Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

Since the discovery of the intercalative binding mode, almost half a century ago, intense efforts have been devoted to design, synthesize and test new small molecules that can bind nucleic acids with improved recognition and affinity. Among them, metal bearing compounds play a principal role. Despite the plethora of different metal complexes which have been designed to react with DNA and which have been tested, the binding mechanisms have often not been analysed. This is unfortunate, considering the importance of understanding of the binding features in depth in order to optimise their biological effects. This review covers articles where an analysis of the kinetic aspects of the interaction between the target metal compound and nucleic acids has been carried out and details of the reaction mechanism are provided. Flat metal complexes (porphyrins), spherical complexes with protruding intercalating residues, azamacrocycle metallo-intercalators and intercalators with metal bearing pendant arms are the classes of molecules that have been taken into account. The limits of the SDS method, employed to measure the rates of drug dissociation from polynucleotides, are also discussed.     

钙铝层状双氢氧化物的改性及表征

采用离子交换法,将铝酸三钙(C3A)投加至十二烷基硫酸钠(sodium dodecyl sulfate,SDS)溶液中,通过调节pH值和反应温度,制备出插入SDS阴离子的钙铝层状双氢氧化物(CaAl-SDS-layered double hydroxide,CaAl-SDS-LDH)。通过X射线衍射、红外光谱、透投射电镜及热重-差热分析等手段对样品分析表征。结果表明,在SDS浓度为0.2mol·L-1,pH值11,合成温度25℃为最佳合成工艺条件,所得CaAl-SDS-LDH层间距为2.79nm,SDS阴离子在层间以双分子层的形式垂直于层板形成交错有序的排布;CaAl-SDS-LDH中有机物质量分数为40%。经SDS改性后的CaAl-SDS-LDH具有层状结构,晶粒尺寸较小,粒径分布集中,晶粒有序度较高。     

Water-promoted unprecedented chemoselective nucleophilic substitution reactions of 1,4-quinones with oxygen nucleophiles in aqueous micelles

Unique nucleophilic substitution and addition reactions of nitrogen and sulfur nucleophiles with 1,4-quinones in aqueous suspension with amines and thiols have recently been demonstrated by us.² However, the reactivity of oxygen nucleophiles toward nucleophilic substitution compared to nitrogen and sulfur nucleophiles ‘on water’ is not facile. An unprecedented economical, green methodology approach using ordinary laundry detergent (LD; washing powder, 0.5 mol %, reusable)/SDS as surfactant ‘in water’ for nucleophilic substitution by oxygen nucleophiles in 1,4-quinones in excellent yields has been demonstrated.     

Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis

Sample preparation is a fundamental step in proteomic methodologies. The quality of the results from a proteomic experiment is dependent on the nature of the sample and the properties of the proteins. In this study, various pre-treatment methods were compared by proteomic analysis; we analysed various rat brain structures after chloroform/methanol, acetone, TCA/acetone and TCA protein precipitation procedures. The protein content of the supernatant was also examined by 2-DE. We found that for four of the rat brain structures, precipitation with chloroform/methanol and acetone delivered the highest protein recovery for top-down proteomic analysis; however, TCA precipitation resulted in good protein separation and the highest number of protein spots in 2-DE. Moreover, TCA precipitation also gave high efficiency of protein recovery if prior sonication procedure was performed.     

Loss of PEG chain in routine SDS‐PAGE analysis of PEG‐maleimide modified protein

SDS‐PAGE represents a quick and simple method for qualitative and quantitative analysis of protein and protein‐containing conjugates, mostly pegylated proteins. PEG‐maleimide (MAL) is frequently used to site‐specifically pegylate therapeutic proteins via free cysteine residue by forming a thiosuccinimide structure for pursuing homogeneous products. The C–S linkage between protein and PEG‐MAL is generally thought to be relatively stable. However, loss of intact PEG chain in routine SDS‐PAGE analysis of PEG‐maleimide modified protein was observed. It is a thiol‐independent thioether cleavage and the shedding of PEG chain exclusively happens to PEG‐MAL modified conjugates although PEG‐vinylsulfone conjugates to thiol‐containing proteins also through a C–S linkage. Cleavage kinetics of PEG40k‐MAL modified ciliary neurotrophic factor showed this kind of degradation could immediately happen even in 1 min incubation at high temperature and could be detected at physiological temperature and pH, although the rate was relatively slow. This may provide another degradation route for maleimide‐thiol conjugate irrespective of reactive thiol, although the specific mechanism is still not very clear for us. It would also offer a basis for accurate characterization of PEG‐MAL modified protein/peptide by SDS‐PAGE analysis.     

On the interaction of bovine serum albumin with ionic surfactants: temperature induced EPR changes of a maleimide nitroxide reflect local protein dynamics and probe solvent accessibility

The interaction of bovine serum albumin (BSA) with the ionic surfactants sodium dodecylsulfate (SDS, anionic), cetyltrimethylammonium chloride (CTAC, cationic) and N-hexadecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate (HPS, zwitterionic) was studied by electron paramagnetic resonance (EPR) spectroscopy of spin label covalently bound to the single free thiol group of the protein. EPR spectra simulation allows to monitor the protein dynamics at the labeling site and to estimate the changes in standard Gibbs free energy, enthalpy and entropy for transferring the nitroxide side chain from the more motionally restricted to the less restricted component. Whereas SDS and CTAC showed similar increases in the dynamics of the protein backbone for all measured concentrations, HPS presented a smaller effect at concentrations above 1.5mM. At 10mM of surfactants and 0.15 mM BSA, the standard Gibbs free energy change was consistent with protein backbone conformations more expanded and exposed to the solvent as compared to the native protein, but with a less pronounced effect for HPS. In the presence of the surfactants, the enthalpy change, related to the energy required to dissociate the nitroxide side chain from the protein, was greater, suggesting a lower water activity. The nitroxide side chain also detected a higher viscosity environment in the vicinity of the paramagnetic probe induced by the addition of the surfactants. The results suggest that the surfactant-BSA interaction, at higher surfactant concentration, is affected by the affinities of the surfactant to its own micelles and micelle-like aggregates. Complementary DLS data suggests that the temperature induced changes monitored by the nitroxide probe reflects local changes in the vicinity of the single thiol group of Cys-34 BSA residue.     

Automated flow-based anion-exchange method for high-throughput isolation and real-time monitoring of RuBisCO in plant extracts

In this work, a miniaturized, completely enclosed multisyringe-flow system is proposed for high-throughput purification of RuBisCO from Triticum aestivum extracts. The automated method capitalizes on the uptake of the target protein at 4 °C onto Q-Sepharose Fast Flow strong anion-exchanger packed in a cylindrical microcolumn (105 × 4 mm) followed by a stepwise ionic-strength gradient elution (0-0.8 mol/L NaCl) to eliminate concomitant extract components and retrieve highly purified RuBisCO. The manifold is furnished downstream with a flow-through diode-array UV/vis spectrophotometer for real-time monitoring of the column effluent at the protein-specific wavelength of 280 nm to detect the elution of RuBisCO. Quantitation of RuBisCO and total soluble proteins in the eluate fractions were undertaken using polyacrylamide gel electrophoresis (PAGE) and the spectrophotometric Bradford assay, respectively. A comprehensive investigation of the effect of distinct concentration gradients on the isolation of RuBisCO and experimental conditions (namely, type of resin, column dimensions and mobile-phase flow rate) upon column capacity and analyte breakthrough was effected. The assembled set-up was aimed to critically ascertain the efficiency of preliminary batchwise pre-treatments of crude plant extracts (viz., polyethylenglycol (PEG) precipitation, ammonium sulphate precipitation and sucrose gradient centrifugation) in terms of RuBisCO purification and absolute recovery prior to automated anion-exchange column separation. Under the optimum physical and chemical conditions, the flow-through column system is able to admit crude plant extracts and gives rise to RuBisCO purification yields better than 75%, which might be increased up to 96 ± 9% with a prior PEG fractionation followed by sucrose gradient step.     

铽-环丙沙星-SDS敏化荧光猝灭法检测雷公藤红素

在pH=9.26的氨-氯化铵缓冲溶液中,铽Ⅲ与环丙沙星反应形成络合物,而后加入十二烷基硫酸钠(SDS)形成了三元体系,其最佳激发、发射波长分别为λex= 330nm、λem=545 nm.在该反应体系中加入适量雷公藤红素溶液,铽Ⅲ与环丙沙星络合物的激发、发射波长位置不变,但荧光强度有规律下降.利用这一现象,建立了测定雷...     

Surfactant addition and alternating current electrophoretic oscillation during size fractionation of nanoparticles in channels with two or three different height segments

An array of parallel planar nanochannels containing two or three segments with varying inner heights was fabricated and used for size fractionation of inorganic and biological nanoparticles. A liquid suspension of the particles was simply drawn through the nanochannels via capillary action. Using fluorescently labeled 30 nm polyacrylonitrile beads, different trapping behaviors were compared using nanochannels with 200-45 nm and 208-54-30 nm height segments. Addition of sodium dodecyl sulfate (SDS) surfactant to the liquid suspension and application of an AC electric field were shown to aid in the prevention of channel clogging. After initial particle trapping at the segment interfaces, significant particle redistribution occurred when applying a sinusoidal 8V peak-to-peak oscillating voltage with a frequency of 150 Hz and DC offset of 4V. Using the 208-54-30 nm channels, 30 nm hepatitis B virus (HBV) capsids were divided into three fractions. When the AC electric field was applied to this trapped sample, all of the virus particles passed through the interfaces and accumulated at the channel ends.     

Influence of chemical agents on interactions in dairy products: Effect of SDS on casein micelles

The addition of SDS during skim milk reconstitution is an original approach to study the effect of an ionic amphiphilic molecule on the milk system and particularly on the casein micelle component. SDS-induced changes in casein micelles were investigated by turbidimetry, rheology, scanning electron microscopy (SEM) and biochemical measurements (including soluble proteins analysis). This study shows that casein micelles were able to interact together to form micellar aggregates or milk gel without coagulating agents addition, when milk was reconstituted in the presence of SDS. This micellar aggregation, depending on the SDS concentration, is confirmed by SEM observations showing that the general aspect of casein micelles was affected by SDS treatment. Biochemical analysis indicated that SDS induced micellar casein dissociation. SDS-induced milk gel formation required a defined level of casein dissociation which could be also related to a particular micellar state.