Quantum-mechanical exploration of the properties of the sugar rings

Theab initio SCF method is used for computing the main electronic properties of the ribose unit of the nucleic acids. The present study is devoted to the ribose in the C₃-endo,gg conformation. The properties investigated include the distribution of the electronic charges, the electrostatic molecular potential around the four oxygens of the unit, the hydration and the Na⁺ binding schemes studied in the supermolecule approximation. The possibilities of through-water binding of the cation to the sugar are also explored. The predictions of the computation in particular with regard to cation binding to the ribose ring are correlated with recent experimental results.     

Réactions de germylènes avec divers oxirannes et le thiiranne. Mise en évidence de germanones et germathiones intermédiaires. Communication préliminaire

Complexed dialkylgermylenes R₂GeNR₃ or R₂GePy react with oxiranes or thiirane and lead to dialkylgermanone and germathione via germaoxetanes or germathiacyclobutane. The formation of germadioxolanes or germadithiolane finally observed arises from condensation of dialkylgermanone (or germathione) on oxiranes (or thiirane).     

QUENCHING OF TYROSINE FLUORESCENCE BY PHOSPHATE IONS: A MODEL STUDY FOR PROTEIN-NUCLEIC ACID COMPLEXES

Abstract— In order to test the ability of phosphate groups to quench the tyrosine fluorescence in nucleic acid-protein complexes, we have studied the effect of several phosphate ions on the fluorescence of tyrosine derivatives. Mono and bianions (H₂PO₄ and HPO₄^2–) which are good proton acceptors quenched the fluorescence of all the phenolic compounds studied except that of O -methyl tyrosine. With the other derivatives (tyrosine, N -acetyl tyrosinamide and lysyl-tyrosyl-α lysine) fluorescence inhibition was accompanied by the appearance of a long wavelength emission (345 nm) attributed to tyrosinate anions. The quenching of tyrosine emission was due to the deprotonation of the phenolic group promoted in the excited state by phosphate ions and leading to the weakly fluorescent tyrosinate ion. Mono and dianions of phosphate mono ester inhibited tyrosine fluorescence as did unesterified phosphates. However, phosphate diester did not have any effect on the fluorescence of tyrosine derivatives. We conclude from this study that in nucleic acid-protein complexes phosphate groups are not able to quench tyrosine fluorescence except at the end of polynucleotide chains. Since monoester and diester monoanions have a different behavior, we propose that quenching of tyrosine fluorescence by monoanions requires the formation of two hydrogen bonds. This complex cannot form with diesters which consequently do not quench tyrosine fluorescence.     

Drying dissipative structures of the aqueous suspensions of monodisperse bentonite particles

Macroscopic and microscopic dissipative structural patterns formed in the course of drying the fractionated and monodisperse bentonite particles (plate-like in their shape) in aqueous deionized suspension and in the presence of NaCl have been studied on a cover glass. The patterns coexisted with the broad ring of the hill accumulated with the particles and with the round hills are formed around the outside edges of the film and in the center, respectively, in the macroscopic scale. By the addition of NaCl the pattern shifts from the broad ring to the round hill in the center. The spoke-like cracks, which have been observed for the suspensions of the spherical particles so often hitherto, are not observed at all for the bentonite suspensions. The characteristic convection flow of the particles and the interactions among the particles and substrate are important for the macroscopic pattern formation. Wrinkled, branch-like and/or star-like fractal patterns are observed in the microscopic scale. These patterns are determined mainly by the electrostatic and polar interactions between the particles and/or between the particle and the substrate in the course of drying.     

Gas-phase reactivity of the O=P(OCH3)2+ phosphonium ion with aliphatic esters in a quadrupole ion trap. Spontaneous elimination of ketenes

Ion-molecule reactions between the O=P(OCH(3))(2) (+) phosphonium ions and five aliphatic esters (methyl acetate, methyl propionate, methyl 2-methylpropionate, methyl butyrate and ethyl acetate) were performed in a quadrupole ion trap mass spectrometer. The O=P(OCH(3))(2) (+) phosphonium ions, formed by electron ionization from neutral trimethyl phosphite, were found to react with aliphatic esters to give an adduct ion [RR'CHCOOR", O=P(OCH(3))(2)](+), which loses spontaneously a molecule of ketene CH(2)=CO or substituted ketenes RR'C=CO. Isotope-labeled methyl acetate was used to elucidate fragmentation mechanisms. The potential energy surface obtained from B3LYP/6-31G(d,p) calculations for the reaction between O=P(OCH(3))(2) (+) and methyl acetate is described.     

Double silyl migration converting ORe[N(SiMe(2)CH(2)PCy(2))(2)] to NRe[O(SiMe(2)CH(2)PCy(2))(2)] substructures

The reaction of (R(2)PCH(2)SiMe(2))(2)NM (PNP(R)M; R = Cy; M = Li, Na, MgHal, Ag) with L(2)ReOX(3) [L(2) = (Ph(3)P)(2) or (Ph(3)PO)(Me(2)S); X = Cl, Br] gives (PNP(Cy))ReOX(2) as two isomers, mer,trans and mer,cis. These compounds undergo a double Si migration from N to O at 90 degrees C to form (POP(Cy))ReNX(2) as a mixture of mer,trans and fac,cis isomers. Additional thermolysis effects migration of CH(3) from Si to Re, along with compensating migration of halide from Re to Si. DFT calculations on various structural isomers support the greater thermodynamic stability of the POP/ReN isomer vs PNP/ReO and highlight the influence of the template effect on the reactivities of these species.     

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.     

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.