Automated in-line gel filtration for native state mass spectrometry

Characterization of protein-ligand complexes by nondenaturing mass spectrometry provides direct evidence of drug-like molecules binding with potential therapeutic targets. Typically, protein-ligand complexes to be analyzed contain buffer salts, detergents, and other additives to enhance protein solubility, all of which make the sample unable to be analyzed directly by electrospray ionization mass spectrometry. This work describes an in-line gel-filtration method that has been automated and optimized. Automation was achieved using commercial HPLC equipment. Gel column parameters that were optimized include: column dimensions, flow rate, packing material type, particle size, and molecular weight cut-off. Under optimal conditions, desalted protein ions are detected 4 min after injection and the analysis is completed in 20 min. The gel column retains good performance even after >200 injections. A demonstration for using the in-line gel-filtration system is shown for monitoring the exchange of fatty acids from the pocket of a nuclear hormone receptor, peroxisome proliferator activator-delta (PPARdelta) with a tool compound. Additional utilities of in-line gel-filtration mass spectrometry system will also be discussed.     

Chemische Vitamin D<Subscript>3</Subscript>-Bestimmung in Lebertran

The different aspects of Vitamin D₃ determination and the data reported in the literature are discussed. The spectrophotometric determination of Vitamin D₃ in cod-liver oil is carried out after the alkaline saponification, extraction of unsaponified parts, precipitation of accompanying sterols and the column- and thin-layer chromatographic purification and separation of vitamin D₃ on 40 cm plates from other vitamins. The dyestuff α-naphtholbenzein is suited well as standard substance for the better location and identification of vitamin D₃ zone on the thin-layer plate. The results obtained from the chemical method were checked through the simultaneous biological determination.     

An Improved Protocol for DNA Extraction from Alkaline Soil and Sediment Samples for Constructing Metagenomic Libraries

An improved single-step protocol has been developed for extracting pure community humic substance-free DNA from alkaline soils and sediments. The method is based on direct cell lysis in the presence of powdered activated charcoal and polyvinylpolypyrrolidone followed by precipitation with polyethyleneglycol and isopropanol. The strategy allows simultaneous isolation and purification of DNA while minimizing the loss of DNA with respect to other available protocols for metagenomic DNA extraction. Moreover, the purity levels are significant, which are difficult to attain with any of the methods reported in the literature for DNA extraction from soils. The DNA thus extracted was free from humic substances and, therefore, could be processed for restriction digestion, PCR amplification as well as for the construction of metagenomic libraries.     

Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

A patent data base of 6.7 million compounds generated by a very high performance computer (Blue Gene) requires new techniques for exploitation when extensive use of chemical similarity is involved. Such exploitation includes the taxonomic classification of chemical themes, and data mining to assess mutual information between themes and companies. Importantly, we also launch candidates that evolve by “natural selection” as failure of partial match against the patent data base and their ability to bind to the protein target appropriately, by simulation on Blue Gene. An unusual feature of our method is that algorithms and workflows rely on dynamic interaction between match-and-edit instructions, which in practice are regular expressions. Similarity testing by these uses SMILES strings and, less frequently, graph or connectivity representations. Examining how this performs in high throughput, we note that chemical similarity and novelty are human concepts that largely have meaning by utility in specific contexts. For some purposes, mutual information involving chemical themes might be a better concept.     

Identification of human hepatocellular carcinoma-related proteins by proteomic approaches

Hepatocellular carcinoma (HCC) is the most common malignant liver tumor. Analysis of human serum from HCC patients using two-dimensional gel electrophoresis (2DE) combined with nano-high-performance liquid chromatography electrospray ionization tandem mass spectrometry (nano-HPLC–ESI-MS/MS) identified fourteen different proteins differentially expressed between HCC patients and the control group. Twelve proteins were up-regulated and two down-regulated. By using nano-HPLC–MS/MS system to analyze proteome in human serum, 317 proteins were identified, twenty-nine of which to high confidence levels (protein matched at last two unique peptide sequences). Of these twenty-nine proteins, six were present only in HCC patients and may serve as biomarkers for HCC. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

The art of building small: from molecular switches to molecular motors

Molecular switches and motors are essential components of artificial molecular machines. In this perspective, we discuss progress in our design, synthesis, and functioning of photochemical and electrochemical switches and chemical and light-driven molecular motors. Special emphasis is given to the control of a range of functions and properties, including luminescence, self-assembly, motion, color, conductance, transport, and chirality. We will also discuss our efforts to control mechanical movement at the molecular level, a feature that is at the heart of molecular motors and machines. The anchoring of molecular motors on surfaces and molecular motors at work are discussed.     

Synthesis and study of the fluorescent behavior of 3-pyridinecarbonitriles

Abstract  A series of (2E)-3-(1-chloro-6-methoxy-3,4-dihydronaphthalen-2-yl)-1-(4-aryl)prop-2-en-1-ones (chalcones) have been synthesized by a new synthetic route. The 3-pyridinecarbonitrile derivatives were synthesized by the Michael reaction of malononitrile (in base) and aroylacetonitriles (in acid) with chalcones in one pot. The fluorescent properties and quantum yields of these compounds were studied. Graphical Abstract        

Label-free detection of nucleic acids by turn-on and turn-off G-quadruplex-mediated fluorescence

In this study we have used two fluorescent probes, tetrakis(diisopropylguanidino)-zinc-phthalocyanine (Zn-DIGP) and N-methylmesoporphyrin IX (NMM), to monitor the reassembly of “split” G-quadruplex probes on hybridization with an arbitrary “target” DNA. According to this approach, each split probe is designed to contain half of a G-quadruplex-forming sequence fused to a variable sequence that is complementary to the target DNA. Upon mixing the individual components, both base-pairing interactions and G-quadruplex fragment reassembly result in a duplex–quadruplex three-way junction that can bind to fluorescent dyes in a G-quadruplex-specific way. The overall fluorescence intensities of the resulting complexes were dependent on the formation of proper base-pairing interactions in the duplex regions, and on the exact identity of the fluorescent probe. Compared with samples lacking any “target” DNA, the fluorescence intensities of Zn-DIGP-containing samples were lower, and the fluorescence intensities of NMM-containing samples were higher on addition of the target DNA. The resulting biosensors based on Zn-DIGP are therefore termed “turn-off” whereas the biosensors containing NMM are defined as “turn-on”. Both of these biosensors can detect target DNAs with a limit of detection in the nanomolar range, and can discriminate mismatched from perfectly matched target DNAs. In contrast with previous biosensors based on the peroxidase activity of heme-bound split G-quadruplex probes, the use of fluorescent dyes eliminates the need for unstable sensing components (H₂O₂, hemin, and ABTS). Our approach is direct, easy to conduct, and fully compatible with the detection of specific DNA sequences in biological fluids. Having two different types of probe was highly valuable in the context of applied studies, because Zn-DIGP was found to be compatible with samples containing both serum and urine whereas NMM was compatible with urine, but not with serum-containing samples.     

Trace detection of inorganic oxidants using desorption electrospray ionization (DESI) mass spectrometry

Desorption electrospray ionization (DESI), an established ambient ionization method in mass spectrometry (MS) for the analysis of organic compounds, is applied here to trace detection of inorganic salts, including inorganic oxidants. In-situ surface analysis of targeted compounds, including nitrogen-, halogen- and sulfur-salts, down to sub-nanogram levels, was performed using DESI-MS. Successful experiments were carried out in both the negative and the positive ion modes; simple anions and cations as well as small cluster ions were observed. Various surfaces are examined and surface porosity effects were briefly explored. Absolute detection limits on porous polytetrafluoroethylene (PTFE) of 120 pg (surface concentration 0.07 ng mm⁻²) and 50 pg (surface concentration 0.03 ng mm⁻²), were achieved for sodium chlorate and sodium perchlorate, respectively. The compounds of interest were examined in the presence of a hydrocarbon mixture to assess matrix effects: only a two- or three-fold decrease in the target ion intensity was observed. Commercial fireworks were analyzed to determine perchlorate salts in complex mixtures. This work demonstrates the potential applicability of ambient ionization mass spectrometry to forensic investigations involving improvised explosives.      

Modulation in comprehensive two-dimensional gas chromatography: 20 years of innovation

With almost 20 years having passed since John B. Phillips described the first comprehensive two-dimensional gas chromatography (GC × GC) separation, much has occurred in this ever-expanding field of separation science. GC × GC is currently one of the most effective techniques for the separation and analysis of complex mixtures, offering significantly greater peak capacities than conventional chromatographic methods. The technique is generally based upon separations performed on two chromatographic columns characterized by considerably different selectivities, joined together through a modulating interface. The modulator periodically traps or samples the primary column effluent, usually refocuses it into a narrow chromatographic band and injects the focused fraction into the secondary column. The modulator is often referred to as the ‘heart’ of the instrument, since a GC × GC separation is impossible without its use. This article reviews major innovations in GC × GC modulator development since its first use by Phillips in 1991. Emphasis has been placed on modulator design and function.