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.     

Preparation, Structure, and Thermal Decomposition of Co(II) Complexeswith 2,3- and 2,5-Dichlorobenzoic Acid and Imidazole

Summary.  The reaction products of Co(II)-2,3- and -2,5-dichlorobenzoate with imidazole (1, 2; CoL ₂⋯2imdċ2H₂O, L=C₇H₃Cl₂O, imd=imidazole) were characterized by their spectroscopic and thermochemical properties. The compounds crystallize in the monoclonic system with space group = P2₁/c, a=13.848(3), b=12.841(3) ?, c= 7.064(2) ?, β=98.12 °, V=1243.5(4) ?³, Z=2 for 1 and space group =P2₁/n, a=13.293(3), b= 6.964(2), c=13.800(3) ?, β=108.92(3) °, V=1208.6(4) ?³, Z=2 for 2. The complexes lose their crystal water in one step at 333 K and subsequently decompose to CoO with intermediate formation of Co₃O₄. Received August 9, 1999. Accepted (revised) February 11, 2000     

Revisiting Thin-Layer Chromatography as a Lipophilicity Determination Tool. Part III — A Study on CN Adsorbent Layers

JPC – Journal of Planar Chromatography – Modern TLC -     

Formation of (E) 1-alkoxy-1,3-butadienes from corresponding propargyl ethers; vicarious nucleophilic substitution in alkoxyallenes

Propargyl ethers treated with dimsyl anion in DMSO at 80-100°C undergo terminal methylenation to afford corresponding (E) 1-alkoxy-1,3-butadienes. The reaction proceeds via an alkoxy-allene.     

H-bonding dependent structures of (NH4+)3H+(SO4 2-)2. Mechanisms of phase transitions

The role of different H-bonds in phases II, III, IV, and V of triammonium hydrogen disulfate, (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2), has been studied by X-ray diffraction and (1)H solid-state MAS NMR. The proper space group for phase II is C2/c, for phases III and IV is P2/n, and for phase V is P onemacr;. The structures of phases III and IV seem to be the same. The hydrogen atom participating in the O(-)-H(+).O(-) H-bond in phase II of (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2) at room temperature is split at two positions around the center of the crucial O(-)-H(+).O(-) H-bonding, joining two SO(4)(2)(-) tetrahedra. With decreasing temperature, it becomes localized at one of the oxygen atoms. Further cooling causes additional differentiation of possibly equivalent sulfate dimers. The NH(4)(+) ions participate mainly in bifurcated H-bonds with two oxygen atoms from sulfate anions. On cooling, the major contribution of the bifurcated H-bond becomes stronger, whereas the minor one becomes weaker. This is coupled with rotation of sulfate ions. In all the phases of (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2), some additional, weak but significant, reflections are observed. They are located between the layers of the reciprocal lattice, suggesting possible modulation of the host (NH(4)(+))(3)H(+)(SO(4)(2)(-))(2) structure(s). According to (1)H MAS NMR obtained for phases II and III, the nature of the acidic proton disorder is dynamic, and localization of the proton takes place in a broader range of temperatures, as can be expected from the X-ray diffraction data.     

Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry

Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1‐azabicyclo[2.2.2]octane (ABCO) or 1,4‐diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI‐MS) and longer retention times on the reverse‐phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision‐induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a‐ and b‐type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision‐induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI‐MS/MS sequencing of peptides. Copyright © 2014 John Wiley & Sons, Ltd.     

Molecular Characterization of DNA Double Strand Breaks with Tip‐Enhanced Raman Scattering

DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of P? O? H and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure.     

A definitive RNAA method for determination of selenium in biological samples: uncertainty evaluation and assessment of degree of accuracy

This article describes work on the development of a highly accurate RNAA method for determination of selenium in biological samples. The analytical post-irradiation procedure is based on a combination of cation-exchange and extraction chromatography with final selective and quantitative fixation of selenium on a column packed with 3,3′-diaminobenzidine (DAB) supported on Amberlite XAD4, followed by gamma-ray spectrometric measurement. The suitability and accuracy of the method was demonstrated by analysing CRMs with certified selenium content. The uncertainty budget for Se determination in standard reference material Peach Leaves NBS 1547 was estimated; the combined standard uncertainty was calculated as 1.7%. The described method fulfils all the criteria for definitive methods. It was subsequently used for determination of selenium in biological materials intended as new CRMs and proficiency test samples.     

Addition Reactions of Sulfenyl and Sulfinyl Chlorides with 3‐Phenyl‐1‐azabicyclo[1.1.0]butane

The reactions of 3‐phenyl‐1‐azabicyclo[1.1.0]butane with α‐chlorosulfenyl chlorides and sulfinyl chlorides lead to the corresponding sulfenamides and sulfinamides, respectively, which possess an azetidine ring. It is proposed that a two‐step mechanism occurs involving an intermediate carbenium ion, which is formed by the addition of the electrophile at the N‐atom and cleavage of the N(1)? C(3) bond. The structures of 9b and 10b are established by X‐ray crystallography.     

Porphyrin‐Ryleneimide Hybrids: Low‐Bandgap Acceptors in Energy‐Transfer Cassettes

Energy‐transfer cassettes consisting of naphthaleneimide‐fused metalloporphyrin acceptors (M=Zn and Pd) and BODIPY donors have been designed and synthesized. These systems have rigid pseudo‐tetrahedral structures with a donor‐acceptor separation of ca. 17.5 Å. Spectroscopic investigations, including femtosecond transient absorption measurements, showed efficient excitation energy transfer (EET) occurring according to the Förster mechanism. Strong fluorescence of the donor units and significant spectral overlap of the donor and acceptor subunits are prerequisites for the efficient EET in these systems.