 with carboxylic acids 4 gives phosphorylated ketamides 5 and 12. Ring closure of ketamides 5 and 12 with triphenylphosphine and hexachloroethane in the presence of triethylamine leads to the formation of phosphorylated oxazoles 8 and 13.     

Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides,m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.