The Renner effect in triatomic molecules with application to CH+, MgNC and NH2

We have developed a computational procedure, based on the variational method, for the calculation of the rovibronic energies of a triatomic molecule in an electronic state that become degenerate at the linear nuclear configuration. In such an electronic state the coupling caused by the electronic orbital angular momentum is very significant and it is called the Renner effect. We include it, and the effect of spin-orbit coupling, in our program. We have developed the procedure to the point where spectral line intensities can be calculated so that absorption and emission spectra can be simulated. In order to gain insight into the nature of the eigenfunctions, we have introduced and calculated the overall bending probability density function f(p) of the states. By projecting the eigenfunctions onto the Born-Oppenheimer basis, we have determined the probability density functions f+(rho) and f-(rho) associated with the individual Born-Oppenheimer states phi(-)elec and phi(+)elec. At a given temperature the Boltzmann averaged value of the f(p) over all the eigenstates gives the bending probability distribution function F(rho), and this can be related to the result of a Coulomb Explosion Imaging (CEI) experiment. We review our work and apply it to the molecules CH2+, MgNC and NH2, all of which are of astrophysical interest.     

Direct identification of all oncogenic mutants in KRAS exon 1 by cycling temperature capillary electrophoresis

Over the past few decades, advances in genetics and molecular biology have revolutionized our understanding of cancer initiation and progression. Molecular progression models outlining genetic events have been developed for many solid tumors, including colon cancer. Previous reports in the literature have shown a relationship between different KRAS mutations and prognosis and response to medical treatment in colon cancer patients. Furthermore, the presence of a mutated KRAS has been correlated with different clinicopathological variables including age and gender of patients and tumor location. To our knowledge, few institutions screen for KRAS mutations on regular basis in colon cancer patients despite such evidence that knowledge of KRAS exon 1 status is informative. Here, we report on a mutation analysis method adapted to a 96-capillary electrophoresis instrument that allows identification of all 12 oncogenic mutations in KRAS exon 1 under denaturing conditions. To determine the optimal parameters, a series of DNA constructs generated by site-directed mutagenesis was analyzed and the migration times of all mutant peaks were measured. A classification tree was then made based on the differences in migration time between the mutants and an internal standard. A randomized series of 500 samples constructed with mutagenesis as well as 60 blind samples from sporadic colon carcinomas was analyzed to test the method. No wild-type samples were scored as mutants and all mutants were correctly identified. Post polymerase chain reaction (PCR) analysis time of 96 samples was performed within 40 min.     

Altered Lipid Composition of Secretory Cells Following Exposure to Zinc Can Be Correlated to Changes in Exocytosis

A micromolar concentration of zinc has been shown to significantly change the dynamics of exocytosis as well as the vesicle contents in a model cell line, providing direct evidence that zinc regulates neurotransmitter release. To provide insight into how zinc modulates these exocytotic processes, neurotransmitter release and vesicle content were compared with single cell amperometry and intracellular impact vesicle cytometry with a range of zinc concentrations. Additionally, time-of-flight secondary ion mass spectrometry (ToF-SIMS) images of lipid distributions in the cell membrane after zinc treatment correlate to changes in exocytosis. By combining electrochemical techniques and mass spectrometry imaging, we proposed a mechanism by which zinc changes the fusion pore and the rate of neurotransmitter release by changing lipid distributions and results in the modulation of synaptic strength and plasticity.     

Method development for identification of ketobemidone metabolites in microdialysate samples by coupled-column capillary liquid chromatography-tandem mass spectrometry

Methodologies for identification of ketobemidone metabolites in microdialysate samples utilizing coupled-column capillary liquid chromatography-electrospray quadrupole time-of-flight tandem mass spectrometry are presented. Two different methods were developed to efficiently analyze the metabolites norketobemidone, ketobemidone N-oxide and hydroxyketobemidone, respectively. Both methods include on-line desalting and trapping of the analytes on micro-solid-phase extraction columns with different retention mechanisms. Norketobemidone and ketobemidone N-oxide were trapped on a C18 column and then eluted by back-flush followed by isocratic separation on a fluorinated reversed-phase type silica gel column (Fluofix). Retention equations are proposed for the chromatographic observations made on the Fluofix column. Hydroxyketobemidone was trapped on a phenylboronic acid column by complex formation at basic pH and then eluted at acidic pH directly into to the mass spectrometer. Oxidation of hydroxyketobemidone to its corresponding quinone was also observed. The methods were successfully used to analyze synthetic ketobemidone metabolites in dilute low-volume microdialysis samples.     

Chlorine isotope fractionation of a semi-volatile organochlorine compound during preparative megabore-column capillary gas chromatography

Chlorine isotope fractionation during preparative capillary gas chromatography (pcGC) was investigated using 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) as a model compound for semi-volatile organochlorine (OCl) molecules. Chlorine isotope analysis by thermal ionization mass spectrometry revealed no significant alteration of the chlorine isotope composition when the whole peaks were collected in pcGC (delta37Cl -3.2 per thousand versus -3.6 per thousand for the unprocessed DDT, +/-0.5 per thousand SD). However, distinct isotope fractionations were measured for the front (delta37Cl -5.1 per thousand) and tail (delta37Cl -1.8 per thousand) segments of partially collected samples. Isolation of individual OCls by pcGC enables accurate off-line chlorine isotope analysis, and thus facilitates the investigation of naturally occurring OCls.     

Gapmer Antisense Oligonucleotides Containing 2′,3′-Dideoxy-2′-fluoro-3′-C-hydroxymethyl-β-d-lyxofuranosyl Nucleotides Display Site-Specific RNase H Cleavage and Induce Gene Silencing

Off-target effects remain a significant challenge in the therapeutic use of gapmer antisense oligonucleotides (AONs). Over the years various modifications have been synthesized and incorporated into AONs, however, precise control of RNase H-induced cleavage and target sequence selectivity has yet to be realized. Herein, the synthesis of the uracil and cytosine derivatives of a novel class of 2′-deoxy-2′-fluoro-3′-C-hydroxymethyl-β-d -lyxo-configured nucleotides has been accomplished and the target molecules have been incorporated into AONs. Experiments on exonuclease degradation showed improved nucleolytic stability relative to the unmodified control. Upon the introduction of one or two of the novel 2′-fluoro-3′-C-hydroxymethyl nucleotides as modifications in the gap region of a gapmer AON was associated with efficient RNase H-mediated cleavage of the RNA strand of the corresponding AON:RNA duplex. Notably, a tailored single cleavage event could be engineered depending on the positioning of a single modification. The effect of single mismatched base pairs was scanned along the full gap region demonstrating that the modification enables a remarkable specificity of RNase H cleavage. A cell-based model system was used to demonstrate the potential of gapmer AONs containing the novel modification to mediate gene silencing.     

Electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry in the electron energy range 0-50 eV

Electron capture dissociation (ECD) of polypeptide cations was obtained with pencil and hollow electron beams for both sidekick and gas-assisted dynamic ion trapping (GADT) using Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) with an electrostatic ion transfer line. Increasing the number of trapped ions by multiple ICR trap loads using GADT improved the ECD sensitivity in comparison with sidekick ion trapping and ECD efficiency in comparison with single ion trap load by GADT. Furthermore, enhanced sensitivity made it possible to observe ECD in a wide range of electron energies (0-50 eV). The degree, rate and fragmentation characteristics of ECD FTICR-MS were investigated as functions of electron energy, electron irradiation time, electron flux and ion trapping parameters for this broad energy range. The results obtained show that the rate of ECD is higher for more energetic (>1 eV) electrons. Long electron irradiation time with energetic electrons reduces average fragment ion mass and decreases efficiency of formation of c- and z-type ions. The obtained dependencies suggest that the average fragment ion mass and the ECD efficiency are functions of the total fluence of the electron beam (electron energy multiplied by irradiation time). The measured electron energy distributions in low-energy ECD and hot ECD regimes are about 1 eV at full width half maximum in employed experimental configurations.     

Alkylation and acylation of basic salts of anthranilic acid

The O-nucleophilicity of basic anthranilic acid salts was documented, analyzed, and utilized in synthesis. Specifically substitutions leading to esters instead of secondary amines, and formation of anthranilic acid anhydrides were studied.