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.     

Experimental evidence for multiple oxidation pathways in the (salen) Mn-catalyzed epoxidation of alkenes

The substrate electronic effects on the selectivity in the catalytic epoxidation of para-substituted cis stilbenes 2a-i were investigated by using (R,R)-[N,N'-bis(3,5-di-tBu-salicylidene)-1,2-cyclohexanediamine]manganese(III) chloride 1 in benzene as the catalyst with iodosobenzene as the terminal oxidant. A Hammett study of the selectivity results reveals a stronger electrophilic character than previously assumed in the (salen)Mn-catalyzed reaction. In general, the best correlations with the experimental values were obtained by using the Hammett sigma + values, which gave rho = -1.37 for the rate of cis-epoxide formation and rho = -0.43 for the rate of the stepwise process leading to the corresponding trans product. The reaction involves two separate pathways as indicated also by the competitive breakdown of the intermediate on the path to trans epoxide for methoxy-substituted substrates. The asynchronicity in the concerted pathway leading to cis epoxide is apparent for 4-methoxy-4'-nitrostilbene, which yields cis epoxide with 75% ee entirely as a result of electronic effects.     

Kekulé structure counts for some classes of all-benzenoid and all-coronoid hydrocarbons

Summary A general formula for the Kekulé structure count (K) is deduced for the class of catacondensed all-benzenoids with unbranched backbones. The formula is extended to thin pericondensed all-benzenoids, where allowance is made for pyrene units. In this treatment the fragmentation matrices are employed. A generalization of these matrices is furnished. Next some generalK formulas for classes of catacondensed and thin pericondensed all-coronoids are deduced. Again the fragmentation matrices are employed, but the problem is also studied in terms of certain polynomials.Dedicated to the memory of Professor Oskar E. Polansky, who died in January 1989. He was the one who coined the term all-benzenoid.     

Exploiting C3-symmetry in the dynamic coordination of a chiral trisoxazoline to copper(II): improved enantioselectivity, and catalyst stability in asymmetric lewis acid catalysis

Chiral C3-symmetric trisoxazolines are highly efficient stereodirecting ligands in enantioselective Cu(II) Lewis acid catalysis which is based on the concept of a stereoelectronic hemilability of the divalent copper; in direct comparison with the analogous bisoxazoline systems they are more efficient in the enantioselective alpha-amination as well as the enantioselective Mannich reaction of prochiral beta-ketoesters.     

Deviation from Ohm's law in electric field assisted capillary liquid chromatography

Earlier studies of electric field assisted LC (EF-LC) have shown that the effect on charged analytes of the application of an electric field over a capillary LC column is relatively small. Charged analytes can only be affected by the electric field while present in the mobile phase, which makes the effective time for influence of the electric field t(0) independent of retention time. Because the charged analytes only can be affected for a short time the electric field strength ought to be high in order to increase the impact of the electric field on the separation. We have, however, found that only a relatively low electric field strength can be used in EF-LC when pressure is used as main driving force. The useful field strength was limited by a dramatic increase in the current. This increase in current was found to origin from an increased concentration of buffer ions that have an electrophoretic mobility towards the pumped flow.     

Synthesis of 2•,3•-Dideoxy-3•-<Emphasis Type="Italic">C</Emphasis>-hydroxymethylcytidine Phosphonomethyl Derivatives

Phosphonomethyl substituted 2?,3?-Dideoxy-3?-C-hydroxymethylcytidines have been synthesized and evaluated for their anti HIV-1 activities. The sugar moiety was synthesized starting from (S)-5-hydroxymethylfuran-2-(5H)-one using photocatalyzed addition of methanol. Reduction of the lactone, condensation with silylated 4-methoxy-2(1H)pyrimidinone, followed by phosphonomethylation and deprotection gave the title compounds. The compounds were tested for inhibition of HIV-1 activity but did not show any significant antiviral activity.     

Chip-Firing Games on Directed Graphs

We consider the following (solitary) game: each node of a directed graph contains a pile of chips. A move consists of selecting a node with at least as many chips as its outdegree, and sending one chip along each outgoing edge to its neighbors. We extend to directed graphs several results on the undirected version obtained earlier by the authors, P. Shor, and G. Tardos, and we discuss some new topics such as periodicity, reachability, and probabilistic aspects.Among the new results specifically concerning digraphs, we relate the length of the shortest period of an infinite game to the length of the longest terminating game, and also to the access time of random walks on the same graph. These questions involve a study of the Laplace operator for directed graphs. We show that for many graphs, in particular for undirected graphs, the problem whether a given position of the chips can be reached from the initial position is polynomial time solvable.Finally, we show how the basic properties of the probabilistic abacus can be derived from our results.     

Synthesis and characterization of dinuclear ruthenium complexes covalently linked to Ru(II) tris-bipyridine: an approach to mimics of the donor side of photosystem II

To mimic the electron-donor side of photosystem II (PSII), three trinuclear ruthenium complexes (2, 2a, 2b) were synthesized. In these complexes, a mixed-valent dinuclear Ru2(II,III) moiety with one phenoxy and two acetato bridges is covalently linked to a Ru(II) tris-bipyridine photosensitizer. The properties and photoinduced electron/energy transfer of these complexes were studied. The results show that the Ru2(II,III) moieties in the complexes readily undergo reversible one-electron reduction and one-electron oxidation to give the Ru2(II,III) and Ru2(III,III) states, respectively. This could allow for photooxidation of the sensitizer part with an external acceptor and subsequent electron transfer from the dinuclear ruthenium moiety to regenerate the sensitizer. However, all trinuclear ruthenium complexes have a very short excited-state lifetime, in the range of a few nanoseconds to less than 100 ps. Studies by femtosecond time-resolved techniques suggest that a mixture of intramolecular energy and electron transfer between the dinuclear ruthenium moiety and the excited [Ru(bpy)3]2+ photosensitizer is responsible for the short lifetimes. This problem is overcome by anchoring the complexes with ester- or carboxyl-substituted bipyridine ligands (2a, 2b) to nanocrystalline TiO2, and the desired electron transfer from the excited state of the [Ru(bpy)3]2+ moiety to the conduction band of TiO2 followed by intramolecular electron transfer from the dinuclear Ru2(II,III) moiety to photogenerated Ru(III) was observed. The resulting long-lived Ru2(III,III) state decays on the millisecond timescale.     

UHF-CI studies of energy barriers for the abstraction and exchange reactions in the system H + CH4

UHF and CI calculations, using the direct CI method, and double-zeta plus polarization functions basis sets, have been performed on the more important parts of the energy hypersurface for CH₅. The abstraction H + CH₄ → H₂ + CH₃ and the inversion substitution reaction H′ + CH₄ → CH₃H′ + H have been studied in detail. The predicted barriers for these two reactions are 13.5 and 36.6 kcal/mol, respectively. The abstraction reaction is, in agreement with experiment, found to be almost thermo-neutral with a heat of reaction of 1.5 kcal/mol.