Stabilizing or destabilizing oligodeoxynucleotide duplexes containing single 2'-deoxyuridine residues with 5-alkynyl substituents

The 5-position of pyrimidines in DNA duplexes offers a site for introducing alkynyl substituents that protrude into the major groove and thus do not sterically interfere with helix formation. Substituents introduced at the 5-position of the deoxyuridine residue of dU:dA base pairs may stabilize duplexes and reinforce helices weakened by a low G/C content, which would otherwise lead to false negative results in DNA chip experiments. Here we report on a method for preparing oligonucleotides with a 5-alkynyl substituent at a 2'-deoxyuridine residue by on-support Sonogashira coupling involving the fully assembled oligonucleotide. A total of 25 oligonucleotides with 5-alkynyl substituents were prepared. The substituents either decrease the UV melting point of the duplex with the complementary strand or increase it by up to 7.1 degrees C, compared with that of the unmodified control duplex. The most duplex-stabilizing substituent, a pyrenylbutyramidopropyne moiety, is likely to intercalate but does not prevent sequence-specific base pairing of the modified deoxyuridine residue or the neighboring nucleotides. It also increases the signal for a target strand when employed on a small oligonucleotide microarray. The ability to tune the melting point of a DNA dodecamer duplex with a single side chain over a temperature range of >11 degrees C may prove useful when developing DNA sequences for biomedical applications.     

New method for the differentiation of the isomers of aminophenol

Summary Pyridine-2,6-dialdehyde is used as a reagent in a very simple and fast method for differentiating between theo- andp-isomers of aminophenol.

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Zusammenfassung Pyridin-2,6-aldehyd wurde für die einfache und schnelle Unterscheidung zwischen den o- und p-Isomeren des Aminophenols verwendet.

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Résumé On décrit une méthode simple et rapide dans laquelle Pyridine 2–6 aldehyde est employé pour distinguer entre les isomères de l'aminophénol.

     

Prediction of liquid chromatographic retention for differentiation of structural isomers

A liquid chromatography (LC) retention time prediction software, ACD/ChromGenius, was employed to calculate retention times for structural isomers, which cannot be differentiated by accurate mass measurement techniques alone. For 486 drug compounds included in an in-house database for urine drug screening by liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/Q-TOFMS), a retention time knowledge base was created with the software. ACD/ChromGenius calculated retention times for compounds based on the drawn molecular structure and given chromatographic parameters. The ability of the software for compound identification was evaluated by calculating the retention order of the 118 isomers, in 50 isomer groups of 2–5 compounds each, included in the database. ACD/ChromGenius predicted the correct elution order for 68% (34) of isomer groups. Of the 16 groups for which the isomer elution order was incorrectly calculated, two were diastereomer pairs and thus difficult to distinguish using the software. Correlation between the calculated and experimental retention times in the knowledge base tested was moderate, r² = 0.8533. The mean and median absolute errors were 1.12 min, and 0.84 min, respectively, and the standard deviation was 1.04 min. The information generated by ACD/ChromGenius, together with other in silico methods employing accurate mass data, makes the identification of substances more reliable. This study demonstrates an approach for tentatively identifying compounds in a large target database without a need for primary reference standards.     

Color and constitution. Part 8 . Some novel dyestuffs containing indoxyl residues

Novel dyes containing C-likned indoxyl residues are prepared by two routes: (a) by the reaction of C-electrophiles with N-acetylindoxyl and (b) by the reaction of active methylene compounds with 2-chloroindole-3-one. The visible absorption spectra are recorded and discussed.     

Preparation of polymers containing sugar residues

The synthesis of five different polymers containing sugar residues on side chain is described. 1-O-Methacryloyltetra-O-acetyl-D -glucose, 1-O-methacryloyltetra-O-acetyl-D -galactose, and 6-O-methacryloyltetra-O-acetyl-D -glucose were prepared and polymerized. The polymethacrylates obtained were converted into water-soluble polymers by removing the acetyl protective group with sodium methoxide. 6-O-Methacryloyldiisopropylidene-D -galactose was also prepared and polymerized. The isopropylidene protective group was removed by acid hydrolysis. Poly (N-methacryloylglucosamine) was prepared directly by the polymerization of N-methacryloyl-D -glucosamine without the use of any protective group.     

Hydrogel containing L-valine residues as a platform for cisplatin chemotherapy

Two acrylic hydrogels, of low cross-linking content and carrying the L-valine residues, were synthesized and studied as a platform to load and release the chemotherapeutic agent cisplatin. The platinum(II)-complex species showed a well-defined stoichiometric ratio in which two carboxylate groups of the collapsing gel coordinate a metal center; this was confirmed by FT-IR spectra. When loaded in water, a zero-order release rate of platinum(II)-species was shown in the physiologic solution (PBS, pH 7.40) for more than one week. Moreover, the amount of platinum(II)-species released from the hydrogel may be improved either by the cross-linking degree and by the temperature. Any increase of the cross-links results in a decreased slope of the straightline Pt(II)/gel (mg/g) versus time, whereas the increasing temperature results in a greater amount of platinum(II)-species in solution. The chemical- and swelling-controlled release are the main mechanisms supervising the whole release process. On the other hand, the loading of cisplatin and temsirolimus in DMF showed a characteristic two phase releasing pattern; the initial burst effect was always followed by the zero-order release rate for a week. In this case only a swelling-controlled mechanism was mainly invoked. The cytotoxic activity towards Me665/2/21 human melanoma cell line, afforded by the cisplatin-loaded hydrogel, was close and in some cases higher compared to the native cisplatin at the same concentration; an interesting synergy in term of cytotoxicity was observed when a combined treatment of temsirolimus and cisplatin was used, although temsirolimus exerted only a moderate inhibition of cell proliferation.     

Synthesis of regular polypeptides,containing arginine residues

Conclusions Using the method of activated ethers, we synthesized the regular polypeptides: H-(Ala-Arg)_n-OH, H-(Ala-Ala-Arg)_n-OH, H-(Ala-Arg-Arg)_n-OH, and H-(Gly-Arg-Arg)_nlOH with a M_av of 1200–7000.Deceased.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2596–2597, November, 1972.     

The stereochemical assignments of the four 8-azaestrone configurational isomers

Complete correlation has now been accomplished for the four possible isomers in the 8-azacstrone scries, synthesized by two different synthetic routes.     

Adsorption properties of silica-based sorbents containing phosphonic acid residues

Isotherms are measured for nitrogen, n-hexane, triethylamine, and water vapor adsorption on silicas of different origins, the surface layers of which contain functional groups of the ??Si(CH₂)₂P(O)(OH)₂ composition, namely, ethylene- and phenylene-bridged polysilsesquioxane xerogels produced by the sol-gel method, silica microspheres synthesized from tetraethoxysilane in the presence of [CH₃(CH₂)₁₇N(CH₃)₃]Br as a template by spray-drying method, and SBA-15 mesoporous silica produced based on tetraethoxysilane using Pluronic 123 as a template. It is shown that all of the samples possess high specific surface areas, while the types of adsorption isotherms and the accessibility of active acidic sites for adsorption interactions with electron-donor molecules depend on the structures of pores and surface layers, which are governed by the methods of synthesis and postsynthesis sample treatment.     

Synthesis of azo compounds containing triazole and tetrazole residues

Triazole- and tetrazolediazonium sulfates were coupled with aromatic azo components. The effect of the structure and medium on the chromaticity of the azo compounds was studied.     

Efficient copper-catalyzed synthesis of poly-N-heterocycles containing amino acid residues

An efficient copper-catalyzed method has been developed for the synthesis of poly-N-heterocycles containing amino acid residues. The protocol uses readily available 2-halobenzamides containing amino acids and their methyl esters, substituted phenylacetonitriles, and malononitrile as the starting materials and the reactions were performed well under mild conditions. The method should provide a novel and useful strategy for synthesis of N-heterocyclic compounds.     

The transport properties of polyimide isomers containing hexafluoroisopropylidene in the diamine residue

The effect of modification of the central moiety of the dianhydride residue and isomerism on the gas transport and physical properties were compared for six polyimides containing the hexafluoroisopropylidene group in the diamine residue. Substitution of bulkier groups within the dianhydride residue resulted in disruption of chain packing and slight increases in resistance to chain motions which led to an increase in permeability with little loss in selectivity. The permeabilities and diffusivities in the meta connected polyimide isomers were considerably lower than in the para connected polyimide isomers. Similarly, the permselectivities in the meta connected isomers were consistently higher than in the para connected isomers. These lower permeabilities and higher permselectivities were a result of the more dense packing and a significant suppression of small scale motions in the meta connected isomers. The suppression of segmental mobility in the meta connected isomers was indicated by an increase in the sub Tg transition temperatures in these materials relative to the para connected isomers. The differences in transport properties for these polyimides were attributed to contributions by several factors, including: (1) total free volume (2) distribution of free volume (3) intersegmental resistance to chain motions, and (4) intrasegmental resistance to chain motions. © 1994 John Wiley & Sons, Inc.     

Photochemical generation of C4'-oxidized abasic site containing oligodeoxynucleotide and its efficient amine modification

[Structure: see text] We synthesized oligodeoxynucleotide (ODN, 3), which contains 4'-o-nitrobenzyloxythymidine (4) as a caged precursor of C4'-oxidized abasic site (1). Photoirradiation of 3 at 365 nm followed by amine treatment under neutral conditions afforded the lactam (2) efficiently. Duplexed ODN 3 was converted to 1 faster and more efficiently than single stranded 3, whereas amine treatment of 1 formed from single stranded 3 resulted in slightly faster lactam formation than with the duplex.     

Tandem mass spectrometry based investigation of cinnamylideneacetophenone derivatives: valuable tool for the differentiation of positional isomers

Cinnamylideneacetophenones have been extensively used as versatile starting materials in numerous different transformations. The structural characterization of this type of compounds is, therefore, of crucial importance since it can give information on the chemistry, reactivity and also the potential biological activity of this type of compounds. Thus, 24 derivatives were systematically studied by tandem mass spectrometry (MS²) with electrospray ionization (ESI), in positive ion mode. The protonated molecules, [M + H]⁺, formed under ESI conditions were induced to dissociate and the fragmentation patterns were studied. The information collected provided important structural information on the type of substituents present and constitute an important database concerning this family of compounds. Overall, it was found that the substitution pattern of the cinnamylideneacetophenone derivatives changes the ESI‐MS² fragmentation considerably. These results indicate that ESI‐MS² is a useful technique for distinguishing positional isomers of these cinnamylideneacetophenone derivatives. Copyright © 2011 John Wiley & Sons, Ltd.     

Substitution effects on the absorption spectra of nitrophenolate isomers

Charge-transfer excitations highly depend on the electronic coupling between the donor and acceptor groups. Nitrophenolates are simple examples of charge-transfer systems where the degree of coupling differs between ortho, meta and para isomers. Here we report the absorption spectra of the isolated anions in vacuo to avoid the complications of solvent effects. Gas-phase action spectroscopy was done with two different setups, an electrostatic ion storage ring and an accelerator mass spectrometer. The results are interpreted on the basis of CC2 quantum chemical calculations. We identified absorption maxima at 393, 532, and 399 nm for the para, meta, and ortho isomer, respectively, with the charge-transfer transition into the lowest excited singlet state. In the meta isomer, this π-π* transition is strongly redshifted and its oscillator strength reduced, which is related to the pronounced charge-transfer character, as a consequence of the topology of the conjugated π-system. Each isomer's different charge distribution in the ground state leads to a very different solvent shift, which in acetonitrile is bathochromic for the para and ortho, but hypsochromic for the meta isomer.     

Charge transfer complexes of polyimines containing trans-1,2-bis-9-carbazolylcyclobutane

Polyimines containing trans-1,2-bis-9-carbazolylcyclobutane (CzD) and a spacer of a variable number of methylene groups (3–10 and 12) were synthesized from the diformylated CzD and the corresponding aliphatic diamine. The charge transfer complexes (CTCs) of these polyimines with electron-acceptors such as tetracyanoethylene (TCNE) and 2,4,7-trinitro-9-fluorenone (TNF) were analyzed in solution and in the solid state using electronic and CP-MAS ¹³C-NMR spectra. Model studies indicate that TCNE does not form a stable complex in the solid state with CzD, while TNF forms a complex in the molar ratio of 1 : 1. Solid-state CTCs of the polyimines with either acceptor retain some solvent which helps in formation of some supramolecular organization. After the solvent is eliminated the CTCs are amorphous and do not show decomplexation. Cross-polarization experiments and T_1ρH measurements in the solid-state NMR spectra demonstrate that the polymer CTCs are very mobile, with a solution-like behavior. © 1992 John Wiley & Sons, Inc.     

Thermal analysis of fluidised bed combustion residues containing limestone scavenger

A method has been developed using thermoanalytical techniques for the analysis of residues from coal-burning fluidised bed plant where limestone is used as a sulphur scavenger. This completely eliminates the need for lengthy wet chemical analyses and allows the derivation of parameters necessary for efficient plant operation, such as limestone addition rate, calcium utilisation efficiency and calcium to sulphur mole ratio. The method also gives values for the unburned carbon content and the ratio of coal ash to limestone derivatives in the sample.