Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

Metabolite-sensing mRNAs, or "riboswitches," specifically interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, capable of ligand-induced structural changes, and downstream regions, harboring expression-controlling elements. We report the crystal structures of the add A-riboswitch and xpt G-riboswitch aptamer modules that distinguish between bound adenine and guanine with exquisite specificity and modulate expression of two different sets of genes. The riboswitches form tuning fork-like architectures, in which the prongs are held in parallel through hairpin loop interactions, and the internal bubble zippers up to form the purine binding pocket. The bound purines are held by hydrogen bonding interactions involving conserved nucleotides along their entire periphery. Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively.     

Binding of hexacyanoferrate(II) by aliphatic amines in aqueous solution

The stability of hexacyanoferrate(II)-amine(methylamine, ethylenediamine, diethylenetriamine and tetraethylenepentamine) was determined potentiometrically. Species Fe(CN)₆(A)H _j ^(j–4) (A=amine) are formed in all the systems investigated, with j=1...n+2 (n=number of aminogroups). Some other complexes Fe(CN)₆(A)_iH_j (with i>1) were also found. The stability of these complexes is fairly high: the full protonated amine species, show for the reaction Fe(CN)₆ ^4- + H_nAⁿ⁺ = Fe(CN)₆(A)H_n ^(n-4) an equilibrium constant given by logK=0.686+2.10n. Factors affecting the stability are discussed in comparison with similar systems, together with the importance of interferences.     

The surface of ordered mesoporous benzene-silica hybrid material: an infrared and ab initio molecular modeling study

Joint IR and computational results allow a detailed characterization of the surface properties of a mesoporous benzene-silica hybrid material with crystal-like wall structure. After outgassing at 450 degrees C, hydroxyl species mainly consist of noninteracting silanols, with both O-H and Si-O stretching modes at lower frequencies than those of SiOH in silica. Interaction with several probe molecules, followed both by experiment and calculus, shows that the aryl group in the coordination sphere of Si imparts a lesser acidity with respect to the isolated silanol in silica. In contrast, adsorption isotherms indicate that the interaction with acetone is stronger with benzene-silica than with silica: this is interpreted in terms of secondary interactions taking place between the slightly acidic CH in acetone and the electronic cloud in benzene-like rings. This suggests that both the inorganic component and the organic one play a role in dictating the surface behavior.     

Wechselwirkungen in Kristallen. 106. Mitteilung. Die Klaviatur der Na⊕-Koordinationszahlen in ihren Carbazolanion-Salzen

Interaction in Crystals: The Keyboard of Na⊕ Coordination Numbers in Its Carbazole Anion Salts Some local minima in the shallow potential of the system carbazole anion, sodium cation, and the ethers tetrahydrofuran, 1,2-dimethoxyethane, diglyme, triglyme, tetraglyme, 15-crown-5 as well as 2.2.1-cryptand are explored experimentally and by quantum-chemical calculations. Three prototype contact-ion multiples of Na⊕-solvated carbazole anion M? salts have been crystallized and structurally characterized: polyether-solvated monomers [M?Na⊕_solv]₁, solvent-shared dimers [M?Na⊕_solv]₂, and solvent-separated polyions [(M?)nNa?_solv](^n?1)? [Na⊕_solv](n_?1). The Na⊕ coordination numbers stretch from 3 to 7 as illustrated by the compounds [(M?)₃Na+]??[Na+(2.2.1-crytand)]₂ for 3 and 7, [(M?)₂Na+(THF)₂]? [Na⊕(2.2.1-cryptand)] for 4 and 7, [M? Na+(diglyme)]₂ for 5, or [M? Na+(l 5-crown-5)] for 6. Structural comparison is based on literature analogies as well as on results of MNDO calculations concerning charge distribution and enthalpies of formation. Taken together, the results demonstrate the delicate energy balance, by which cation solvation can influence the formation of organic salts.     

A kinetic method for <Emphasis Type="Italic">para</Emphasis>-nitrophenol determination based on its inhibitory effect on the catalatic reaction of catalase

The inhibitory effect of para-nitrophenol on the catalytic reaction of catalase was investigated. Michaelis-Menten kinetic parameters were determined from Lineweaver-Burk plots obtained in the absence or in the presence of the inhibitor. The inhibitor pattern, revealed by the Lineweaver-Burk plots, suggested a fully mixed inhibition mechanism. Spectrophotometric monitoring of the indicator reaction: in conjunction with initial rate measurements was employed for the kinetic determination of the inhibitor. Calibration plots of initial rate vs. para-nitrophenol concentration were linear in the concentration range 0.9·10⁻⁵–2.5·10⁻⁵ mol/L and the detection limit was 3·10⁻⁶ mol/L (417 μg/L) para-nitrophenol. Interferences from other phenolic compounds like orto-cresole, meta-and orto-nitrophenol were observed.     

Quantification of free and total salicylic acid in plants by solid-phase extraction and isocratic high-performance anion-exchange chromatography

Salicylic acid (SA) is an important signaling compound in plants and is involved in various defense responses. Here we report a new method for quantification of free and total soluble SA in Arabidopsis thaliana with 5-fluorosalicylic acid (5-FSA) as internal standard. The SA was isolated from leaf extracts by solid-phase extraction with phenyl-phase cartridges and selectively eluted as the cationic iron(III)-complex. Recoveries of SA and 5-FSA were equal and exceeded 90%. Free SA was subsequently released from the iron(III)-complex by addition of 2,2-bipyridyl and high-performance anion-exchange chromatography was performed on an NH₂ column. The SA appeared as last peak with a retention time of 15 min, baseline-separated from other substances. On-line detection was performed fluorimetrically for both SA and 5-FSA at an excitation wavelength of 300 nm and an emission wavelength of 410 nm, because both substances give similar fluorescence spectra. The detection limit for SA was 5 ng g^–1 FW for a sample size of 100 mg. Thus the main advantages of the method are highly selective sample preparation, increased sensitivity, reduced analysis time compared with reversed-phase HPLC, and use of a novel internal standard detectable under the same conditions as SA. The techniques described are applicable to other plant materials.     

Synthesis and characterization of PAni–SiO2 and PTh–SiO2 nanocomposites' thin films by plasma polymerization

In the present work, we explore the possibility to deposit polyaniline–silicon dioxide (PAni–SiO₂) and polythiophene–silicon dioxide (PTh–SiO₂) nanocomposites through a plasma polymerization route. The films were generated by spraying of mixtures of nano-sized silica particles dispersed in the liquid monomer into a plasma stream of the DC-plasma discharge reactor. The silica in the resulted polymer matrix changes the conduction mechanisms varying from ohmic to ballistic and traps inducing the space charged limited currents (SCLC). The silica modifies the morphology and composition of the deposited films.     

A density functional theory study of the gas-phase elimination reactions of 4-arylideneimino-1,2,4-triazol-3(2H )-ones and their 3(2H )-thione analogues

Theoretical studies on the thermolysis in the gas phase of 4-arylideneimino-1,2,4-triazol-3(2H)-ones and 4-arylideneimino-1,2,4-triazol-3(2H)-thiones were carried out using density functional theory methods, at the B3LYP/6-31G(d) and B3LYP/6-311+G(2d,p) levels of theory. The proposed reaction mechanism occurs in one step, leading to the formation of 3-hydroxy-(2H)-1,2,4-triazole or 3-mercapto-(2H)-1,2,4-triazole and a 4-substituted benzonitrile, via a six-membered cyclic transition state. The progress of the reactions was followed by means of the Wiberg bond indices. The results indicate that the transition states have character intermediate between reactants and products, and the calculated synchronicities show that the reactions are slightly asynchronous, in the case of triazolones, and show a higher asynchronicity in the case of triazolthiones. The bond-breaking processes are slightly more advanced than the bond-forming ones, indicating a small bond deficiency in the transition states. Kinetic and activation parameters for the reactions studied have been calculated and compared with available experimental data.From the Proceedings of the 28th Congreso deQuímicos Teóricos de Expresión Latina (QUITEL 2002)     

Antimalarial activity of n(6)-substituted adenosine derivatives (part 2)

We have investigated the in vitro antimalarial activity of a new series of adenosine derivatives. The results show that N(6)-(1-naphthylmethyl)-5'-deoxy-5'-(amido)adenosines as well as N(6)-(4-phenylbenzyl)-5'-deoxy-5'-(amido)adenosines display significant activity against the malaria-causing parasites, with the sterically demanding bisubstituted species reported being active in most cases in the low-micromolar range. The novel compounds with unusual substitution pattern were obtained applying an efficient convergent polymer-assisted solution-phase (cPASP) synthesis protocol. Thus, we were able to prepare a series of substituted derivatives in parallel that would have been difficult to synthesize by standard techniques. The scope and limitations of the synthetic methodology are discussed.