A new family of sequence-specific DNA-cleaving agents directed by triple-helical structures: benzopyridoindole-EDTA conjugates

Sequence-specific DNA recognition can be achieved by oligonucleotides that bind to the major groove of oligopyrimidine x oligopurine sequences. These intermolecular structures could be used to modulate gene expression and to create new tools for molecular biology. Here we report the synthesis and biochemical characterization of triple helix-specific DNA cleaving reagents. It is based on the previously reported triplex-specific ligands, benzo[e]pyridoindole (BePI) and benzo[g]pyridoindole (BgPI), covalently attached to ethylenediaminotetraacetic acid (EDTA). In the presence of iron, a reducing agent and molecular oxygen, BgPI-EDTA x FeII but not BePI-EDTA x FeII induced a double-stranded cut in a plasmid DNA at the single site where a triplex-forming oligonucleotide binds. At single nucleotide resolution, it was found that upon triplex formation BePI-EDTA x FeII led to cleavage of the pyrimidine strand and protection of the purine strand. BgPI-EDTA x FeII cleaved both strands with similar efficiency. The difference in cleavage efficiency between the two conjugates was rationalized by the location of the EDTA x FeII moiety with respect to the grooves of DNA (major groove: BePI-EDTA x FeII, minor groove: BgPI-EDTA x FeII). This work paves the way to the development of a new class of triple helix directed DNA cleaving reagents. Such molecules will be of interest for sequence-specific DNA cleavage and for investigating triple-helical structures, such as H-DNA, which could play an important role in the control of gene expression in vivo.     

Composition of the black crusts from the Saint Denis Basilica, France, as revealed by gas chromatography-mass spectrometry

The organic fraction of black crusts from Saint Denis Basilica, France, is composed of a complex mixture of aliphatic and aromatic compounds. These compounds were studied by two different analytical approaches: tetramethyl ammonium hydroxide (TMAH) thermochemolysis in combination with gas chromatography-mass spectrometry (GC-MS), and solvent extraction, fractionation by silica column, and identification of the fraction components by GC-MS. The first approach, feasible at the microscale level, is able to supply fairly general information on a wide range of compounds. Using the second approach, we were able to separate the complex mixture of compounds into four fractions, enabling a better identification of the extractable compounds. These compounds belong to different classes: aliphatic hydrocarbons (nalkanes, n-alkenes), aliphatic and aromatic carboxylic acids (n-fatty acids, alpha,omega-dicarboxylic acids, and benzenecarboxylic acids), polycyclic aromatic hydrocarbons (PAH), and molecular biomarkers (isoprenoid hydrocarbons, diterpenoids, and triterpenoids). With each approach, similar classes of compounds were identified, although TMAH thermochemolysis failed to identify compounds present at low concentrations in black crusts. The two proposed methodological approaches are complementary, particularly in the study of polar fractions.     

The preparation of precisely defined lithium isotope mixtures

The need for accurate (< 0.06%) isotopic blends of ⁶Liand ⁷Li is explained and their preparation is discussed. It is shown that lithium must be determined at an accuracy level better than 0.035%. Four methods — acid-base titration with hydrochloric acid or benzoic acid, and weighing as sulphate or carbonate — were tested and improved for the precise and accurate analysis of lithium hydroxide solutions. The results of these four methods for a 0.1 M solution agreed within ± 0.02%. The preparation of pure isotopically enriched lithium hydroxide solutions, with specially purified cation- and anion-exchangers, is described. The prepared products contain as little as 100 μg of other alkali metals and 50 μg of alkaline-earth metals per gram of lithium, and are sufficiently free of anions to permit accurate chemical assay of lithium. No changes in the isotopic compositions of 99% ⁶Li or 99.99% ⁷Li were detected during the treatment.     

Stable and soluble oligo(3,4-ethylenedioxythiophene)s end-capped with alkyl chains

The synthesis of a new series of stable and soluble EDOT oligomers end-capped with n-hexyl groups is described. Optical and electrochemical results indicate that the synergy between the direct electron-releasing effects of the ethylenedioxy groups and the self-rigidification resulting from intramolecular interactions controls to a large extent the HOMO-LUMO gap.     

Analytical study of highly condensed non ionic surfactants. Separation on cation exchangers

Summary This study was aimed at optimizing the separation of non-ionic surfactants, resulting from the condensation of ethylene oxide with natural fatty alcohols in the C₁₆ and C₁₈ range (saturated and unsaturated), and presenting a high degree of condensation, i.e. 20 and 25 ethylene oxide units (Brij 99 and KM 25). The cation exchange stationary phase is a partially ionized silica, conditioned in different ways. We have studied the influence of the nature of cations on the separation selectivity. Cations studied included alkali metals (Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺), alkaline earth metals (Mg²⁺, Ca²⁺, Sr²⁺, Ba²⁺), transition metals (Zn²⁺, Cd²⁺, Hg²⁺, Pb²⁺, Cu²⁺), and quaternary ammonium (NH ₄ ⁺ , NMe ₄ ⁺ ) ions as well as a proton (acetic acid). The influences of ionic strength, pH and addition of cosolvent were examined. A study of the influence of temperature on the system selectivity evidenced a strong interdependance of these two parameters. The optimized conditions [mobile phase: CH₃CN/H₂O (92/8), pH 7.4, sodium acetate 5.10^–3 M; temperature gradient between 25 and 50°C] allowed for the first time the distributions of Brij 99 and KM 25 to be obtained.     

On a numerical approach to Stefan-like problems

Summary This paper is devoted to the numerical analysis of a bidimensional two-phase Stefan problem. We approximate the enthalpy formulation byC ⁰ piecewise linear finite elements in space combined with a semi-implicit scheme in time. Under some restrictions related to the finite element mesh and to the timestep, we prove positivity, stability and convergence results. Various numerial tests are presented and discussed in order to show the accuracy of our scheme.This work is supported by the Fonds National Suisse pour la Recherche Scientifique.