Method for detection of single-base mismatches using bimolecular beacons

This paper describes a method for the detection of single-base mismatches using DNA microarrays in a format that does not require labeling of the sample ("target") DNA. The method is based on disrupting fluorescence energy transfer (FRET) between a fluorophore attached to an immobilized DNA strand ("probe") and a quencher-containing sequence that is complementary except for an artificial mismatch (e.g. 5-nitroindole, 3-nitropyrole, or abasic site) at the site of interrogation. As the displacement of the FRET acceptor and hybridization of the unlabeled probe are bimolecular, the term "bimolecular beacons" is used to describe this approach. The analysis of a mismatch was based on differences in the amount of disruption in FRET upon hybridization of perfectly matched DNA targets and those containing single-base mismatches. Using this method and an oligonucleotide model system, A/C single-base mismatches were successfully discriminated at levels greater than that observed using surface-immobilized molecular beacons. The amount of discrimination was dependent on the identity of the artificial mismatch; greater discrimination was observed with 5-nitroindole (a "universal" base) than with an abasic site. G/T mismatches, considered to be particularly difficult to detect, were also successfully discriminated when quencher sequences containing 5-nitroindole were used.     

A variational coupled cluster theory for closed shells using a propagator modification procedure

A general partial summation method for including arbitrary classes of diagrams to all orders in the coupled cluster based size consistent energy functional for closed shell states is developed. Since the various reduced density matrices which appear in the energy functional are essentially the time-independent analogues of the corresponding many body Green functions, it is possible to derive Dyson-like equations for these quantities. By expanding the associated proper self energy parts in terms of the T-amplitudes, one can carry out partial summations in the reduced density matrices and thus in energy. At a higher level, higher order terms in a proper self energy can also be generated by renormalizing the internal propagators in it, and considering only the irreducible self-energy terms.     

Application of nanosized zeolites in methanol conversion processes: A short review

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Investigation of the separation efficiency in one-stage and multistage extractions by a numerical method

Theoretical separation efficiencies in one-stage static and multistage dynamic models of liquid-liquid extraction have been studied mathematically. By the use of the iterative numerical method the maximum difference between separation efficiencies in these two models, as well as the absolute values of the respective separation efficiencies were calculated at this maximum. The maximum difference between multistage and one-stage separation efficiencies amounts to 20.36%, when the respective separation efficiencies are about 91.89% and 71.56%.     

Favorable interactions of amine- and ester-terminated PAMAM with cationic surfactants: photophysical and transport studies

Conductivity (kappa), turbidity (tau), and fluorescence (I1/I3) studies of hexadecyltrimethylammonium bromide (HTAB), hexadecylpyridinium bromide (HPyBr), and hexadecylpyridinium chloride (HPyCl) in aqueous poly(amido amine) (PAMAM) dendrimers of generations 0 to 2.5 G have been carried out. The complexation of surfactant monomers with the PAMAM surface groups is demonstrated by the critical aggregation concentration (cac), which is two to three orders of magnitude less than the micellization of cationic surfactants in aqueous PAMAM and denoted by critical micelle concentration (cmc*). In the presence of aqueous amine-terminated PAMAM, the cmc* value for each surfactant was much lower than the cmc in pure water, while they remain close to each other in the presence of aqueous ester-terminated PAMAM for each surfactant. The fluorescence studies demonstrated that both amine- and ester-terminated PAMAM interact with the cationic surfactants, though the mode of interaction varied due to the different nature of surface groups.     

Complexation of 6-Deoxy-6-(aminoethyl)amino-β-cyclodextrin with Sodium Cholate and Sodium Deoxycholate

In order to study its guest binding and the inclusion phenomena, 6-deoxy-6-(aminoethyl)amino--cyclodextrin (CDN) was synthesised and its binding properties examined. The complexation phenomena of sodium cholate (NaC) and sodium deoxycholate (NaDC) with CDN has been monitored by the NMR method using ¹³C chemical shift data. The method of continuous variation Job's method has been used to determine the stoichiometry of these supramolecular complexes. The Job's plot confirms the 1 : 1 supramolecular complex for NaC: CDN and the 1 : 2 supramolecular complex for NaDC: CDN. The interaction of NaC and NaDC with CDN has been obtained through two-dimensional Rotational Nuclear Overhauser Effect Spectroscopy (ROESY) NMR. Equilibrium constants were also obtained from ¹³C chemical shift data (C-1, C-3 & C-4) at different pH values (7, 9, & 11).     

Oxomolybdenum(VI) and (IV) complexes of pyrazole derived ONO donor ligands – synthesis,crystal structure studies and spectroelectrochemical correlation

Four cis-dioxomolybdenum complexes of general formula [MoO₂(Lⁿ)EtOH] (n = 1–4) and one oxomolybdenum(IV) complex [MoO(L⁴)EtOH], with potentially tridentate Schiff bases derived from 5-methyl pyrazole-3-carbohydrazide and salicylaldehyde/substituted salicylaldehyde/o-hydroxy acetophenone have been prepared. The Mo(IV) complex is derived from the Mo(VI) dioxo complex by oxotransfer reaction with PPh₃. The complexes are characterized by elemental analysis, electronic spectra, IR, ¹H NMR, and by cyclic voltammetry. All the Mo(VI) species are crystallographically characterized. The complexes have a distorted octahedral structure in which the ligand behaves as a binegative donor one, leaving the pyrazole –N uncoordinated towards the metal center. It is also revealed from the crystal structure that the Mo(VI) center enjoys an NO₅ donor environment.     

Dual Solvatochromism of Neutral Red

Abstract— The effect of solvent polarity on the electronic absorption and fluorescence properties of neutral red (NR), a phenazine-based dye of biological importance has been investigated in several neat and mixed solvents. An unusual dual solvatochromic behavior has been observed that reveals the existence of two closely spaced electronic excited states in NR. In low-polarity solvents the fluorescence of the NR is mainly emitted from the localized excited state, whereas in high-polarity solvents the emission from the charge transfer state dominates. The dipole moments of the localized and charge transfer states of NR have been estimated from the solvatochromic shifts. The dipole moment of the localized excited state (4.8 D) is only slightly higher than that of the ground state (2.0 D), while that of the charge transfer state is drastically higher (17.5 D). Fluorescence quantum yields and the life-times of NR have been determined in different solvents and correlated with the solvatochromic shifts.     

Experimental and theoretical study of the reaction between bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine and 2-[(2-allylphenoxy)methyl]oxirane

In reactions of bicyclo[2.2.1]hept-5-en-endo-2-ylmethylamine with 2-[(2-allylphenoxy)methyl]oxirane alongside the product of amine monoalkylation a compound was obtained and isolated by chromatography on silica gel resulting from the reaction of the monoalkylated substance with the initial epoxide. The structure of new aminoalcohols and the regiochemistry of the oxirane opening were examined using IR, 1H NMR, and mass spectra. The features of the reaction mechanism were considered applying quantum-chemical calculations in the level of theory PCM/B3LYP/6-3aG(d).     

Polyhydroxamic Acid Sorbents for Uranium Recovery

Crosslinked polyacrylamides were synthesized by solution polymerization using benzoyl peroxide as the radical initiator. The water–insoluble polymer obtained was functionalized by reacting with hydroxylamine to convert the amide group into hydroxamic acid group. The resultant functionalized polymer was characterized in terms of moisture uptake, elemental composition, IR spectra, thermal stability, exchange capacity and heavy metal sorption. The sorbent, obtained in particulate form, was investigated for its sorption properties with respect to uranium from uranyl nitrate solutions under unstirred batch conditions. This paper will concentrate on preparation, characterization and performance evaluation with respect to uranium sorption as a function of concentration, time, solution pH and temperature. The potential of this sorbent for uranium and other heavy metal ion recovery from sea water is ascertained.