Developing DNA tiles for oligonucleotide hybridization assay with higher accuracy and efficiency

We demonstrate the versatility of a DNA tile system for oligonucleotide hybridization assay and explored the detection limit of the probe tiles for DNA targets of varied lengths.     

Isotropic chemical shifts in magic-angle spinning NMR spectra of proteins

Here we examine the effect of magic-angle spinning (MAS) rate upon lineshape and observed peak position for backbone carbonyl (C') peaks in NMR spectra of uniformly-(13)C,15N-labeled (U-(13)C,15N) solid proteins. 2D N-C' spectra of U-(13)C,15N microcrystalline protein GB1 were acquired at six MAS rates, and the site-resolved C' lineshapes were analyzed by numerical simulations and comparison to spectra from a sparsely labeled sample (derived from 1,3-(13)C-glycerol). Spectra of the U-(13)C,15N sample demonstrate large variations in the signal-to-noise ratio and peak positions, which are absent in spectra of the sparsely labeled sample, in which most 13C' sites do not possess a directly bonded 13CA. These effects therefore are a consequence of rotational resonance, which is a well-known phenomenon. Yet the magnitude of this effect pertaining to chemical shift assignment has not previously been examined. To quantify these effects in high-resolution protein spectra, we performed exact numerical two- and four-spin simulations of the C' lineshapes, which reproduced the experimentally observed features. Observed peak positions differ from the isotropic shift by up to 1.0 ppm, even for MAS rates relatively far (a few ppm) from rotational resonance. Although under these circumstances the correct isotropic chemical shift values may be determined through simulation, systematic errors are minimized when the MAS rate is equivalent to approximately 85 ppm for 13C. This moderate MAS condition simplifies spectral assignment and enables data sets from different labeling patterns and spinning rates to be used most efficiently for structure determination.     

Kinetic studies on the oxidation of aryl methyl sulfides and sulfoxides by dimethyldioxirane; absolute rate constants and activation parameters for 4-nitrophenyl methyl sulfide and sulfoxide

The oxidations of methyl 4-nitrophenyl sulfide and sulfoxide by dimethyldioxirane, in acetone and mixtures of acetone with water, methanol, acetonitrile and hexane, have been followed by UV-Vis spectroscopy to monitor the decay of the substrates. The data show that, under all the conditions studied, both oxidations obey second-order kinetics. Grunwald-Winstein and Kamlet-Taft analyses of the influence of solvents on the second-order rate constants have been used to obtain mechanistic information on the two reactions. Activation parameters for the two oxidations in acetone and aqueous acetone have been calculated from rate constants for reactions in the temperature range 283-313 K and compared with those from sulfide and sulfoxide oxidations with other oxidants. For sulfoxide oxidations in acetone and 1-20% v/v water in acetone, the results support a concerted nucleophilic displacement by sulfur of oxygen from dimethyldioxirane with the rate being dependent on the solvent's polarity. Sulfide oxidations in acetone and 1-5% v/v water in acetone also proceed by a concerted mechanism. However, in the most polar solvent system studied, 20% v/v water in acetone, the mechanism changes in favour of a two-step reaction involving a betaine intermediate. Importantly, the sulfide oxidation shows a different solvent dependence to that of the sulfoxide, with the rate of oxidation being determined by the hydrogen bond donor capacity and electron-pair donicity of the solvent.     

Remote site photosubstitution in metalloporphyrin-rhenium tricarbonylbipyridine assemblies: photo-reactions of molecules with very short lived excited states

The synthesis is reported of a series of metalloporphyrins (and the corresponding free-base porphyrin), mono-meso-substituted with a bipyridyl group via an amide link at the 4-position of one phenyl group: [Re(CO)(3)(Pic)Bpy-MTPP][OTf], where M = Mg, Zn, Pd or 2H, Pic = 3-picoline, Bpy = 2,2'-bipyridine, TPP = tetraphenylporphyrin. The photochemical reactions of the assemblies with the sacrificial electron donor triethylamine have been investigated by IR spectroscopy and compared to the behaviour of analogues of the type Bpy-MTPP without rhenium. Selective long-wavelength irradiation of the metalloporphyrin unit in the presence of excess picoline leads to reduction at the rhenium bipyridine centre. In the absence of 3-picoline, the latter is not reduced, but substituted by added halide or by the THF solvent. Mechanistic analysis highlights the differences between the zinc and magnesium chelate on the one hand and the palladium porphyrin on the other. The free-base assembly, [Re(CO)(3)(Pic)Bpy-H(2)TPP][OTf] is unreactive. The zinc and magnesium porphyrin assemblies initially coordinate Et(3)N before undergoing photo-induced inner-sphere electron transfer from the triethylamine to form a charge-shifted excited state of the assembly. In contrast, the palladium-based dyad reacts via outer-sphere reductive quenching of a porphyrin-based excited state. The substitution products are postulated to form by a mechanism involving an electron-transfer chain.     

Kinetics and products from reaction of Cl radicals with dioctyl sebacate (DOS) particles in O(2): a model for radical-initiated oxidation of organic aerosols

The reaction of Cl radicals with bis (2-ethylhexyl) sebacate (also known as dioctyl sebacate, DOS) particles in the presence of O(2) is studied as a model of radical-initiated oxidation of organic aerosols. The uptake coefficient as measured from the rate of loss of DOS is gamma(DOS) = 1.7 (+/-0.3) indicating that a radical chain is operative. It is observed that nearly all of the detected products, accounting for 86% (+/-12%) of the reacted DOS, remain in the particles indicating that they are not efficiently volatilized. Correspondingly, the particles do not decrease in volume even after 60% of the DOS has reacted; upon further reaction the volume does decrease by up to 20%. Additionally, the mass of a DOS film increases with reaction indicating that the density increases. The two primary products identified are the ketone (38 +/- 10% yield) and alcohol (14 +/- 4% yield) resulting from reactions of alkylperoxy radicals originating from DOS oxidation. The fact that the ketone/alcohol ratio is >1 implies that the Russell mechanism, the typical fate of alkylperoxy radicals in liquids whereby both a ketone and an alcohol are generated, is not the only source of ketones. In fact, the ketone yield demonstrates a Langmuir-Hinshelwood type dependence on the O(2) concentration indicating that 44% (+/-8%) of the ketone is created from the reaction of alkoxy radicals with O(2) at the surface of the particles (at 20% O(2)). While this is a common reaction in the gas phase, it is generally not considered to occur in organic solvents. Furthermore, the appearance of gas-phase H(2)O(2) suggests that peroxy radicals react to form two ketones and H(2)O(2)via the Bennett and Summers mechanism. The absence of aldehyde products, both in the gas phase and in the particles, indicates that beta-scission of the alkoxy radicals is not significant. The results of this study suggest that organic aerosols in the troposphere are efficiently oxidized by gas-phase radicals but that their chemical transformation does not lead to their removal through volatilization.     

Facile Cu-free Sonogashira cross-coupling of nucleoside C-6 arylsulfonates with terminal alkynes

The combination of PdCl₂[CH₃CN]₂ with XPhos is an efficient catalytic system for the Sonogashira-type cross-coupling of 2′-deoxyguanosine O⁶-arylsulfonates with terminal alkynes. The reactions generally proceed under mild conditions requiring no Cu co-catalyst to give the corresponding C-6-alkynylated deoxynucleosides in moderate to good yields.     

Stereoselective synthesis of a dialkylhydantoin featuring an asymmetric Strecker reaction on an acyclic dialkyl ketone

A diastereoselective Strecker reaction using (R)-(?)-phenylglycinol forms the basis of a concise scalemic route to dialkylhydantoin 1. The phenylglycinol functionality was exploited in the manipulation of the aminonitrile Strecker product through to the dialkylhydantoin via a short, efficient sequence involving crystalline intermediates.     

Biomimetic processes. IV. Carbocationic polymerization of isoprene initiated by dimethyl allyl alcohol

In this article, we investigate a new bio‐inspired synthetic route towards NR homologs based on the carbocationic polymerization of isoprene initiated by dimethyl allyl alcohol (DMAOH)/TiCl₄ or BF₃.Et₂O as the catalytic system. This study is the continuation of our studies related to the proof of principle that NR biosynthesis is based on a carbocationic mechanism. It is shown that using the biomimetic strategy of initiation by allylic carbocations, polyisoprene carrying a dimethyl allyl head group is produced almost exclusively via 1,4 addition, yielding repeating units with cis and trans configurations. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 2181–2189, 2009