Unprecedented hour-long residence time of a cation in a left-handed G-quadruplex

Cations are critical for the folding and assembly of nucleic acids. In G-quadruplex structures, cations can bind between stacked G-tetrads and coordinate with negatively charged guanine carbonyl oxygens. They usually exchange between binding sites and with the bulk in solution with time constants ranging from sub-millisecond to seconds. Here we report the first observation of extremely long-lived K⁺ and NH₄⁺ ions, with an exchange time constant on the order of an hour, when coordinated at the center of a left-handed G-quadruplex DNA. A single-base mutation, that switched one half of the structure from left- to right-handed conformation resulting in a right–left hybrid G-quadruplex, was shown to remove this long-lived behaviour of the central cation.

An extremely long-lived cation has been detected in left-handed G-quadruplexes.     

Kinetic Determination of Microquantities of Rutin by Perturbation of the Bray-Liebhafsky Oscillatory Reaction in an Open System

A kinetic method is described for the microquantitative (microconcentration/microvolume) determination of rutin based on potentiometric monitoring of the concentration perturbations of the Bray-Liebhafsky (BL) oscillatory reaction being in a non-equilibrium stationary state close to a bifurcation point. The experiments are carried out in an open reactor. The response of the matrix system to perturbations by different concentrations of rutin ethanolic solutions is followed by a Pt-electrode. In the concentration range between 7.8×10^–8moldm^–3 and 9.1×10^–6mol dm^–3, we found a linear dependence of the maximal potential shift, E_m, on the logarithm of the rutin concentrations. The unknown concentrations can be determined from the calibration curve up to an accuracy of ±5%. The detection limit is 3.6×10^–8mol dm^–3. The amount of required sample can be as small as 10µL.     

Reaction and mass transfer effects in a catalytic monolith reactor

Zeolite-based monoliths (Cu/ZSM-5 on cordierite) are prepared and used to catalyze direct decomposition of nitrogen monoxide. Two-dimensional heterogeneous model is applied to describe the behavior of the monolith reactor, with the emphasis on the features introduced due to coupling of flow, mass transfer and chemical reaction. The proposed model has been verified by comparing computer simulation data with laboratory experimental data. It is shown that both inter- and intraphase diffusion limitations have to be considered when modeling complex reactor configuration, such as monolith reactors, especially when monolith with thicker catalytic layer are used at higher temperatures.     

Influence of response factors on determining equilibrium association constants of non-covalent complexes by electrospray ionization mass spectrometry

A method for determining the equilibrium association constant of a complexation reaction A + B left harpoon over right harpoon AB by electrospray ionization mass spectrometry is described. The method consists in measuring the relative intensities of the peaks corresponding to A and to AB in equimolar A-B solutions at different concentrations C(0). The results are fitted by a non-linear least-squares procedure, with the two variable parameters being the equilibrium association constant K(a) and a factor R, defined by I(AB)/I(A) = R x [AB]/[A]. The factor R is the ratio between the response factors of AB and A, and corrects for the relative electrospray responses of the complex and the free substrate A, mass discrimination of instrumental origin and/or moderate in-source dissociation. The method is illustrated with the following two systems: complexes between a double-stranded 12-base pair oligonucleotide and minor groove binders, and cyclodextrin complexes with alpha,omega-dicarboxylic acids. For the oligonucleotide complexes, it is found that the response of the complex is not dramatically different to the response of the free oligonucleotide duplex, as the double helix conformation is disturbed by the drug only to a minor extent. In the case of cyclodextrin complexes, these complexes were found to have a much higher response than free cyclodextrin. This may be due to the fact that cyclodextrin is neutral in solution, whereas the complex is charged, but it can also stem from the fact that a significant proportion of the complex is in a non-inclusion geometry. The present method requires the exact determination of the concentrations of the reactants and is applicable to 1 : 1 complexes.     

In Situ Amperometric Detection of Vesicles and Microgel Phases in an Aggregating System: Calcium Alginate

In situ amperometric characterization of an aggregating system in terms of molecular adsorption and single microparticle interactions at the electrode interface is demonstrated using a model system: alginate/Ca(II) in an aqueous electrolyte solution. Recording of chronoamperometric curves of oxygen reduction at the dropping mercury electrode is designed for detection of dip‐shaped signals of individual gel microparticles. By addition of Ca(II) decrease of alginate adsorption is accompanied by appearance of signals indicating vesicle type association of alginate molecules and microparticles of gel phase. AFM imaging provided evidence of initial stage in calcium alginate gel formation.     

Triplex and quadruplex DNA structures studied by electrospray mass spectrometry

DNA triplex and quadruplex structures have been successfully detected by electrospray ionization mass spectrometry (ESI-MS). Circular dichroism and UV-melting experiments show that these structures are stable in 150 mM ammonium acetate at pH 7 for the quadruplexes and pH 5.5 for the triplexes. The studied quadruplexes were the tetramer [d(TGGGGT)](4), the dimer [d(GGGGTTTTGGGG)](2), and the intramolecular folded strand dGGG(TTAGGG)(3), which is an analog of the human telomeric sequence. The absence of sodium contamination allowed demonstration of the specific inclusion of n - 1 ammonium cations in the quadruplex structures, where n is the number of consecutive G-tetrads. We also detected the complexes between the quadruplexes and the quadruplex-specific drug mesoporphyrin IX. MS/MS spectra of [d(TGGGGT)](4) and the complex with the drug are also reported. As the drug does not displace the ammonium cations, one can conclude that the drug binds at the exterior of the tetrads, and not between them. For the triplex structure the ESI-MS spectra show the detection of the specific triplex, at m/z values typically higher than those typically observed for duplex species. Upon MS/MS the antigene strand, which is bound into the major groove of the duplex, separates from the triplex. This is the same dissociation pathway as in solution. To our knowledge this is the first report of a triplex DNA structure by electrospray mass spectrometry.     

Interaction between antitumor drugs and a double-stranded oligonucleotide studied by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry was used to investigate the complex formation between a double-stranded oligonucleotide and various antitumor drugs belonging to two categories: intercalators (ethidium bromide, amsacrine and ascididemin) and minor groove binders (Hoechst 33258, netropsin, distamycin A, berenil and DAPI). The goal of this study was to determine whether the relative intensities in the mass spectra reflect the relative abundances of the species in the solution phase. The full-scan mass spectra suggest non-specific binding for the intercalators and specific binding for the minor groove binders. The preferential stoichiometries adopted by each minor groove binder were determined by studying the influence of the drug concentration on the spectra. We obtained 2:1 > 1:1 for distamycin, 1:1 > 2:1 for Hoechst 33258 and DAPI and only the 1 : 1 complex for netropsin and berenil. These features reflect their known behavior in solution. The compared tandem mass spectra of the 1 : 1 complexes with Hoechst 33258 and netropsin, when correlated with published crystallographic data, suggest the possibility of inferring some structural information. The relative binding affinities of the drug for the considered duplex were deduced with two by two competition experiments, assuming that the relative intensities reflect the composition of the solution phase. The obtained affinity scale is netropsin > distamycin A > DAPI > Hoechst 33258 > berenil. These examples show some of the potential uses of mass spectrometry as a useful tool for the characterization of specific drug binding to DNA, and possibly a rapid drug screening method requiring small amounts of materials.     

Thermogravimetric and EPR study of the solid-state reactions between zinc chromate and zinc oxalate

The formation of some catalytically active Cr(V) and Cr(III) species is studied when the progressive thermal reduction of zinc chromate is enhanced by the addition of solid zinc oxalate, the reducing agent CO being formed in situ, during thermal analysis.When compared with the decomposition of pure ZnCrO₄, Cr(VI) reduction, as followed by EPR, is similar concerning the nature of the intermediate Cr species formed: Cr(V), Cr(III) in a Cr₂O₃-like bulk phase and Cr(III) dispersed in ZnO. However, the temperature range of Cr₂O₃ formation, as well as the magnitude of the Cr(III)-Cr(III) interaction in such a phase is found to be strongly dependent on the amount of ZnO formed. On the other hand, after the Cr(V) species resulting from progressive oxygen release have disappeared, some other stable Cr(V) species are formed again at higher temperatures. Their formation may be related to a further reduction of the remaining Cr(VI) species by CO stemming from the oxalate.

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Zusammenfassung Die Bildung einiger katalytisch aktiver Cr(V) und Cr(III) Species wird für den Fall untersucht, bei dem die progressive thermische Reduktion von Zinkchromat durch Zugabe von festem Zinkoxalat gefördert wird, wobei das Reduktionsmittel CO in situ, während der Thermoanalyse gebildet wird.Ein Vergleich mit der Zersetzung der reinen ZnCrO₄ ergibt die ÄhnIichkeit der durch EPR verfolgten Cr(VI)-Reduktion hinsichtlich der Beschaffenheit der gebildeten Cr Intermediärspecies: Cr(V), Cr(III) in einer Cr₂O₃-artigen Hauptphase und Cr(III) in ZnO dispergiert. Jedoch sind Temperaturbereich der »Cr₂O₃«-Bildung sowie der Umfang der Cr(III)-Cr(III) Wechselwirkung in einer solchen Phase stark von der Menge des gebildeten ZnO abhängig. Andererseits werden nach dem Verschwinden der durch die progressive Sauerstoff-Freisetzung entstandenen Cr(V)-Species wider einige andere stabile Cr(V)-Species bei höheren Temperaturen gebildet. Ihre Bildung mag mit einer weiteren Reduktion der noch vorhandenen Cr(VI)-Species durch aus dem Oxalat stammendes CO verbunden sein.

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Cr(V) Cr(III) , , , , . , Cr(VI), ZnCrO₄ . , Cr : Cr(V) Cr(III) , Cr₂₃, Cr(III) ZnO. , «Cr₂₃», Cr(III)-Cr(III) . , , Cr(V) , Cr(V) . Cr(VI) , .

     

TG and DSC investigation of the dehydration of the extra large pore aluminophosphate molecular sieve VPI-5 and related materials

The dehydration of a series of VPI-5 and H3 samples, synthesized under various conditions, as well as the solid state transformation of VPI-5 to AlPO₄-8 have been investigated using combined TG-DTG-DSC and high-resolution solid state³¹P-NMR. The TG curves show a quasi-continuous release of water, the total loss being characteristic for each sample. Complete dehydration is achieved when the samples are heated from 20°C to about 150°C at various beating rates. Besides the main dehydration effect, several weak endothermic peaks are observed. These generally non-reproducible modulated peaks, recorded at high heating rates, are presumably due to the interactions of the water molecules leaving the channels of VPI-5 with the randomly positioned fragments stemming from the destruction of the water triple helix assemblage. The non-isothermal kinetic parameters of the dehydration have been evaluated from the TG and DTG curves recorded at low heating rates. In celebration of the 60^th birthday of Dr. Andrew K. Galwey