Synthesis of a novel linear polymer of a macrocyclic polyamine copper (II) complex and its interaction with plasmid DNA

The novel linear polymer of a macrocyclic polyamine copper (II) complex, which has many cyclen groups linked by epichlorohydrin, has been synthesized as a DNA cleavage agent. The structure of the polymer 3 was identified by ¹HNMR and IR and its molecular weight was measured by GPC. The result of agarose gel electrophoresis assay showed that Cu-(II) complex 4 could act as a powerful catalyst for the cleavage of plasmid DNA under physiological conditions.     

Strong Indirect Effects of a Submersed Aquatic Macrophyte, Vallisneria americana, on Bacterioplankton Densities in a Mesotrophic Lake

Phytoplankton and allochthonous matter are important sources of dissolved organic carbon (DOC) for planktonic bacteria in aquatic ecosystems. But in small temperate lakes, aquatic macrophytes may also be an important source of DOC, as well as a source or sink for inorganic nutrients. We conducted micro- and mesocosm studies to investigate the possible effects of an actively growing macrophyte, Vallisneria americana, on bacterial growth and water chemistry in mesotrophic Calder Lake. A first microcosm (1 L) study conducted under high ambient NH ₄ ⁺ levels (NH ₄ ⁺ 10 µM) demonstrated that macrophytes had a positive effect on bacterial densities through release of DOC and P. A second microcosm experiment, conducted under NH ₄ ⁺ -depleted conditions (NH ₄ ⁺ < 10 µM), examined interactive effects of macrophytes and their sediments on bacterial growth and water chemistry. Non-rooted macrophytes had negative effects on bacterial numbers, while rooted macrophytes had no significant effects, despite significant increases in DOC and P. A 70-L mesocosm experiment manipulated macrophytes, as well as N and P supply under surplus NH ₄ ⁺ conditions (NH ₄ ⁺ 10 µM), and measured effects on bacterial growth, Chl a concentrations, and water chemistry. Bacterial growth and Chl a concentrations declined with macrophyte additions, while bacterial densities increased with P addition (with or without N). Results suggest that the submersed macrophyte Vallisneria exerts a strong but indirect effect on bacteria by modifying nutrient conditions and/or suppressing phytoplankton. Effects of living macrophytes differed with ambient nutrient conditions: under NH ₄ ⁺ -surplus conditions, submersed macrophytes stimulated bacterioplankton through release of DOC or P, but in NH ₄ ⁺ -depleted conditions, the influence of Vallisneria was negative or neutral. Effects of living macrophytes on planktonic bacteria were apparently mediated by the macrophytes use and/or release of nutrients, as well as through possible effects on phytoplankton production.     

Some Examples of the Use of Trifluoromethane Sulfonic Anhydride in Nucleic Acid Chemistry

Abstract

Trifluoromethane sulfonic anhydride has been used for the inversion of configuration at the 3′-position of 2′-deoxypurine nucleosides, for the modification of the base moiety of purine and pyrimidine nucleosides, for nucleophilic substitution in the sugar moiety, for the synthesis of O²,3′-cyclothymidine and for sugar-base condensation reactions. Reaction can be carried out under very mild conditions. The conditions for these reactions are quite different so that a good selectivity can be obtained when different reactive groups are present.     

The structure of Pseudomonas fluorescens biofilms in contact with flowing systems

Using a specially designed flow system Pseudomonas fluorescens has been grown on the inside of glass tubes under carefully controlled conditions. Results show that films developed from water flowing at 0–5 m.s^‐1 are less compact and thicker than with a water velocity of 2–5 m.s^‐1. In the latter all the cells are aligned in the direction of flow whereas in the former the individual cells directly attached to the surface, are randomly distributed with groups of cells lying parallel to the tube axis.     

Efficient photodynamic inactivation of Leishmania parasites mediated by lipophilic water-soluble Zn(II) porphyrin ZnTnHex-2-PyP4+

BackgroundPhotodynamic inactivation (PDI) is emerging as a promising alternative for cutaneous leishmaniasis (CL). The chemotherapy currently used presents adverse effects and cases of drug resistance have been reported. ZnTnHex-2-PyP⁴⁺ is a porphyrin with a high potential as a photosensitizer (PS) for PDI, due to its photophysical properties, structural stability, and cationic/amphiphilic character that can enhance interaction with cells. This study aimed to investigate the photodynamic effects mediated by ZnTnHex-2-PyP⁴⁺ on Leishmania parasites.MethodsZnTnHex-2-PyP⁴⁺ stability was evaluated using accelerated solvolysis conditions. The photodynamic action on promastigotes was assessed by (i) viability assays, (ii) mitochondrial membrane potential evaluation, and (iii) morphological analysis. The PS-promastigote interaction was studied. PDI on amastigotes and the cytotoxicity on macrophages were also analyzed.ResultsZnTnHex-2-PyP⁴⁺, under submicromolar concentration, led to immediate inactivation of more than 95% of promastigotes. PDI promoted intense mitochondrial depolarization, loss of the fusiform shape, and plasma membrane wrinkling in promastigotes. Fluorescence microscopy revealed a punctate PS labeling in the parasite cytoplasm. PDI also led to reductions of ca. 64% in the number of amastigotes/macrophage and 70% in the infection index after a single treatment session. No noteworthy toxicity was observed on mammalian cells.ConclusionsZnTnHex-2-PyP⁴⁺ is stable against demetallation and more efficient as PS than the ethyl analogue ZnTE-2-PyP⁴⁺, indicating readiness for evaluation in in vivo studies as an alternative approach to CL.General significanceThis report highlighted promising photodynamic effects mediated by ZnTnHex-2-PyP⁴⁺ on Leishmania parasites, opening up perspectives for applications in CL pre-clinical assays and PDI of other microorganisms.     

Identification of acylation products in SHAPE chemistry

SHAPE chemistry (selective 2′-hydroxyl acylation analyzed by primer extension) has been developed to specifically target flexible nucleotides (often unpaired nucleotides) independently to their purine or pyrimidine nature for RNA secondary structure determination. However, to the best of our knowledge, the structure of 2′-O-acylation products has never been confirmed by NMR or X-ray data. We have realized the acylation reactions between cNMP and NMIA under SHAPE chemistry conditions and identified the acylation products using standard NMR spectroscopy and LC–MS/MS experiments. For cAMP and cGMP, the major acylation product is the 2′-O-acylated compound (>99%). A trace amount of N-acylated cAMP has also been identified by LC–UV–MS². While for cCMP, the isolated acylation products are composed of 96% of 2′-O-acylated, 4% of N,O-diacylated, and trace amount of N-acylated compounds. In addition, the characterization of the major 2′-O-acylated compound by NMR showed slight differences in the conformation of the acylated sugar between the three cyclic nucleotides. This interesting result should be useful to explain some unexpected reactivity of the SHAPE chemistry.     

Attachment Behavior of Shewanella putrefaciens onto Magnetite under Aerobic and Anaerobic Conditions

In this study, batch experiments were used to characterize attachment behavior of Shewanella putrefaciens strain 200R to ferrihydrite and magnetite. Attachment was quantified in batch experiments with a 0.01 M NaNO ₃ solution as a function of pH (ranging from 3 to 10), sorbed anion (PO₄ ^{3 ?} ), and growth conditions (aerobic vs. anaerobic). Electrophoretic mobility data was collected for S. putrefaciens cells and magnetite grains and used as a means to interpret the role of electrostatic interaction in attachment studies. Little difference in attachment behavior was observed as a function of growth conditions or surface treatments. The exception was at pH ranging from 2 to 4, under anaerobic conditions, where increased attachment was measured on magnetite surfaces with sorbed PO₄ ^{3 ?} . This increased attachment was attributed to development of Fe-PO₄ surface complexes or secondary mineral phases, resulting in altered surface interactions between cell and mineral surfaces. Attachment was irreversible and increased with time under anaerobic conditions even under elevated pH conditions unfavourable to electrostatic interactions between cells and mineral surfaces. These results suggest that electrophoretic mobility data in this system is not a good predictor of attachment behavior, while surface charge development via protonation and deprotonation of surface functional groups is consistent with experimental attachment data. In this study, S. putrefaciens appears to utilize polymers or pili to remain attached to Fe-oxides and this process may facilitate Fe reduction on these surfaces. Results from this study underscore the need for quantitative bulk measurements of microbial attachment to accurately predict partitioning of dissimilatory iron reducing bacteria between solution and solid phases.     

Opioid Peptides: Synthesis and Biological Activity of New Endomorphin Analogues

Summary Syntheses are described of new endomorphin 1 and 2 peptoid–peptide hybrids in which Tyr¹ and either one or both Phe³ and Phe⁴ have been replaced by N-substituted-glycine. The preparation is also described of two glycosylated Hyp²-endomorphin 2 analogues in which either 2,3,4,6-tetra-O-acetyl glucose or glucose are β-O-glycosidically linked to the hydroxyproline residue. The Hyp²-endomorphin sequences have also been elongate by adding a C-terminal β-alanine residue and several linear dimers have been prepared by coupling either the native peptides or the modified analogues. The cyclo endomorphin 2 has also been synthesized. Preliminary pharmacological experiments on isolated organ preparations showed that the agonist activities of both endomorphin 1 and 2 are not significantly affected by the Pro/Hyp substitution. Phe⁴/Nphe substitution in the endomorphin 1 reduced the potency on guinea pig ileum (GPI) by about 100 times and abolished the agonist activity on mouse vas deferens (MVD) preparation. The decrease of the agonist activity induced by modification of one phenylalanine residue only, either Phe³ or Phe⁴, is lower on endomorphin 2. Either modification of both Phe³ and Phe⁴ or glycosylation of the Hyp²-endomorphin 2 cancelled any agonist activity on both preparations. The linear peptide dimers [endomorphin 1]₂, [endomorphin 2]₂, [Hyp²-endomorphin 1]₂, [Hyp²-endomorphin 2]₂, [Hyp²-endomorphin 1-Hyp²-endomorphin 2]₂ or [Hyp²-endomorphin 2-Hyp²-endomorphin 1]₂, are 7–19 times less potent than endomorphin 1 on GPI and significantly less active than endomorphins 1 and 2 on MVD. The other afforded modifications significantly affected or abolished the agonist activity of the resulting endomorphin analogues on both GPI and MVD preparations.The α-amino acid residues are of the L-configuration. Standard abbreviations for amino acid derivatives and peptides are according to the suggestions of the IUPAC-IUB Commission on Biochemical Nomenclature (1984) Eur. J. Biochem., 138, 9–37. Abbreviations listed in the guide published in (2003) J. Peptide Sci., 9, 1–8 are used without explanation.     

Purine Based Combinatorial Chemistry: Solution Phase Simultaneous Addition of Functionalities. Iterative Deconvolution by Orthogonal Protection to a Single Compound with Potent Antibacterial Activity

Abstract

We have recently described a method to prepare combinatorial chemistry libraries by solution phase simultaneous addition of functionalities (SPSAF).^1–2 SPSAF has been used to create libraries based on the purine heterocycle. The nucleophilic sites (secondary nitrogens) in the planer heteroaromatic purine scaffold were built in via linkers. Thus, to continue the use of electophilic functionalities, as in previous libraries, a bifunctional nucleophilic linker was required. Piperazines readily served this purpose. Nucleophilic displacement of the chloro groups on 2,6-dichloropurine with piperazines provides reactive, constrained secondary amines for combinatorialization (Figure 1, 1). An additional piperazine was placed in the 9-position by alkylation of 2,6-dipiperazinylpurine. In this manner, the functionality that differentiates each pool (sublibrary) could be placed last in the synthetic scheme (fix last concept).¹     

8-AZA-7-DEAZAADENINE AND 7-DEAZAGUANINE: SYNTHESIS AND PROPERTIES OF NUCLEOSIDES AND OLIGONUCLEOTIDES WITH NUCLEOBASES LINKED AT POSITION-8

The 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin-4-amine) N⁸-(2′-deoxy-ribonucleoside) (2) and the 7-deazaguanine (pyrrolo[3,4-d]pyrimidine-2-amin-(3H)-4-one) C⁸-(2′-deoxyribonucleoside) (4) were synthesized and incorporated in oligonucleotides employing phosphoramidite chemistry. Oligonucleotides carrying compound 2 are able to form base pairs with the four canonical DNA constituents without significant structural discrimination. The nucleoside 4 was obtained from the corresponding ribonucleoside by deoxygenation. Oligonucleotides containing compound 4 showed similar base pairing properties as those with 2′-deoxyisoguanosine.     

Synthesis and DNA Binding Studies of Novel Heterocyclic Substituted Quinoline Schiff Bases: A Potent Antimicrobial Agent

The present article deals with the synthesis of 2-chloroquinoline-3-carbaldehyde [(2-hydroxy-1-naphthyl) methylene] hydrazone (CQCMH) (2a-c) and 2-chloroquinoline-3-carbaldehyde [4-(dimethylamino) benzylidene] hydrazone (CQCDBH) (3a-c) from quinoline derivatives under suitable experimental conditions. The synthesized compounds were characterized by elemental analysis, FTIR, ¹HNMR, and mass spectral data. The selected compounds were studied for interaction with calf thymus-DNA (CT-DNA) by electronic spectra, viscosity measurements as well as thermal denaturation studies. On binding to DNA, the absorption spectrum underwent bathochromic and hypochromic shifts. The binding constant (K_b) had value of 2.3×10³ M^?1 for (2a) and 2.5×10⁴ M^?1 for (3a). The viscosity measurements indicated that the viscosity of sonicated rod like DNA fragments increased. The synthesized derivatives have been screened for antibacterial and antifungal activities.     

DNA binding,prominent photonuclease activity and antibacterial PDT of cobalt(II) complexes of phenanthroline based photosensitizers

Abstract

The chemistry of Co(II) complexes showing efficient light induced DNA cleavage activity, binding propensity to calf thymus DNA and antibacterial PDT is summarized in this article. Complexes of formulation [Co(mqt)(B)₂]ClO₄ 1–3 where mqt is 4-methylquinoline-2-thiol and B is N,N-donor heterocyclic base, viz. 1,10-phenanthroline (phen 1), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq 2) and dipyrido[3,2-a:2′,3′-c]phenazine (dppz 3) have been prepared and characterized. The DNA-binding behaviors of these three complexes were explored by absorption spectra, viscosity measurements and thermal denaturation studies. The DNA binding constants for complexes 1, 2 and 3 were determined to be 1.6?×?10³?M^?1, 1.1?×?10⁴?M^?1 and 6.4?×?10⁴?M^?1 respectively. The experimental results suggest that these complexes interact with DNA through groove binding mode. The complexes show significant photocleavage of supercoiled (SC) DNA proceeds via a type-II process forming singlet oxygen as the reactive species. Antimicrobial photodynamic therapy was studied using photodynamic antimicrobial chemotherapy (PACT) assay against E. coli and all complexes exhibited significant reduction in bacterial growth on photoirradiation.     

马利亚霉菌(Mariannaeasp.) HJ合成金属硒化物及机理研究

[背景] 金属硒化物因其优异的光电和催化特性,近年来在半导体、电化学及抗癌等领域成为了研究热点。相较于传统的化学还原法,生物合成金属硒化物具有环境友好、耗能较低等优势。然而,目前有关生物合成金属硒化合物的微生物资源较少且相关合成机理尚不明晰。[目的] 利用马利亚霉菌（Mariannaea sp.） HJ合成了3种金属硒化物并对其合成机理进行了初步探索。[方法] 利用X射线衍射（X-Ray Diffraction,XRD）和傅里叶转换红外线光谱（Fourier Transform Infrared Spectroscopy,FTIR）对菌株HJ合成的金属硒化物进行了初步的表征,考察了纳米材料合成过程中总巯基含量、总抗氧化性能及自由基含量变化,并且验证了转运蛋白DMT1在金属硒化物合成中所起的关键性作用。[结果] XRD结果表明菌株HJ能够在Bi³⁺、Pb²⁺、Co²⁺与SeO₃^2-作用下分别合成Bi₄Se₃、PbSe和CoSe₂纳米颗粒,其合成的最优pH条件分别为6.0、7.0、8.0。FTIR结果表明,合成的金属硒化物表面含有氨基、羧基、羟基等官能团。3种金属硒化物的合成反应体系与空白对照组相比,总巯基含量明显下降,而总抗氧化性能却有所提高,这表明巯基等酶促体系或氨基酸金属蛋白类的非酶促体系可能参与了SeO₃^2-的还原过程。苄基异硫脲盐酸盐屏蔽实验表明,转运蛋白DMT1在SeO₃^2-转运和金属硒化物分泌过程中起到关键作用。此外,Bi³⁺、Pb²⁺和Co²⁺的加入使得菌株HJ产生氧化应激反应,在胞外分泌了大量的过氧化氢、羟基自由基和超氧自由基,而上述自由基可通过诱导热激效应的方式增强金属离子或纳米颗粒的转运过程。[结论] 利用马利亚霉菌（Mariannaeasp.） HJ合成了Bi₄Se₃、PbSe和CoSe₂纳米颗粒,为研究金属硒化物的生物合成及机理提供了一定的理论参考。     

A Reinvestigation of Sulfenyl Groups as Amino Protecting Groups for the Synthesis of Oligonucleotides on Solid Support by Phosphoramidite Chemistry†

Abstract

Although sulfenyl groups as protectors of heterocyclic amines of nucleosides appeared satisfactory during the synthesis of DNA and RNA via the phosphotriester approach, their usefulness in automated synthesis of oligonucleotides using phosphoramidite chemistry has not been investigated. Herein, we examined the stability and efficiency of 2-nitrophenylsulfenyl- and tritylsulfenyl-nucleosides upon the conditions applied in oligonucleotide synthesis by the phosphoramidite approach.

     

Conformational diversity of the quercetin molecule: a quantum-chemical view

Abstract

This paper focuses on the comprehensive conformational analysis of the quercetin molecule with a broad range of the therapeutic and biological actions. All possible conformers of these molecule, corresponding to the local minima on the potential energy hypersurface, have been obtained by the sequential rotation of its five hydroxyl groups and also by the rotation of its (A?+?C) and B rings relatively each other. Altogether, it was established 48 stable conformers, among which 24 conformers possess planar structure and 24 conformers – nonplanar structure. Their structural, symmetrical, energetical and polar characteristics have been investigated in details. Quantum-mechanical calculations indicate that conformers of the quercetin molecule are polar structures with a dipole moment, which varies within the range from 0.35 to 9.87 Debay for different conformers. Relative Gibbs free energies of these conformers are located within the range from 0.0 to 25.3?kcal·mol^?1 in vacuum under normal conditions. Impact of the continuum with ε?=?4 leads to the decreasing of the Gibbs free energies (–0.19–18.15?kcal·mol^?1) and increasing of the dipole moment (0.57–12.48?D). It was shown that conformers of the quercetin molecule differ from each other by the intramolecular specific contacts (two or three), stabilizing all possible conformers of the molecule – H-bonds (both classical ОН…О and so-called unusual С′Н…О and ОН…С′) and attractive van-der-Waals contacts О…О. Obtained conformational analysis for the quercetin molecule enables to provide deeper understanding of the ‘structure-function’ relationship and also to suggest its mechanisms of the therapeutic and biological actions.

Communicated by Ramaswamy H. Sarma     

Impact of tropospheric ozone on the Euro‐Mediterranean vegetation

The impact of ozone (O₃) on European vegetation is largely under‐investigated, despite huge areas of Europe are exposed to high O₃ levels and which are expected to increase in the next future. We studied the potential effects of O₃ on photosynthesis and leaf area index (LAI) as well as the feedback between vegetation and atmospheric chemistry using a land surface model (ORCHIDEE) at high spatial resolution (30 km) coupled with a chemistry transport model (CHIMERE) for the whole year 2002. Our results show that the effect of tropospheric O₃ on vegetation leads to a reduction in yearly gross primary production (GPP) of about 22% and a reduction in LAI of 15–20%. Larger impacts have been found during summer, when O₃ reaches higher concentrations. During these months the maximum GPP decrease is up to 4 g C m^?2 day^?1, and the maximum LAI reduction is up to 0.7 m² m^?2. Since CHIMERE uses the LAI computed by ORCHIDEE to estimate the biogenic emissions, a LAI reduction may have severe implications on the simulated atmospheric chemistry. We found a large change in O₃ precursors that however leads to small changes in tropospheric O₃ concentration, while larger changes have been found for surface NO₂ concentrations.     

Kinetic study of DNA binding of cisplatin and of a bicycloalkyl-substituted (ethylenediamine)dichloroplatinum(II) complex

 Salmon sperm DNA platination has been conducted under strictly pseudo-first-order conditions with cisplatin (1) and rac-{(1S,2S,4S)-exo-2-(aminomethyl)-2-amino-7-bicyclo[2.2.1]heptane}dichloroplatinum(II) (2). An aquation step first occurs for both complexes, with the rate constants k ₁ = 1.12(0.02)×10^–4 s^–1 and 1.47(0.02)×10^–4 s^–1 respectively for 1 and 2 at 37  °C, values in agreement with those previously reported. It is followed by the actual platination step whose second-order rate constant has been determined for the first time by physicochemical techniques. The values for 1 and 2 respectively are: k ₂ = 2.08(0.07) M^–1 s^–1 and 3.9(0.4) M^–1 s^–1. These kinetic data are discussed in the context of a comparison of several biological properties of the two complexes. Received: 15 May 1998 / Accepted: 26 June 1998     

Effect of polycyclic aromatic hydrocarbons on laccase production by white rot fungus <Emphasis Type="Italic">Pleurotus ostreatus</Emphasis> D1

The effect of polycyclic aromatic hydrocarbons (PAHs) on the time course of laccase production by the fungus Pleurotus ostreatus D1 under conditions of submerged cultivation on Kirk’s medium has been studied. It has been shown that phenanthrene, fluoranthene, pyrene, and chrysene actively induce this enzyme, whereas fluorene and anthracene had a smaller effect. Addition of Mn²⁺ ions to cultivation medium elevates the laccase activity twofold and more in the presence of all the studied PAHs. Electrophoresis under nondenaturing conditions demonstrates induction of additional laccase forms by xenobiotics. Ligninolytic peroxidase activities are undetectable under the conditions used.     

Novel TSAO Derivatives Modified at Positions 3′ and 4′ Of the Spiro Moiety

Abstract

We have explored the introduction of different functional groups at positions 3′ and 4′ of the spiro moiety of TSAO-T. Alkylation of this spiro moiety afforded mixtures of N and/or C-alkylated derivatives, while acylation occurs, exclusively, on the amino group. Position 3′ has been selectively functionalized by halogenation followed by Stille-cross coupling reaction with organostannanes under a variety of experimental conditions.     

Adaptation of the black tiger shrimp, Penaeus monodon, to different salinities through an excretory function of the antennal gland

Black tiger shrimps (Penaeus monodon) are able to survive and can be reared under various salinities, possibly by the cellular adaptation of their excretory system, particularly the antennal gland, which is known to regulate body fluid in crustaceans. We have investigated the morphological and biochemical alterations of the antennal glands in shrimp reared in 7, 15, or 30 ppt seawater. Drastic changes occur in animals reared under 7 ppt conditions. Ultrastructural studies of the antennal gland in shrimps reared in 7 ppt seawater have revealed that podocytic cells in the coelomosacs ramify with more cytoplasmic processes forming the filtration slits, and that the tubular labyrinth cells possess more mitochondria in their basal striation and a wider tubular lumen than those found in the other groups. Many apical cytoplasmic blebs from labyrinth cells have also been seen in the lumen of the labyrinths under 7 ppt conditions, a feature that is not as prominent under the other conditions. The expression and activity of the Na⁺/K⁺-ATPase in the antennal gland are also correlated with the surrounding environment: the lower the salinity, the higher the expression and activity of the enzyme. Immunohistochemistry results have demonstrated the highest staining intensity in the labyrinth cells of shrimps reared under 7 ppt conditions. Our findings thus suggest that one of the adaptation mechanisms of this shrimp to the surrounding salinity is the regulation of Na⁺/K⁺-ATPase expression in the antennal gland, in conjunction with subcellular changes in its excretory cells.