Circular dichroism signatures of features simultaneously present in structured guanine-rich oligonucleotides: a combined spectroscopic and electrophoretic approach

In order to identify possible signatures of the most typical structures adopted by guanine-rich oligonucleotides, we submitted them to the crossed fire of circular dichroism (CD) and electrophoresis. These signatures show up in the circular dichroism spectra even when simultaneously present within the same molecule. Guanine-rich oligonucleotides, when structured, manifest themselves by CD contributions around 260 or 295 nm. For instance, positive bands at 264 nm and 295 nm, respectively, signal the parallel and antiparallel guanine quartets, while a positive band around 261 nm may indicate the presence of a (parallel?) Hoogsteen duplex. A positive band at 264 nm may also reflect the presence of rigidly and unusually oriented GpT and TpG steps within loops. The signatures are additive with those of other structural features of the same molecule, such as hairpins or Watson-Crick duplexes, whose bands are observed at 280 nm.     

Development and validation of a liquid chromatography-ultraviolet absorbance detection assay using derivatisation for the novel marine anticancer agent ES-285 x HCl [(2S,3R)-2-amino-3-octadecanol hydrochloride] and its pharmaceutical dosage form

ES-285 x HCl [(2S,3R)-2-amino-3-octadecanol hydrochloride] is a novel investigational anticancer agent, which has shown in vitro and in vivo cytotoxic activity against various tumor cell lines with selectivity for certain solid tumors. The pharmaceutical development of ES-285 x HCl warranted the availability of an assay for the quantification and purity determination of ES-285 x HCl active pharmaceutical ingredient (API) and its pharmaceutical dosage form. A liquid chromatographic method (LC) comprising of derivatisation of ES-285 x HCl with phenylisothiocyanate and UV-detection was developed. The method was found to be linear, precise and accurate. The assay also proved selectivity as determined by analysing ES-285 x HCl in combination with 15 analogues and in combination with hydroxypropyl-beta-cyclodextrin, the excipient used in the lyophilised pharmaceutical dosage form. Stress testing showed that the degradation products were separated from the parent compound, confirming its stability indicating capacity. The method was found robust as determined with design of experiments (DoE), which made it possible to predict system suitability responses in worst case experimental conditions and to define criteria for system suitability testing.     

Single-run analysis of retinal isomers, retinol and photooxidation products by high-performance liquid chromatography

A high-performance liquid chromatographic (HPLC) procedure was developed to allow the rapid separation, in a single run, of a mixture of the main retinal isomers (all-trans, 13-cis, 9-cis), all-trans-retinol, and of the two major photooxygenated photoproducts (5,8-peroxyretinal and 5,6-epoxyretinal). The mixture was separated by HPLC on an octadecyl (ODS) column with 16% (v/v) diethyl ether in hexane as mobile phase and anthracene as the internal standard. A commercial type cosmetic formulation containing 0.05% all-trans-retinal was analyzed successfully for this analyte.     

The thermodynamic properties of acetals+heptane mixtures at 298.15 K

Excess enthalpies and excess volumes were determined at 298.15 K for: dimethoxymethane+heptane, diethoxymethane+heptane, 1,1-dimethoxyethane+heptane, 1,1-diethoxyethane+heptane, 2,2-dimethoxypropane+heptane and 1,1-diethoxypropane+heptane.     

Assessing weak intramolecular donor-acceptor interactions using 1H-117Sn J-HMQC spectroscopy

It is demonstrated that long-range nJ(1H,117Sn) coupling constants down to 0.3 Hz, can be accurately quantified from non-linear fitting of the sine modulation of the associated 1H-117Sn correlation cross-peak intensities sampled as a function of the heteronuclear antiphase coherence preparation time in the 1H-117Sn J-HMQC pulse sequence. The contribution of additional, undesired modulations is illustrated and assessed using the product operator formalism, and is traced back to contributions that arise from miss-setting of the wandering 180 degrees pulse angle in the constant time period. The power of the method and its use in the characterization of weak intramolecular donor-acceptor interactions are illustrated by the determination of long-range nJ(1H,117Sn) coupling constants of bis[3-(dimethylamino)propyl]tin derivatives, [Me2N(CH2)3]2SnR2 (', R = Me; 3, R = Ph; 4, R = t-Bu). By comparing these with the values found for the corresponding bis(4-methylpentyl)tin derivatives, [Me2CH(CH2)3]2SnR2 (2', R = Me; 3', R = Ph), which lack such interactions, the use of long-range coupling constants to detect intramolecular donor-acceptor interactions is evaluated. It is concluded that nJ(1H,117Sn) couplings up to six bonds through an organic carbon chain can be quantified, whether donor-acceptor interactions are present or not. Furthermore, evidence is presented that, when two scalar coupling pathways co-exist, the pathway involving an intramolecular donor-acceptor interaction can have opposite sign, thus decreasing the overall coupling constant to a value smaller than that actually measured in the absence of a donor-acceptor interaction, where only one coupling pathway is active. There is nevertheless clear numerical value discrimination in the series of compounds investigated between long-range couplings in derivatives without weak intramolecular donor-acceptor interactions and those where such interactions can exist.     

A doubly deprotonated form of calix[6]arene: Crystal and molecular structure of (calix[6]arene-2H)2−·(HNEt 3 + )2

The doubly deprotonated form of calix[6]arene, with two protonated triethylamines as counter-ions, crystallizes in the monoclinic system: space groupP2₁/n,a=8.465(4),b=17.822(8),c=15.182(6) Å,=90.18(4)°,V=2291(2) ų,Z=2. Refinement led to a final conventionalR value of 0.063 for 1046 reflections. The macrocycle conformation is not apinched cone, usual for freeR-calix[6]arene, but a distorted 1,2,3-alternate cone, since the molecule lies on a symmetry center. Furthermore, one of the torsion angles defined by the methylene bridges is near to zero, which is unusual in calixarene structures. Supplementary Data relating to this article (atomic coordinates for hydrogen atoms, anisotropic displacement parameters for oxygen and nitrogen atoms, and observed and calculated structure factors) are deposited with the British Library as Supplementary Publication No. SUP 82182 (7 pages).     

PHOTOSENSITIZING PROPERTIES OF BACTERIOCHLOROPHYLLIN a and BACTERIOCHLORIN a, TWO DERIVATIVES OF BACTERIOCHLOROPHYLL a

Abstract The photosensitizing properties of two water soluble derivatives of bacteriochlorophyll a , bacteriochlorophyllin a and bacteriochlorin a (lacking the central Mg-ion) were investigated and compared to those of hematoporphyrin derivatives. At physiological pH the oxygen consumption rate of histidine, tryptophan, dithiothreitol and guanosine upon illumination was 3 to 4 times higher when bacteriochlorin a was used as photosensitizer than when hematoporphyrin derivatives were used. Especially bacteriochlorin a proved to be an effective sensitizer for the killing of L929 cells. Because bacteriochlorin a has an absorption maximum at 765 nm in phosphate buffered saline (allowing a light penetration in tissue about ten times larger than at 630 nm) and a high molar absorption coefficient (32 000 M cm⁻¹) it has promising possibilities for the application in photodynamic therapy.     

Effect of dose rate of gamma irradiation on biochemical quality and browning of mushrooms Agaricus bisporus

In order to enhance the shelf-life of edible mature mushrooms Agaricus bisporus, 2 kGy ionising treatments were applied at two different dose rates: 4.5 kGy/h (I⁻) and 32 kGy/h (I⁺). Both I⁺ and I⁻ showed 2 and 4 days shelf-life enhancement compared to the control (C). Before day 9, no significant difference (p>0.05) in L^* value was detected in irradiated mushrooms. However, after day 9, the highest observed L^* value (whiteness) was obtained for the mushrooms irradiated in I⁻. Analyses of phenolic compounds revealed that mushrooms in I⁻ contained more phenols than I⁺ and C, the latter containing the lower level of phenols. The polyphenol oxidase (PPO) activities of irradiated mushrooms, analysed via catechol oxidase and dopa oxidase substrates, resulted in being significantly lowered (p0.05) compared to C, with a further decrease in I⁺. Analyses of the enzymes indicated that PPO activity was lower in I⁺, contrasting with its lower phenol concentration. Ionising treatments also increased significantly (p0.05) the phenylalanine ammonia-lyase (PAL) activity. The observation of mushrooms cellular membranes, by electronic microscopy, revealed a better preserved integrity in I⁻ than in I⁺. It is thus assumed that the browning effect observed in I⁺ was caused by both the decompartimentation of vacuolar phenol and by the entry of molecular oxygen into the cell cytoplasm. The synergetic effect of the residual active PPO and the molecular oxygen, in contact with the phenols, allowed an increased oxidation rate and, therefore, a more pronounced browning in I⁺ than in I⁻.     

Does alpha-fluorination affect the structural trans-influence and kinetic trans-effect of an alkyl ligand? Molecular structures of Pd(TMEDA)(CH(3))(R(F)) and a kinetic study of the trans to cis isomerization of Pt(TMEDA)(CH(3))(2)I(R(F)) [R(F) = CF(2)CF(3), CFHCF(3), CH(2)CF(3)

Reaction of Pd(TMEDA)(CH(3))(2) [TMEDA = tetramethylethylenediamine] with fluoroalkyl iodides R(F)I affords a series of square planar Pd(II) complexes Pd(TMEDA)(CH(3))(R(F)) [R(F) = CF(2)CF(3) (9), CFHCF(3) (10), CH(2)CF(3) (11)], presumably by oxidative addition followed by reductive elimination of CH(3)I. The solid-state structures of each compound have been determined by single crystal X-ray diffraction studies, allowing the effect of increasing alpha-fluorination on the structural trans-influence of alkyl ligands to be examined. In these compounds there is no significant difference observed in the trans-influence of the three fluorinated alkyl ligands toward the trans-N atom, although a significant cis-influence on the neighboring methyl ligand is apparent. Oxidative addition of the same series of fluoroalkyl ligands to the corresponding Pt(TMEDA)(CH(3))(2) affords octahedral Pt(IV) complexes trans-Pt(TMEDA)(CH(3))(2)(R(F))I [R(F) = CF(2)CF(3) (12), CFHCF(3) (13), CH(2)CF(3) (14)] as the kinetic products. In each case, subsequent isomerization to the corresponding all cis-isomers is observed; in the case of 13, the stereocenter at the alpha-carbon results in two diastereomeric cis-isomers, which are formed at different rates. The molecular structures of 13 and its more stable all cis-isomer 16b have been crystallographically determined. Kinetic studies of the trans-cis isomerization reactions show the mechanism to involve a polar transition state, presumably involving iodide dissociation, followed by rearrangement of the cation, and iodide recombination. High dielectric solvents increase the rate, but solvent coordinating ability has no effect. Dissolved salts (LiI, LiOTf) show normal accelerative salt effects, with no inhibition in the case of added iodide, consistent with the formation of an intimate ion pair intermediate. The kinetic parameters show that the trans-effects of fluoroalkyl ligands in these compounds follow the order expected from the relative sigma-donor properties of the ligands, with CF(2)CF(3) < CFHCF(3) < CH(2)CF(3).     

Laser-induced fluorescence detection schemes for the analysis of proteins and peptides using capillary electrophoresis

Over the past few years, a large number of studies have been prepared that describe the analysis of peptides and proteins using capillary electrophoresis (CE) and laser-induced fluorescence (LIF). These studies have focused on two general goals: (i) development of automatic, selective and quick separation and detection of mixtures of peptides or proteins; (ii) generation of new methods of quantitation for very low concentrations (nm and subnanomolar) of peptides. These two goals are attained with the use of covalent labelling reactions using a variety of dyes that can be readily excited by the radiation from a commonly available laser or via the use of noncovalent labelling (immunoassay using a labelled antibody or antigen or noncovalent dye interactions). In this review article, we summarize the works which were performed for protein and peptide analysis via CE-LIF.