Molecular mechanics and dynamics of DNA-furocoumarin complexes: effect of the aromatization of the pyrone ring on the intercalation geometry

Results of molecular mechanics and dynamics calculations on intercalation complexes of DNA with various furocoumarins (psoralen, angelicin, 7-methylpyrido[3,4-c]psoralen and 7-methylpyrido[4,3-c]psoralen) and their corresponding aromatized derivatives are presented. These calculations were undertaken with the aim to elucidate the roles of the pyrone and pyridine moieties in the interactions which tend to orient the furocoumarins and pyridopsoralens between DNA base pairs. It appears that the intercalation geometries are very similar for the furocoumarins and related aromatized compounds. Therefore the oxygen and nitrogen atoms of the pyrone and pyridine moieties are not important in the orientation of the drug within the oligonucleotide.     

Synthesis,Characterization and Applications of Immobilized Iminodiacetic Acid-Modified Silica

Porous immobilized iminodiacetic acid modified silica of the general formula S—(CH₂)₃—N(CH₂COOH)₂, (where S represents [Si—O] _n siloxane network) has been prepared by replacement of the iodide in 3-iodopropyl modified silica with diethyliminodiacetate. The immobilized-diethyliminodiacetate ligand system (S-DIDA) was then hydrolyzed by hydrochloric acid to produce the immobilized iminodiacetic acid ligand system (S-IDA). The iodo functionalized modified silica (S-I) was prepared by polycondensation of Si(OEt)₄ and (MeO)₃Si(CH₂)₃I. The XPS and CP/MAS ¹³C NMR spectra showed that not all iodine atoms are replaced and that the hydrolysis of ethyl acetate groups are incomplete upon treatment with HCl. The immobilized iminodiacetic acid ligand system exhibits high potential for the uptake of various di- and trivalent metal ions such as (Mn²⁺, Fe³⁺, Co²⁺, Ni²⁺, Cu²⁺ and Zn²⁺). Complexation of the iminodiacetate ligand system for the metal ions at the optimum conditions was found in the order: Cu²⁺ > Fe³⁺ > Ni²⁺ > Co²⁺ > Mn²⁺ > Zn²⁺. Stability studies of the iminodiacetate ligand system showed that a degradation of the siloxane network and leaching of some species occurred upon treatment with strong acid and base aqueous solutions.     

A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA

The effect of interaction with DNA and oligonucleotides on the photophysical properties of two thiazole orange (TO) derivatives, with different side chains (-(CH2)3-N+(CH3)3 and -(CH2)6-I)) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one called TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to oligonucleotides with the aim of being used for specific in situ detection of biomolecular interactions. Both photophysical measurements and molecular calculations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 x 10(-5) and 2 x 10(-4), respectively. However, upon binding to double-stranded DNA, large spectroscopic changes result and the quantum yield of fluorescence is enhanced by four orders of magnitude, reaching values up to phi F = 0.2 and 0.3, respectively, as a result of an intercalation mechanism between DNA base pairs. A modulation of the quantum yield is observed as a function of the base sequence. The two derivatives also bind with single-stranded oligonucleotides, but the fluorescence quantum yield is not so great as that when bound to double-stranded samples. Typical fluorescence quantum yields of 7 x 10(-3) to 3 x 10(-2) are observed when the dyes interact with short oligonucleotides, whereas the fluorescence quantum yield remains below 10(-2) when interacting with single-stranded oligonucleotides. This slight but significant quantum-yield increase is interpreted as a folding of the single strand around the dye, which reduces the internal rotation of the two heterocycles around the central methine bridge that links the two moieties of the dye. From these properties, it is proposed to link monomer covalently to oligonucleotides for the subsequent detection of target sequences within cells.     

Thermal decomposition of stichtite

The mineral stichtite was synthesised and its thermal decomposition measured using thermogravimetry coupled to an evolved gas mass spectrometer. Mass loss steps were observed at 52, 294, 550 and 670°C attributed to dehydration, dehydroxylation and loss of carbonate. The loss of carbonate occurred at higher temperatures than dehydroxylation.     

Grafting of swelling clay materials with 3-aminopropyltriethoxysilane

The grafting reaction between a trifunctional silylating agent and two kinds of 2:1 type layered silicates was studied using FTIR, XRD, TGA, and 29Si CP/MAS NMR. XRD patterns clearly indicate the introduction of 3-aminopropyltriethoxysilane (gamma-APS) into the clay interlayer. In the natural montmorillonite, gamma-APS adopts a parallel-bilayer arrangement, while it adopts a parallel-monolayer arrangement in the synthetic fluorohectorite. These different silane arrangements have a prominent effect on the mechanism of the condensation reaction within the clay gallery. In natural montmorillonite, the parallel-bilayer arrangement of gamma-APS results in bidentate (T2) and tridendate (T3) molecular environments, while the parallel-monolayer arrangement leads to monodentate (T1), as indicated by 29Si CP/MAS NMR spectra. This study demonstrates that the silylation reaction and the interlayer microstructure of the grafting products strongly depend on the original clay materials.     

Spectroscopic investigation of interactions between dipeptides and vanadate(V) in solution

The reaction of vanadate(V) with a series of dipeptides (Val-Gln, Ala-Gln, Gly-Gln, Gly-Glu, and Ala-Gly) was investigated by UV-visible spectroscopy and multinuclear ((51)V, (14)N, (13)C) NMR spectroscopy in solution. It was possible to evaluate the formation constants of the corresponding complexes for which a molecular structure was proposed. Complex formation is favored by the presence of a functionalized or a sterically demanding side chain. The Val-Gln dipeptide which combines both properties exhibits one of the highest formation constant reported so far for dipeptides.     

Oncidinol—a novel diacylglycerol from Ornithophora radicans Barb. Rodr. (Orchidaceae) floral oil

The structure and absolute configuration of a novel diacylglycerol, (2S,3′R,6′R)-1-acetyl-2-[3′,6′-diacetoxyeicosanyl)-glycerol 1, named oncidinol, from the Ornithophora radicans floral oil was elucidated from spectroscopic data and by applying the Mosher method.     

Regioselectivity in aromatic Claisen rearrangements

Theoretical calculations and the isomeric product composition for a series of eight meta-substituted allyl aryl ethers confirm the reliability of a new (1)H NMR methodology used to predict aromatic Claisen regioselectivity from ground-state conformational preference of the reactant allyloxy group. Frontier HOMO-LUMO intramolecular orbital interactions, a classical approach in predicting reactivity and selectivity for Claisen rearrangements of allyl vinyl ethers, is shown to fail to mimic transition-state orbital interactions for aromatic Claisen rearrangements of meta-substituted allyl aryl ethers. B3LYP/6-31G(d,p) calculations on reactants and transition states are shown, however, to correctly predict the outcome of such aromatic Claisen rearrangements from either the preferential reactant ground-state conformation (theoretical predictions that agree with the NMR measurements) or the less energetic transition state, or both.     

INTRAMOLECULAR ENERGY TRANSFER IN NATIVE tRNA AT ROOM TEMPERATURE

Abstract— The odd nucleoside 4-thiouridine, which is present in position 8 of 70% of E. coli tRNAs, possesses unusual spectroscopic properties which make it suitable for intramolecular energy transfer studies. Both its luminescence excitation spectrum and the action spectrum (230–380 nm) for the 8–13 link formation have been established in native E. coli tRNA at room temperature. The spectra are identical and present a new unexpected peak around 260 nm. At this wavelength, they are amplified by a factor of nine as compared with the absorption and excitation spectra of the free nucleoside in aqueous solution.
The origin of this new peak is discussed and it is concluded that energy transfer does occur from the common nucleosides to the 4-thiouridine residue. Using the values of the nucleosides to 4-thiouridine distances inferred from the sets of atomic coordinates obtained on yeast tRNA^phe crystals, a satisfactory account of our finding can be obtained assuming singlet-singlet energy transfer. The efficiency of the mechanism is probably favoured by a good overlap between the emission spectra of the common nucleosides and the absorption spectrum of 4-thiouridine.     

Ab-initio study of Na n F n and Na n F n−1 clusters: atypical structures

Alkali halide clusters Na _n F _n have most frequently cuboid structures and Na _n F _n?1 clusters are derived from Na _n F _n by removing a F^? centre. An excess electron localises on the site of the removed F^? ion. In this paper, other kind of clusters are studied at the SCF level: i) The non-cubic structures. ii) The cubic Na _n F _n?1 for which the excess electron has no defined site. Due to very large size of these species (at least 27 atoms!) some equivalent fictive linear and planar geometries are studied.