Synthesis of oligonucleotides containing an O-G-alkyl-O-G interstrand cross-link

A methodology to synthesize oligonucleotides containing an alkyl interstrand cross-link between the two O6 atoms of deoxyguanosine has been developed. This cross-link is designed to serve as a stable structural mimic of the lesion formed in duplex DNA with the bifunctional alkylating agent hepsulfam. The O6-alkyl coupling is performed via a Mitsunobu reaction between a nucleoside and mono-protected 1,7-heptanediol. Solid-phase oligonucleotide synthesis using a nucleoside bis-phosphoramidite allows for the assembly of the cross-linked duplex. Sufficient quantities of this cross-linked duplex were obtained for various structural and biological investigations.     

Synthesis of new derivatives of 4-amino-2,4-dihydro-1,2,4-triazol-3-one as potential antibacterial agents

Thirty new 2-substituted-4-amino-5-alkyl or aryl-2,4-dihydro-1,2,4-triazol-3-ones and ten 2-substituted-5-alkyl or aryl-4-(5-nitro-2-furfurylidene)amino-2,4-dihydro-1,2,4-triazol-3-ones were synthesized and characterised by their sharp melting points, elemental analysis, ir and ¹H nmr spectra. These new derivatives of 5-nitro-2-furaldehyde were screened for their antibacterial activities. Most of the compounds showed good activity against one test organism, Staphylococcus aureus. For a few compounds, C.M.I. ranged from 4 to 8 μg/ml (higher results than nitrofurantoin).     

'Boomerang'-like insertion of a fusogenic peptide in a lipid membrane revealed by solid-state 19F NMR

Solid state (19)F NMR revealed the conformation and alignment of the fusogenic peptide sequence B18 from the sea urchin fertilization protein bindin embedded in flat phospholipid bilayers. Single (19)F labels were introduced into nine distinct positions along the wild-type sequence by substituting each hydrophobic amino acid, one by one, with L-4-fluorophenylglycine. Their anisotropic chemical shifts were measured in uniaxially oriented membrane samples and used as orientational constraints to model the peptide structure in the membrane-bound state. Previous (1)H NMR studies of B18 in 30% TFE and in detergent micelles had shown that the peptide structure consists of two alpha-helical segments that are connected by a flexible hinge. This helix-break-helix motif was confirmed here by the solid-state (19)F NMR data, while no other secondary structure (beta-sheet, 3(10)-helix) was compatible with the set of orientational constraints. For both alpha-helical segments we found that the helical conformation extends all the way to the respective N- and C-termini of the peptide. Analysis of the corresponding tilt and azimuthal rotation angles showed that the N-terminal helix of B18 is immersed obliquely into the bilayer (at a tilt angle tau approximately 54 degrees), whereas the C-terminus is peripherally aligned (tau approximately 91 degrees). The azimuthal orientation of the two segments is consistent with the amphiphilic distribution of side-chains. The observed 'boomerang'-like mode of insertion into the membrane may thus explain how peptide binding leads to lipid dehydration and acyl chain perturbation as a prerequisite for bilayer fusion to occur.     

Preparation of symmetrical and unsymmetrical monomers towards bridge trifluoromethylated poly(p-phenylenevinylene)

The preparation and identification of a series of trifluoromethylated and bis(trifluoromethylated) precursors and monomers for bridge substituted trifluoromethylated poly(p-phenylenevinylene) (PPV) is reported. These monomers were prepared in several steps from terephthaldicarboxaldehyde and they contain symmetrical and unsymmetrical combinations of leaving groups and/or polarizers, including chlorides, sulfoxides, sulphones, tosylates and S-methyl (and also O-ethyl) xanthates. The electron withdrawing effect of the trifluoromethyl group dominated the regioselectivity of substitution, thus allowing the convenient and selective formation of unsymmetrically substituted products in high yield.     

The effect of the “Inert” support on relative photocatalytic activity in the oxidative decomposition of alcohols on irradiated titanium dioxide composites

Reduced quantum efficiencies for the photocatalytic degradation of cyclohexanol, cyclododecanol, 2-hexanol, and benzyl alcohol are observed on TiO₂ particles included within small pore zeolitic supports suspended in acetonitrile. A modest reduction in photocatalytic activity observed with TiO₂ included within large pore zeolites and pillared clays is attributed to reflective and refractive losses of incident light. No appreciable substrate size selectivity could be observed in this series of supported TiO₂ composites. TS-1, a titanium-containing zeolite with Ti in tetrahedral lattice sites, was photoactive, although ETS-10, a titanium-containing zeolite with Ti in octahedral lattice sites, was less so. The low quantum yield residual photoactivity observed with these alcoholic substrates on unmodified zeolites may derive from surface charge transfer complexation, as suggested by diffuse reflectance absorption measurements.     

A convenient synthesis of new aminomethylenedioxypyrroloindoles via an iminium salt

Cyclization of 2-(1-pyrrolyl)piperonylcarboxamide derivatives gave iminium perchlorates which afforded 9-(N-substituted-imino) and 9-(N-substituted amino)-6,7-methylenedioxypyrrolo[1,2-a]indoles.     

Investigation of the metal binding site in methionine aminopeptidase by density functional theory

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co²⁺ions or Zn²⁺ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. colimethionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.     

A L-RNA aptamer chiral stationary phase for the resolution of target and related compounds

In this paper, we report for the first time an aptamer-based chiral stationary phase (CSP) able to resolve racemates of both target and various related compounds. The enantiomers of tyrosine and analogues (11 enantiomeric pairs) were separated using an immobilized tyrosine-specific L-RNA aptamer as CSP and an aqueous buffer (8 mM Tris-HCl buffer, 25 mM NaCl, 5 mM MgCl2; pH 7.4) as mobile phase, at a column temperature of 10 degrees C. It appeared that the carboxylic and amino groups as well as the aromatic side chain of amino acid controlled the stereospecific recognition. Modifications on the polar groups were strongly detrimental for enantioselectivity while the replacement of the phenolic group by some bicyclic aromatic residues of different polarity, size or shape did not impair the enantioselective interaction. In addition, the effects of the mobile phase composition and column temperature upon the retention and stereoselective properties of the CSP were assessed. Finally, it was found that the immobilized RNA aptamer could be used under hydro-organic mobile phase conditions without alteration of the stationary phase stability.     

New evidence of confinement effects in mesoporous materials and the definition of confined Pitzer acentric factors

In the present work, the corresponding states principle is proposed as a new approach to clarify the comparison between adsorption-desorption isotherms obtained on porous solids. The applicability of this principle at the capillary critical point in adsorption-desorption isotherms is demonstrated. Deviations of the Clausius-Clapeyron curves in reduced coordinates are interpreted in terms of polarizability, and those are perfectly correlated using analogous Pitzer acentric factors in confined environments. New acentric factors are proposed to take confinement effects in mesoporous materials into account. Enthalpic excesses during capillary condensation could be predicted, and those are supported by calorimetric experiments.     

Efforts to expand the genetic alphabet: identification of a replicable unnatural DNA self-pair

Six unnatural nucleotides featuring fluorine-substituted phenyl nucleobase analogues have been synthesized, incorporated into DNA, and characterized in terms of the structure and replication properties of the self-pairs they form. Each unnatural self-pair is accommodated in B-form DNA without detectable structural perturbation, and all are thermally stable and selective to roughly the same degree. Furthermore, the efficiency of polymerase-mediated mispair synthesis is similar for each unnatural nucleotide in the template. In contrast, the efficiency of polymerase-mediated self-pair extension is highly dependent on the specific fluorine substitution pattern. The most promising unnatural base pair candidate of this series is the 3-fluorobenzene self-pair, which is replicated with reasonable efficiency and selectivity.