A new hydrophobic linker effective for the in situ synthesis of DNA-CPG conjugates as tools for SNP analysis

DNA chips consisting of DNA oligonucleotide probes immobilized on the surface of solid supports are very powerful tools for rapid analysis of multiple samples. In this Letter we describe a new method for the efficient synthesis of DNA probes without their serious elimination by use of a new hydrophobic 16-hyroxydecanoic linker and a new non-aqueous reagent of MeNH₂/THF for the deprotection of the base and phosphate protecting groups on CPG resins. The elimination of DNA probes in this new method could be suppressed more than 20-fold compared with the previous method using a hexaethylene glycol linker and concd NH₄OH. Moreover, we carried out SNPs detection by use of our DNA-CPG conjugate to show the utility of our new linker and deprotection conditions.     

A convenient synthesis of phosphoenolpyruvate via silyl-ester intermediate

Phosphoenolpyruvate was synthesized in high yield by a simple procedure starting from pyruvic acid and dimethyl trimethylsilyl phosphite through trimethylsilylation, bromination, and the Perkow reaction.     

Electronic conductivity of pure ceria

The electronic conductivity of pure ceria with two different impurity levels is examined by dc polarization technique based on the Hebb-Wagner ion blocking method. The impurity level for the ceria with 99.999% purity (5N-CeO₂) is about 1/100 of that with 99.9% purity (3N-CeO₂) as confirmed by the fluorescence intensity of impurities obtained by Raman spectroscopy. The electronic conductivity for the 5N-CeO₂ was measured at T = 973 K to 1173 K, and the results are essentially the same as those for the 3N-CeO₂. The electronic conductivity increases with decreasing of P(O₂) following slope values of − 1/4 to − 1/6. The − 1/4 dependent region becomes narrower for the 5N-CeO₂ than that for the 3N-CeO₂. For both types of ceria, the P(O₂) independent region appears in the same region of higher than 10^− 2 and 10^− 3 MPa at T = 1073 K and 973 K, respectively. Activation energies for the 5N-CeO₂ were 2.2 eV, 2.6 eV and 1.9 eV in P(O₂) dependent regions of − 1/6, − 1/4 and 0, respectively.     

Solvent- and environment-dependent fluorescence of modified nucleobases

Fluorescent nucleosides with modified nucleobases are useful tools for detecting nucleic acids and probing their structures and functions. Nucleobases are suitable for modification because 1) intrinsically light-absorbing nucleobases can be converted to fluorescent chromophores by simple chemical modification, 2) attaching substituents to nucleobases at appropriately selected positions does not inhibit base pairing or duplex formation, and 3) duplex formation and protein interactions affect the environment of nucleobases, causing changes in their fluorescence intensities and/or wavelengths. This review summarizes recent fluorescent nucleosides and their photophysical properties, such as absorption wavelength, emission wavelength, and fluorescence quantum yield together with their solvent dependency.     

Squaryl group as a new mimic of phosphate group in modified oligodeoxynucleotides: synthesis and properties of new oligodeoxynucleotide analogues containing an internucleotidic squaryldiamide linkage

This paper describes the synthesis and properties of a new type of modified oligodeoxynucleotide containing a neutral but highly polarized squaryl group as a novel mimic of the phosphate group. A modified thymidine dimer derivative (TsqT) having a squaryldiamide linkage was synthesized in almost quantitative yield by a two-step substitution of diethyl squarate with 3'-amino-5'-O-(4,4'-dimethoxytrityl)-3'-deoxythymidine and 5'-amino-5'-deoxythymidine. The CD and UV studies of TsqT suggest that this dimer has basically a structure similar to that of TpT. The NMR studies of TsqT show a unique property, namely, that the squaryl group of TsqT is influenced by Mg2+ concentration. The ab initio calculations of TsqT showed a highly polarized structure resembling that of a phosphate group. This dimer structural motif was finally incorporated into oligodeoxynucleotides by use of the phosphoramidite approach. The hybridization affinity of these modified oligodeoxynucleotides for the complementary and mismatched oligodeoxynucleotides was studied in detail by using Tm experiments. Consequently, it turned out that in a matched duplex of 5'-d(CGCATsqTAGCC)-3'/5'-d(GGCTAATGCG)-3' the A-T base pairs at the modified site can be preserved, but instead thermal destabilization of the overall structure was observed. To estimate the structure of the duplex, two kinds of fluorescein chromophores (fluorescein (FL) and cyanine 3 (Cy3)) were introduced into the 5'-terminal site of 5'-d(GACGCATsqTAGCCGAT)-3' and 5'-d(ATCGGCTAATGCGTC)-3', respectively. The fluorescence resonance energy transfer experiments using these functionalized oligodeoxynucleotides suggest that the matched duplexes have a bent structure at the modified site. This conclusion was also strongly supported by computational MM and MD simulations.     

Electro-optic effects of colloidal crystals of polymer-modified silica spheres immobilized with gelator

Electro-optic responses of colloidal crystals consist of poly(maleic anhydride-co-styrene)-modified silica spheres (P(MA-ST)/SiO₂) in acetonitrile and the crystals immobilized with a gelator, N-benzyloxycarbonyl-L-isoleucilaminooctadecane (Z-L-Ile-C-18), are studied by reflected-light intensity measurements and time-resolved reflection spectroscopy. Application of an alternating electric field deforms P(MA-ST)/SiO₂ crystal lattices reversibly. The response waveforms from the crystals are dependent on the frequency and strength of the applied electric field; similar dependencies have been qualitatively observed for the colloidal crystals consisting of polystyrene or silica spheres in aqueous media in our previous studies. Both gelated and ungelated P(MA-ST)/SiO₂ crystals change the reflection intensity, however, the amplitude is larger for the latter. The small response for the gelated P(MA-ST)/SiO₂ crystals is attributed to the higher elastic modulus (G). The G value of the gelated P(MA-ST)/SiO₂ crystals in acetonitrile is estimated from the change in the inter-sphere distance to be 8.0 Pa, which is about 2.3 and 2.4 times larger than that for ungelated P(MA-ST)/SiO₂ crystals in acetonitrile and colloidal silica crystals in aqueous media, respectively.     

Crystal engineering for topochemical polymerization of muconic esters using halogen-halogen and CH/pi interactions as weak intermolecular interactions

We now report the molecular and crystal structure design of muconic ester derivatives on the basis of crystal engineering using halogen-halogen contacts and CH/pi interactions. The solid-state photoreaction pathway of the dibenzyl (Z,Z)-muconates as the 1,3-diene dicarboxylic acid monomers depends on the structure of the ester groups. The substitution of a halogen atom for the aromatic hydrogen of a benzyl group induces topochemical polymerization to produce stereoregular polymers in a crystalline form, whereas the unsubstituted benzyl derivative isomerizes to yield the corresponding E,E isomer under similar conditions. The topochemical polymerization process is directly confirmed by the fact that the single-crystal structures before and after the polymerization are very similar to each other. From the crystal structure analysis for a series of substituted benzyl (Z,Z)- and (E,E)-muconates, it has been revealed that the planar diene moieties are closely packed to form a columnar structure in the crystals. The stacking of the polymerizable monomers is characterized by a stacking distance of 4.9-5.2 A along the columns. This structure is supported by a halogen-halogen interaction between the chlorine or bromine atoms introduced at the p position of the benzyl groups in addition to an aromatic stacking due to the CH/pi interaction between the benzylic methylene hydrogens and aromatic rings. The design of a monomer packing corresponds to the type and position of the introduced halogen atom and also the polymorphs. To make a stacking distance of 5 A using both halogen-halogen and CH/pi interactions as supramolecular synthons is important for the molecular design of muconic ester derivatives appropriate for topochemical polymerization.     

Intramolecular stable carbon isotopic analysis of archaeal glycosyl tetraether lipids

Glycolipids are prominent constituents in the membranes of cells from all domains of life. For example, diglycosyl‐glycerol dibiphytanyl glycerol tetraethers (2Gly‐GDGTs) are associated with methanotrophic ANME‐1 archaea and heterotrophic benthic archaea, two archaeal groups of global biogeochemical importance. The hydrophobic biphytane moieties of 2Gly‐GDGTs from these two uncultivated archaeal groups exhibit distinct carbon isotopic compositions. To explore whether the isotopic compositions of the sugar headgroups provide additional information on the metabolism of their producers, we developed a procedure to analyze the δ¹³C values of glycosidic headgroups. Successful determination was achieved by (1) monitoring the contamination from free sugars during lipid extraction and preparation, (2) optimizing the hydrolytic conditions for glycolipids, and (3) derivatizing the resulting sugars into aldononitrile acetate derivatives, which are stable enough to withstand a subsequent column purification step. First results of δ¹³C values of sugars cleaved from 2Gly‐GDGTs in two marine sediment samples, one containing predominantly ANME‐1 archaea and the other benthic archaea, were obtained and compared with the δ¹³C values of the corresponding biphytanes. In both samples the dominant sugar headgroups were enriched in ¹³C relative to the corresponding major biphytane. This ¹³C enrichment was significantly larger in the putative major glycolipids from ANME‐1 archaea (～15‰) than in those from benthic archaea (<7‰). This method opens a new analytical window for the examination of carbon isotopic relationships between sugars and lipids in uncultivated organisms. Copyright © 2010 John Wiley & Sons, Ltd.     

Application of Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to Multi-Element Analysis of Human Organs

Abstract

Elemental concentrations of internal organs (cerebrum, cerebellum, heart, spleen, liver and kidney) of Japanese were measured with inductively coupled plasma mass spectrometry (ICP-MS). Sixty-one elements were determined simultaneously, and concentrations of some trace elements in human organs, on which information are scarcely available in the literature, were obtained. The analytical values obtained by ICP-MS and those by other methods were compared and fairly good agreement was found for Cd, Zn and Fe. Moderate agreement was found for Se and Hg, but discrepancy was observed for Mg and Na. Unacceptable values were obtained for some elements, such as Ti, Sc or Ge, probably due to polyatomic molecular interference.     

A light-controlled reversible DNA photoligation via carbazole-tethered 5-carboxyvinyluracil

We describe a light-controlled template-directed reversible DNA photoligation via carbazole-tethered 5-carboxyvinyluracil. Carbazole-tethered 5-carboxyvinyl-2'-deoxyuridine-containing oligodeoxynucleotide (ODN) can be ligated by irradiation at 366 nm in the presence of template ODN, and the ligated ODN can be split by irradiation at 366 nm in the absence of template ODN.