Carbohydrate-based DNA ligands: sugar-oligoamides as a tool to study carbohydrate-nucleic acid interactions

Sugar-oligoamides have been designed and synthesized as structurally simple carbohydrate-based ligands to study carbohydrate-DNA interactions. The general design of the ligands 1-3 has been done as to favor the bound conformation of Distamycin-type gamma-linked covalent dimers which is a hairpin conformation. Indeed, NMR analysis of the sugar-oligoamides in the free state has indicated the presence of a percentage of a hairpin conformation in aqueous solution. The DNA binding activity of compounds 1-3 was confirmed by calf thymus DNA (ct-DNA) NMR titration. Interestingly, the binding of the different sugar-oligoamides seems to be modulated by the sugar configuration. Semiquantitative structural information about the DNA ligand complexes has been derived from NMR data. A competition experiment with Netropsin suggested that the sugar-oligoamide 3 bind to DNA in the minor groove. The NMR titrations of 1-3 with poly(dA-dT) and poly(dG-dC) suggested preferential binding to the ATAT sequence. TR-NOE NMR experiments for the sugar-oligoamide 3-ct-DNA complex both in D(2)O and H(2)O have confirmed the complex formation and given information on the conformation of the ligand in the bound state. The data confirmed that the sugar-oligoamide ligand is a hairpin in the bound state. Even more relevant to our goal, structural information on the conformation around the N-glycosidic linkage has been accessed. Thus, the sugar asymmetric centers pointing to the NH-amide and N-methyl rims of the molecule have been characterized.     

Salt Stress Proteins Identified by a Functional Approach in Yeast

We have performed functional genomics of salt stress by overexpression of gene libraries in yeast and selection for salt tolerance. Thirty halotolerance genes were isolated from yeast, Arabidopsis, and sugar beet. The results indicate that Na⁺ transport (uptake, efflux, and compartmentation), sulfate activation, RNA processing, and protein synthesis are crucial for salt tolerance.     

Unexpected ferromagnetic interaction in a new tetranuclear copper(II) complex: synthesis, crystal structure, magnetic properties, and theoretical studies

The new tetranuclear carbonate complex [Cu2L)2(CO3)] x 8H2O (1 x 8H2O) (H3L = (2-(2-hydroxyphenyl)-1,3-bis[4-(2-hydroxyphenyl)-3-azabut-3-enyl]-1,3-imidazolidine) has been obtained by two different synthetic routes and fully characterized. Recrystallization of 1 x 8H2O in methanol yields single crystals of {[(Cu2L)2(CO3)]}2 x 12H2O (1 x 6H2O), suitable for X-ray diffraction studies. The crystal structure of 1 x 6H2O shows two crystallographically different tetranuclear molecules in the asymmetric unit, 1a and 1b. Both molecules can be understood as self-assembled from two dinuclear [Cu2L]+ cations, joined by a mu4-eta(2):eta(1):eta(1) carbonate ligand. The copper atoms of each crystallographically different [(Cu2L)2(CO3)] molecule present miscellaneous coordination polyhedra: in both 1a and 1b, two metal centers are in square pyramidal environments, one displays a square planar chromophore and the other one has a geometry that can be considered as an intermediate between square pyramid and trigonal bipyramid. Magnetic studies reveal net intramolecular ferromagnetic coupling between the metal atoms. Density functional calculations allow the assignment of the different magnetic coupling constants and explain the unexpected ferromagnetic behavior, because of the presence of an unusual NCN bridging moiety and countercomplementarity of the phenoxo (or carbonate) and NCN bridges.     

Group 6 heteroatom- and non-heteroatom-stabilized carbene complexes. beta,beta'- and alpha,beta,beta'-annulation reactions of cyclic enamines

Cyclization reactions of group 6 Fischer carbene complexes with cyclopentanone and cyclohexanone enamines are described. Enamine 3a undergoes thermal alpha,beta,beta'-annulation with alkenylcarbene complexes 1 and 2 (THF, 60 degrees C), affording semibullvalenes 5. The metalate intermediates 6, resulting from beta,beta'-annulation of the enamines 3a and 4a, were quantitatively formed by running the reaction in hexane at room temperature. Acid-promoted demetalation of 6 afforded endo-2-bicyclo[3.2.1]octen-8-ones 7 and endo/exo-2-bicyclo[3.3.1]nonen-9-ones 8 (endo/exo = 5:1). Using (S)-methoxymethylpyrrolidine-derived enamines 3b and 4b,c allowed highly enantioenriched cycloadducts endo-(+)-7 as well as endo-(-)-8 and exo-(-)-8 to be accessed. The non-heteroatom-stabilized carbene complex 10 was formed from complex 6 by Me(3)SiOTf-promoted elimination of the methoxy group, characterized by (13)C NMR, and transformed into the organic compounds 7, 7-d, and 11 as well as into bicyclo[3.2.1]octan-2,8-diones 14 and cycloheptanones 15. On the basis of this sequence, enantioenriched cycloheptanones (+)-15 were efficiently prepared in one pot from carbene complexes 2 and enamine 3b (51-55% yield, 91-96% ee). Extension of this work to simple Fischer carbene complexes 16 allowed an appropriate way to generate the nonstabilized pentacarbonyl[(phenyl(alkyl)carbene]tungsten complex 17 to be designed, for which the thermal and chemical behavior leading to compounds 18-21 is described.     

Scanning electrochemical microscopy as a probe of Ag+ binding kinetics at Langmuir phospholipid monolayers

A new method has been developed for measuring local adsorption rates of metal ions at interfaces based on scanning electrochemical microscopy (SECM). The technique is illustrated with the example of Ag+ binding at Langmuir phospholipid monolayers formed at the water/air interface. Specifically, an inverted 25 microm diameter silver disc ultramicroelectrode (UME) was positioned in the subphase of a Langmuir trough, close to a dipalmitoyl phosphatidic acid (DPPA) monolayer, and used to generate Ag+ via Ag electro-oxidation. The method involved measuring the transient current-time response at the UME when the electrode was switched to a potential to electrogenerate Ag+. Since the Ag+/Ag couple is reversible, the response is highly sensitive to local mass transfer of Ag+ away from the electrode, which, in turn, is governed by the interaction of Ag+ with the monolayer. The methodology has been used to determine the influence of surface pressure on the adsorption of Ag+ ions at a phospholipid (dipalmitoyl phosphatidic acid) Langmuir monolayer. It is shown that the capacity for metal ion adsorption at the monolayer increased as the density of surface adsorption sites increased (by increasing the surface pressure). A model for mass transport and adsorption in this geometry has been developed to explain and characterise the adsorption process.     

Colloidal aggregation induced by long range attractions

The structure of colloidal clusters formed by long-range attractive interactions under diluted conditions is studied by means of Monte Carlo simulations. For a not-too-long attraction range, clusters show self-similar internal structure with lower density than that typical for diffusive aggregation. For long-range interactions, low kappa, nonfractal clusters are formed (dense at short scales but open at long ones). The dependence on the volume fraction shows that more-compact clusters are grown the higher the colloidal density for diffusive aggregation and attraction-driven aggregation in the fractal regime. The whole trend is explained in terms of the interpenetration among aggregates. In attraction-driven aggregations, the interpenetration of clusters competes with aggregation in the tips of the clusters, causing low-density clusters.     

Determination of pirimicarb and endosulfan in commercial pesticide formulations by Fourier transform infrared spectrometry

A routine method based on Fourier transform infrared spectrometry was developed for the simultaneous determination of pirimicarb and endosulfan in commercially available pesticide formulations. The method is based on peak area absorbance measurements between 1362 and 1352 cm(-1), corrected with a baseline fixed at 1338 cm(-1), for pirimicarb and peak area absorbance measurements between 919 and 909 cm(-1) with a baseline fixed at 931 cm(-1) for endosulfan; chloroform solutions for analysis were obtained by direct dilution of emulsifiable concentrates or by solvent extraction from solid samples. Various extraction conditions and appropriate band selection were investigated, and interference studies were performed. Under the experimental conditions selected, limits of detection of 13 microg/g for pirimicarb and 150 microg/g for endosulfan were obtained that correspond to 0.13 and 1.6% (w/w), respectively, in commercial samples. Results from analyses of commercial samples by the developed method compared well with those obtained by a liquid chromatography reference method.     

Chiral analysis of pollutants and their metabolites by capillary electromigration methods

Chiral separation of enantiomers is one of the most challenging tasks for any analytical technique including CE. Since the first report in 1985 showing the great possibilities of CE for the separation of chiral compounds, the amount of publications concerning this topic has quickly increased. Although chiral electromigration methods have mainly been used for enantioseparation of drugs and pharmaceuticals, they have also been applied to analyze chiral pollutants. This article intends to provide an updated overview, including works published till January 2005, on the principal applications of CE to the chiral analysis of pollutants and their metabolites, with special emphasis on articles published in the last 10 years. The main advantages and drawbacks regarding the use of CE for chiral separation of pollutants are addressed including some discussion on the foreseen trends of electromigration procedures applied to chiral analysis of contaminants.