Simple reagent for the synthesis of oligonucleotides labeled with 3,3,3′,3′-tetramethyl-2,2′-indodicarbocyanine

Synthesis of a phosphoramidite reagent for the preparation of oligonucleotides labeled at the 5′-end with a fluorescent dye, 3,3,3′,3′-tetramethyl-2,2′-indodicarbocyanine, is described. The efficiency of this reagent is confirmed by the synthesis of several labeled oligonucleotides. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 154–158, January, 2006.     

Different Strategies of Covalent Attachment of Oligonucleotide Probe onto Glass Beads and the Hybridization Properties

The glass bead is a new biochip support material for immobilization biomolecules, due to its independence and convenient rearrangement. In order to optimize the immobilization efficiency of oligonucleotides onto glass beads and obtain the highest hybridization efficiency, three commonly used coupling strategies have been studied for covalently attaching oligonucleotides onto large glass beads. Glass beads with 250 μm diameter were amino-silaned with 2% 3-aminopropyltrimethoxysilane (APTMS) and then reacted separately with glutaraldehyde, succinic anhydride and 1,4-phenylene diisothiocyanate (PDITC) to derive CHO beads, COOH beads and isothiocyanate-modified beads (NCS-Beads) accordingly. Afterwards, amino-terminal oligonucleotides were covalently attached onto the surface of beads achieved by three strategies mentioned above. The immobilization efficiency were studied to compare the three strategies, which turned out 2.55 × 10¹³ probes/cm² for CHO-Beads, 3.21 × 10¹³ probes/cm² for COOH beads and 6.68 × 10¹³ probes/cm² for NCS beads. It meant that the immobilization efficiency based on NCS beads was most acceptable. And the method, developed by attaching amino-terminal oligonucleotides onto these cyanate active beads, could be regarded as an efficient one for immobilizing oligonucleotides onto a solid surface. Moreover, in this paper, the hybridization properties of NCS bead-based oligonucleotides have been studied by employing Cy5-tagged complementary oligonucleotides. It was found that the high probe density NCS beads led to low hybridization efficiency possibly due to the existence of steric crowding. In addition, the equilibrium binding constant K _A was determined by employing Langmuir isotherm model, which was 7.0 × 10⁶ M⁻¹ for NCS beads with the density of 6.7 × 10¹³ probes/cm². Furthermore, it only took 60 min to reach hybridization equilibrium. These large microspheres (>100 μm) can be employed in the mesofluidic systems for automated heterogeneous assays.     

Gas Chromatographic-Ion Trap Mass Spectrometric Analysis of Volatile Organic Compounds by Ion–Molecule Reactions Using the Electron-Deficient Reagent Ion CCl<Stack><Subscript>3</Subscript><Superscript>+</Superscript></Stack>

When using tetrachloromethane as the reagent gas in gas chromatography-ion trap mass spectrometry equipped with hybrid ionization source, the cation CCl₃⁺ was generated in high abundance and further gas-phase experiments showed that such an electron-deficient reagent ion CCl₃⁺ could undergo interesting ion–molecule reactions with various volatile organic compounds, which not only present some informative gas-phase reactions, but also facilitate qualitative analysis of diverse volatile compounds by providing unique mass spectral data that are characteristic of particular chemical structures. The ion–molecule reactions of the reagent ion CCl₃⁺ with different types of compounds were studied, and results showed that such reactions could give rise to structurally diagnostic ions, such as [M + CCl₃ – HCl]⁺ for aromatic hydrocarbons, [M – OH]⁺ for saturated cyclic ether, ketone, and alcoholic compounds, [M – H]⁺ ion for monoterpenes, M^·+ for sesquiterpenes, [M – CH₃CO]⁺ for esters, as well as the further fragment ions. The mechanisms of ion–molecule reactions of aromatic hydrocarbons, aliphatic ketones and alcoholic compounds with the reagent ion CCl₃⁺ were investigated and proposed according to the information provided by MS/MS experiments and theoretical calculations. Then, this method was applied to study volatile organic compounds in Dendranthema indicum var. aromaticum and 20 compounds, including monoterpenes and their oxygen-containing derivatives, aromatic hydrocarbon and sesquiterpenes were identified using such ion–molecule reactions. This study offers a perspective and an alternative tool for the analysis and identification of various volatile compounds.     

Spectroscopic study of protonation of oligonucleotides containing adenine and cytosine

Acidobasic properties of purine and pyrimidine bases (adenine, cytosine) and relevant nucleosides (adenosine, cytidine) were studied by means of glass-electrode potentiometry and the respective dissociation constants were determined under given experimental conditions (I = 0.1 M (NaCl), t = (25.0 ± 0.1) °C): adenine (pK _HL = 9.65 ± 0.04, pK _H2L = 4.18 ± 0.04), adenosine (pK _H2L = 3.59 ± 0.05), cytosine (pK _H2L = 4.56 ± 0.01), cytidine (pK _H2L = 4.16 ± 0.02). In addition, thermodynamic parameters for bases: adenine (ΔH ⁰ = (−17 ± 4) kJ mol⁻¹, ΔS ⁰ = (23 ± 13) J K⁻¹ mol⁻¹), cytosine (ΔH ⁰ = (−22 ± 1) kJ mol⁻¹, ΔS ⁰ = (13 ± 5) J K⁻¹ mol⁻¹) were calculated. Acidobasic behavior of oligonucleotides (5′CAC-CAC-CAC3′ = (CAC)₃, 5′AAA-CCC-CCC3′ = A₃C₆, 5′CCC-AAA-CCC3′ = C₃A₃C₃) was studied under the same experimental conditions by molecular absorption spectroscopy. pH-dependent spectral datasets were analyzed by means of advanced chemometric techniques (EFA, MCR-ALS) and the presence of hemiprotonated species concerning (C⁺-C) a non-canonical pair (i-motif) in titled oligonucleotides was proposed in order to explain experimental data obtained according to literature.     

Accessing HgSe<Subscript><Emphasis Type="Italic">x</Emphasis></Subscript>S<Subscript><Emphasis Type="Italic">1−x</Emphasis></Subscript> Nanoparticles Using the Single-Source Reagent Me<Subscript>3</Subscript>Si–SeS–SiMe<Subscript>3</Subscript>

Mercury-selenosulfide (HgSe _x S _1-x ) nanoparticles have been synthesized using the single-source reagent Me₃Si–SeS–SiMe₃. The reagent distributes Se²⁻ and S²⁻ to the metal core as the reaction between Me₃Si–SeS–SiMe₃ and mercury acetate occurs via a redox pathway, ultimately giving rise to Se–S bond cleavage. Particles are characterized by EDX, TEM and powder X-ray diffraction analysis in conjunction with UV–Visible absorption spectroscopy. Dedicated to Prof. Dr. Dieter Fenske on the occasion of his 65th birthday.     

Determination of phenols in waters using micro-pumped multicommutation and spectrophotometric detection: an automated alternative to the standard procedure

An automated and greener spectrophotometric procedure has been developed for the determination of phenol in water at 700 nm. The method uses the reaction between phenol, sodium nitroprusside, and hydroxylamine hydrochloride in a buffered medium at pH 12.3. The flow manifold comprises four solenoid micro-pumps employed for sample and reagent introduction into the reaction coil and to transport the colored product formed to the detector. The linear dynamic range was 50–3,500 ng mL⁻¹ (R = 0.99997; n = 6) and the method provided a limit of detection (3σ) of 13 ng mL⁻¹. The sampling throughput was estimated to be 65 measurements per hour and the coefficient of variation was 0.5% (n = 10) for a 1.0 μg mL⁻¹ phenol concentration. Recoveries of 92–105% were obtained for phenol determination in spiked water samples at concentration levels from 50 to 5,000 ng mL⁻¹. The use of multicommutation reduced the reagent consumption 25-fold, the sample consumption 225-fold, and the waste generation 30-fold compared with the batch procedure. The proposed method is an environmentally friendly alternative to the official 4-aminoantipyrine method since it avoids the use of chloroform.     

Optical and chromaticity characteristics of palladium(II) complex with 1-nitroso-2-naphthol-3,6-disulfonic acid

Optimal conditions of complexation palladium(II) with 1-nitroso-naphthol-3,6-disulfonic acid were found by the spectrophotometric method (an optimum interval pH 1.2–3.8, a five-multiple surplus reagent). The analytical characteristics of a complex in an interval concentration of palladium(II) (0.94–8.59) × 10⁻⁵ M are determined, ɛ = (9.80 ± 0.02) × 10³ (n = 9, P = 0.95). The function and molar coefficient of chromaticity are determined. The most sensitive functions are G [(7.6 ± 0.1) × 10⁵] and Z [(5.6 ± 0.2) × 10⁵] (n = 5, P = 0.95).     

Enhanced thermal stability of poly(p-dioxanone) in melt by adding an end-capping reagent

For the enhancement of thermal stability of poly(p-dioxanone) (PPDO), the isocyanate end-capping reagent was prepared by treatment of toluene-2,4-diisocyanate with an equivalent of 1-hexyl alcohol. The end-capping reagent and the end-capping PPDO with an inherent viscosity of 0.26 dL g⁻¹ were characterized by FTIR and ¹H-NMR. Thermal stability of the end-capping PPDO with an inherent viscosity of 0.92 dL g⁻¹ was investigated isothermally and non-isothermally under air atmosphere using thermogravimetry. It has been shown that the addition of the prepared isocyanate can enhance significantly the thermal stability of PPDO. The activation energies for non-isothermal degradation estimated by Kissinger method and Friedman method are 91, 81 kJ mol⁻¹ for as-prepared PPDO, and 160, 149 kJ mol⁻¹ for the end-capping PPDO, respectively. The activation energy increases by about 70 kJ mol⁻¹ through the end-capping.     

Utility of <Emphasis Type="Italic">π</Emphasis>-acceptor reagents for spectrophotometric determination of sulphonamide drugs via charge-transfer complex formation

A simple, sensitive and accurate spectrophotometric method for the determination of sulphonamides (sulphamethoxazole (SMZ), sulphaguanidine (SGD), sulphaquinoxaline sodium (SQX), sulphametrole (SMR), and sulphadimidine sodium (SDD)) has been developed. The charge-transfer reactions between sulphonamides as n-electron donors and 7,7,8,8-tetracyanoquinodimethane (TCNQ), 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ), and 2,5-dichloro-3,6-dihydroxy-1,4-benzoquinone (chloranilic acid, p-CLA) as π-acceptors resulting in highly coloured complexes were studied. Experimental conditions for these CT reactions were carefully optimised. Beer’s law is valid over the concentration ranges from 4–280 μg mL⁻¹, 4–260 μg mL⁻¹, 4–200 μg mL⁻¹, and 4–200 μg mL⁻¹ of SMZ, SGD, SQX, and SDD using DDQ reagent, respectively. While the calibration curves are linear in the concentration ranges from 4–180 μg mL⁻¹, 4–80 μg mL⁻¹, 4–60 μg mL⁻¹, 4–180 μg mL⁻¹, and 4–60 μg mL⁻¹ of SMZ, SGD, SQX, SMR, and SDD, respectively, using TCNQ reagent and from 4–380 μg mL⁻¹ and 4–300 μg mL⁻¹ of SQX and SDD, respectively, using p-CLA reagent, respectively. Different analytical parameters, namely molar absorptivity (ε), standard deviation, relative standard deviation, correlation coefficient, limit of detection, and limit of quantification, were calculated. The results obtained by the proposed methods are in good agreement with those obtained by the official method as indicated by the percent recovery values.     

Asymmetric synthesis of β-N-substituted α,β-diamino acidsvia a chiral complex of NiII with a dehydroalanine derivative

Asymmetric synthesis of β-N-substituted (S)-α,β-diamino acids was accomplished by Michael addition of amines to the Ni^II complex of the Schiff base derived from (S)-2-[N-(N′-benzylprolyl)amino]benzophenone (BPB) and dehydroalamine. Diastereoselectivity of the reaction is kinetically and thermodynamically controlled. The chiral auxiliary reagent, BPB, can be recovered and reused. Translated fromIzvestiya Akademii Nauk. Serya Khimicheskaya, No. 3, pp. 504–507, March, 1997.     

Enhanced in-source fragmentation in MALDI-TOF-MS of oligonucleotides using 1,5-diaminonapthalene

The capability to rapidly and confidently determine or confirm the sequences of short oligonucleotides, including native and chemically-modified DNA and RNA, is important for a number of fields. While matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been used previously to sequence short oligonucleotides, the typically low fragmentation efficiency of in-source or post-source decay processes necessitates the accumulation of a large number of spectra, thus limiting the throughput of these methods. Here we introduce a novel matrix, 1,5-diaminonapthalene (DAN), for facile in-source decay (ISD) of DNA and RNA molecular anions, which allows for rapid sequence confirmation. d-, w-, and y-series ions are prominent in the spectra, complementary to the (a-B)- and w- ions that are typically produced by MALDI post-source decay (PSD). Results are shown for several model DNA and RNA oligonucleotides, including combinations of DAN-induced fragmentation with true tandem TOF MS (MS/MS) for pseudo-MS³ and “activated-ion PSD.”     

Preparation of lithium fast ionic conductor by sol-gel-hydrothermal method

The solid fast ionic conductor was synthesized by the sol-gel-hydrothermal method. The influences of the dispersion reagent, the alkalinity and the calcination temperature on the surface morphology of nanopowders, and the electric conductivity were discussed. When PEG 12000 was used as the dispersion reagent, the alkalinity was 1.0% and the calcination temperature was 550°C; the electric conductivity at ambience temperature of the inorganic nanopowder of lithium fast ionic conductor synthesized was 2.59 × 10⁻³ S·cm⁻¹. __________ Translated from Journal of National University of Defense Technology, 2005, 27(2) (in Chinese)     

一锅法可控合成金属有机框架材料Mn-荧光素用于核磁共振/荧光成像

通过一锅法,首次将核磁共振成像试剂Mn2+和荧光成像试剂荧光素(FSD)自组装于一个简单的金属有机框架材料(Mn-FSD)上.实验结果表明,Mn-FSD的粒径可被控制在微纳米水平内并进行生物成像.体外和体内实验结果证实,Mn-FSD可在细胞和裸鼠中显示强绿色荧光.同时,Mn-FSD表现出较高的弛豫值(r1=4.95 L...     

Development of a flow injection method for monitoring cell membrane damage of wine lactic acid bacteria

A flow injection analysis (FIA) system was developed for the determination of phosphate efflux from wine lactic acid bacteria (Oenococus oeni and Lactobacillus hilgardii) as an indication of cell membrane damage. The system allowed the direct injection of the cell suspension, avoiding the filtration step, with minimum sample treatment and minimized reagent consumption. The developed system is characterized by a linear concentration zone between 3.23 × 10⁻⁵ and 4.84 × 10⁻⁴ mol L⁻¹ PO₄ ³⁻ and repeatability better than 2.9%. Bacterial suspensions were exposed to a chemical stress with phenolic acids and injected in the FIA system at regular intervals. The extracellular concentration of phosphate was measured spectrophotometrically. The experimental results obtained indicate that hydroxycinnamic acids (p-coumaric, ferulic and caffeic) induced faster phosphate leakage rates than hydroxybenzoic acids (vanillic and p-hydroxybenzoic) in both strains tested, which could be related to their higher lipophilic character.     

Reduction of carbon monoxide by molybdenum-containing hydroxide systems

The reduction of CO by the nitrogen-fixing systems Ti(OH)₃−Mo(OH)₃ and MgTi₂O₄−Mo(OH)₃ was studied in aqueous and water-methanol media; in the latter,¹⁴CO was used as the reagent. The main reaction product is methanol, whose yield in the H₂O−MeOH−KOH mixture is almost an, order of magnitude higher than that in an aqueous alkaline solution. The data obtained were compared to those for the reduction of N₂ Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10 pp. 2081–2083, October, 1998.     

Adsorption of reactive brilliant red K-2BP on activated carbon developed from sewage sludge

Activated carbon was prepared from the sewage sludge of municipal wastewater treatment plant by chemical activation (activation reagent is ZnCl₂) and was used for the adsorption of dye (reactive brilliant red K-2BP). The impact of adsorbent amount, adsorption time and pH value on adsorption effect, the adsorption kinetics, and the adsorption thermodynamics were discussed according to batch adsorption tests. The results indicated that the activated carbon developed from sewage sludge (ACSS), which was mesoporous, possessed opened porous structures. The iodine number of the ACSS was 326 mg·g⁻¹. The rate of achievement was 51.31%. The BET surface area was 298 m²·g⁻¹ and the contents of heavy metals in the leachate didn’t exceed the contents limit. The adsorption kinetics of reactive brilliant red K-2BP on the ACSS was accorded with the two-step kinetics rate equation and pseudo-second-order kinetics equation. Compared to the Freundlich isotherm equation, the Langmuir isotherm equation showed better applicability for the adsorption. The adsorption which was favorable was an endothermic (enthalpy ΔH > 0) and spontaneous (free energy ΔG < 0) process and was accompanied by an increase in entropy (ΔS > 0). __________ Translated from Journal of Shandong University (Natural Science), 2007, 42(3): 64–70 [译自: 山东大学学报(理学版)]     

Peculiarities of the Interaction of Short Oligonucleotides with Supported Lipid Films and Langmuir Monolayers

Summary.  The method of electrostriction was applied to supported bilayer lipid membranes (sBLM) and Langmuir monolayers with the aim to study the peculiarities of the interaction of short oligonucleotides with lipid films and of the duplex formation between complementary oligonucleotides. The bilayer lipid membranes (sBLM) were formed on an agar support, whereas Langmuir monolayers were generated on the air-water interface. As an oligonucleotide, the 15-mer 5^′-cholesterolphosphoryl-dT15 (CHpdT15) was synthesized. We could show that the interaction of CHpdT15 with sBLM resulted in a considerable increase of the elasticity modulus perpendicular to the membrane plane (E _⊥) and an increase of the surface potential. Interaction of complementary oligodeoxyadenylate (dA15) with sBLM modified by CHpdT15 resulted in a slight increase of the surface potential whereas E _⊥ slightly decreased. CHpdT15 forms monomolecular layers on the air/water interface. Interaction of dA15 with such monolayers resulted in an increase of the surface pressure, probably due to an increase of the surface charge of the monolayer; similar effects were observed for lipid monolayers modified by CHpdT15. Prospects of using such interactions for detecting DNA hybridization are discussed. Received June 23, 2000. Accepted (revised) September 19, 2000     

An efficient chiral synthesis of (R)-N-[3-acetyl-4-(2-hydroxy-3-isopropylamino-propoxy)phenyl]-butanamide with high enantioselectivity

R-Enantiomer of the β-receptor antagonist N-[3-acetyl-4-(2-hydroxy-3-isopropylamino-propoxy)phenyl] butanamide with high enantioselectivity was synthesized from cheap starting materials and enantiopure chiral reagent through an efficient, convenient and practical synthetic strategy. Title product was detected by ¹H NMR, ¹³C NMR, and MS, and the enatiomeric excess was determined by chiral HPLC analysis using a chiracel AD-H column. Supported by the National Natural Science Foundation of China (Grant Nos. 20472090 & 10576034) and PLA General Armament Department (Grant No. 9140A28010707zk7301)     

Reagents for addressed modification of biopolymers

Derivatives of histidine, imidazolylacetic and urocanic acids, containing anN ^Im-2,4-dinitrophenyl moiety and a hydroxy group were synthesized and characterized. The applicability of these reagents for anchoring imidazole residues to oligonucleotides to give potential site-specific artificial ribonucleases was shown taking the synthesis of dinucleotide derivatives as an example. For Part 10. see Ref. 1. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 536–541, March, 2000.     

Determination of total and extractable hydrogen peroxide in organic and aqueous solutions of uranyl nitrate

The development of a spectrophotometric method for the determination of hydrogen peroxide in uranyl nitrate solutions is reported. The method involves the measurement of the absorbance at 520 nm of a vanadyl peroxide species. This species was formed by the addition of a reagent consisting of vanadium (V) (50 mmol·dm⁻³) in dilute sulphuric acid (2 mol·dm⁻³ H₂SO₄). This reagent, after dilution, was also used as an extractant for organic phase samples. The method is simple and robust and tolerant of nitric acid and U(VI). Specificity and accuracy were improved by the application of solid phase extraction techniques to remove entrained organic solvents and Pu(IV). Reverse phase solid phase extraction was used to clean-up aqueous samples or extracts which were contaminated with entrained solvent. A solid phase extraction system based upon an extraction chromatography system was used to remove Pu(IV). Detection limits of 26 μmol·dm⁻³ (0.88 μg·cm⁻³) or 7 μmol·dm⁻³ (0.24 μg·cm⁻³) for, respectively, a 1 and 4 cm path length cell were obtained. Precisions of RSD=1.4% and 19.5% were obtained at the extremes of the calibration curve (5 mmol·dm⁻³ and 50 μmol·dm⁻³ H₂O₂, 1 cm cell). The introduction of the extraction and clean-up stages had a negligible effect upon the precision of the determination. The stability of an organic phase sample was tested and no loss of analyte could be discerned over a period of at least 5 days. The presence of trace levels of reductants interfered with the determination, e.g., hydrazine (<2 mmol·dm⁻³), but this effect was ameliorated by increasing the concentration of the colormetric reagent.