DNA condensation and interaction with zwitterionic phospholipids mediated by divalent cations

Artificial viruses are considered to be a promising tool in gene therapy. To find lipid-DNA complexes with high transfection efficiency but without toxicity is a fundamental aim. Although cationic lipids are frequently toxic for cells, neutral lipids are completely nontoxic. Zwitterionic lipids do not interact with DNA directly; however, the interaction can be mediated by divalent cations. Langmuir monolayers represent a well-defined model system to study the DNA-lipid complexes at the air/water interface (quasi-2D systems). In this work, isotherms, infrared reflection absorption spectroscopy (IRRAS), X-ray reflectivity (XR), grazing incidence X-ray diffraction (GIXD), and Brewster angle microscopy (BAM) measurements are used to study the interaction of calf thymus DNA with DMPE (1,2-dimyristoyl-phosphatidylethanolamine) monolayers mediated by Ca2+ or Mg2+ ions. DNA adsorption is observed only in the presence of divalent cations. At low lateral pressure, the DNA partially penetrates into the lipid monolayer but is squeezed out at high pressure. The adsorption layer has a thickness of 18-19 A. Additionally, GIXD provides information about a one-dimensional ordering of adsorbed DNA. The periodic distance between DNA strands depends on the type of the divalent cation.     

Charge density of divalent metal cations determines RNA stability

RNA molecules are exquisitely sensitive to the properties of counterions. The folding equilibrium of the Tetrahymena ribozyme is measured by nondenaturing gel electrophoresis in the presence of divalent group IIA metal cations. The stability of the folded ribozyme increases with the charge density (zeta) of the cation. Similar scaling is found when the free energy of the RNA folded in small and large metal cations is measured by urea denaturation. Brownian dynamics simulations of a polyelectrolyte show that the experimental observations can be explained by nonspecific ion-RNA interactions in the absence of site-specific metal chelation. The experimental and simulation results establish that RNA stability is largely determined by a combination of counterion charge and the packing efficiency of condensed cations that depends on the excluded volume of the cations.     

Removal and regeneration of aqueous divalent cations by boehmite

Boehmite (Al(OH)O) was employed for the removal of aqueous Mg(2+), Cu(2+), Cd(2+), Pb(2+), and Co(2+) at 298 K. Although boehmite was able to remove these divalent cations, the greater removal rate with boehmite of Pb(2+) (28.7%) than with Mg(2+), Cu(2+), Cd(2+), and Co(2+) (5.6, 25.3, 10.9, and 13.3%, respectively) was observed under acidic conditions. Under stronger alkaline conditions, in which the lead species was completely dissolved, a greater removal rate of Pb(2+) (more than 80%) was observed under the corresponding conditions employed for the acidic conditions. The removed lead species could not be dissolved from boehmite in an acidic solution while an evident dissolution of lead species was detected using an aqueous NaOH solution. The results shown in the present study reveal that boehmite can be employed as a reagent for the removal and regeneration of aqueous metal cations.     

Ternary uranium oxides from thermal decomposition of uranyl butyrates with divalent cations

In order to make DTA accessible to a larger group of interested people a new simple DTA concept was developed. Without large-scale electronics linear changes of temperature in the range of + 20 to + 1000°C are realized. The system seems to be suitable for both laboratory courses and research. Constructional features, the mode of operation and a selection of different DTA curves are reported.     

Electroconduction of rubidium pyrophosphate modified by divalent cations

Solid solutions based on rubidium pyrophosphate are synthesized in the Rb_{4 -2x}M_xP₂O₇ systems (M = Ca, Sr, Ba, Pb). The temperature and concentration dependences of their rubidium-cation conductivity are investigated. The X-ray data for the low and high-temperature forms of Rb₄P₂O₇ and also for solid solutions based on it are reported. The effect exerted by modifying cation M²⁺ on electrical properties of synthesized solid solutions is considered     

Enzymatic lithography of phospholipid bilayer films by stereoselective hydrolysis

The stereoselective phospholipase A2-catalyzed hydrolysis of patterned phospholipid bilayers consisting of the l- and d-isomers of alpha-dilauroylphosphatidylcholine (DLPC) and alpha-dipalmitoylphosphatidylcholine (DPPC) is reported. The stereochemically directed enzyme lithography demonstrated herein allows the parallel modification of large surface areas and constitutes a potentially useful method to structure biomimetic films, given the stereospecific action of many enzymes.     

Photo-cross-linking-assisted thermal stability of DNA origami structures and its application for higher-temperature self-assembly

Heat tolerance of DNA origami structures has been improved about 30 °C by photo-cross-linking of 8-methoxypsoralen. To demonstrate one of its applications, the cross-linked origami were used for higher-temperature self-assembly, which markedly increased the yield of the assembled product when compared to the self-assembly of non-cross-linked origami at lower-temperature. By contrast, at higher-temperature annealing, native non-cross-linked tiles did not self-assemble to yield the desired product; however, they formed a nonspecific broken structure.     

Tuning supramolecular G-quadruplexes with mono- and divalent cations

Supramolecular G-quadruplexes (SGQs) are formed via the cation promoted self-assembly of guanine derivatives into stacks of planar hydrogen-bonded tetramers. Here, we present results on the formation of SGQs made from the 8-(m-acetylphenyl)-2′-deoxyguanosine (mAGi) derivative in the presence of various mono- and divalent cations. NMR and HR ESI-MS data indicate that varying the cation can efficiently tune the molecularity, the fidelity and stability (thermal and kinetic) of the resulting SGQs. The results show that, parallel to the previously reported potassium-templated hexadecamer (mAGi₁₆·3K⁺), Na⁺, Rb⁺ and NH₄⁺ also promote the formation of similar supramolecules with high fidelity and molecularity. In contrast, the divalent cations Pb²⁺, Sr²⁺ and Ba²⁺ template the formation of octamers (mAGi₈), with the latter two inducing higher thermal stabilities. Molecular dynamics simulations for the hexadecamers containing monovalent cations enabled critical insights that help explain the experimental observations.     

First o-glycosylation from unprotected 1-thioimidoyl hexofuranosides assisted by divalent cations

The preparation of O-hexofuranosides was accomplished from unprotected 1-thioimidoyl furanosides as donors. The present methodology was first used for the synthesis of octyl galactofuranoside and further extended to D-galactofuranose-containing disaccharides. Within this study, we emphasized the need for additional complexing cations to maintain the furanose ring in its initial size. After experimentation, calcium ion was first used concomitantly with trimethylsilyl trifluoromethanesulfonate, the latter being able to activate the thioimidate and the former being likely to inhibit ring expansion. Moreover, an improvement was performed by using copper(II) trifluoromethanesulfonate which could then meet the requirements as both promoter and complexing agent.     

Complexes of tetracyclines with divalent metal cations investigated by stationary and femtosecond-pulsed techniques

Spectroscopic techniques both in steady-state (in absorption and emission) and pulsed (absorption of excited states with femtosecond resolution) conditions were used to study the complexation process between six molecules belonging to the tetracycline family and Mg(2+); in the case of TC the study was extended to the metal ions Ca(2+) and Cu(2+). The study was carried out in aqueous solution at various pH values, where one acid-base form of the substrate prevails over the others. The processing of experimental results, performed by means of Singular Value Decomposition and Global Analysis methods, allowed us to evaluate the extent of interaction through the association constants, to identify the number of equilibria present in solution and the stoichiometry (1:1 or 1:2) of the tetracycline:metal ion complex, and to define the spectral and photophysical properties of the latter (in terms of fluorescence quantum yields, lifetimes and rate constants). In fact, the (allowed) radiative decay process is a minor root for the lowest excited state of the complexes which mainly decay to the ground state by internal conversion. Details of the complexation sites are proposed for the various protonated forms of tetracyclines, and for the various cations in the case of TC. In particular, the molecular structure seems to affect significantly the dynamics of interaction when the upper peripheral region of tetracycline is rich in additional hydroxyl groups. Moreover, the state of protonation of the substrate produces changes in the order of the complexation sites, whose affinity for the cation increases significantly when they are negatively charged owing to the loss of protons. Magnesium and calcium (hard cations) give similar interactions, at least in acid solution, while copper(ii) (borderline cation) binds more efficiently on different sites, thus forming complexes with different properties.     

Perturbation of phospholipid bilayer properties by ethanol at a high concentration

Atomistic molecular dynamics (MD) simulations have been carried out at 30 degrees C on a fully hydrated liquid crystalline lamellar phase of dimyrystoylphosphatidylcholine (DMPC) lipid bilayer with embedded ethanol molecules at 1:1 composition, as well as on the pure bilayer phase. The ethanol molecules are found to exhibit a preference to occupy regions near the upper part of the lipid acyl chains and the phosphocholine headgroups. The calculations revealed that the phosphocholine headgroup dipoles (P- --> N+) of the lipids prefer to orient more toward the aqueous layer in the presence of ethanol. It is noticed that the ethanol molecules modify the dynamic properties of both lipids as well as the water molecules in the hydration layer of the lipid headgroups. Both the in-plane "rattling" and out-of-plane "protrusion" motions of the lipids have been found to increase in the presence of ethanol. Most importantly, it is observed that the water molecules within the hydration layer of the lipid headgroups exhibit faster translational and rotational motions in the presence of ethanol. This arises due to faster dynamics of hydrogen bonds between lipid headgroups and water in the presence of ethanol.     

Effect of bacteria growth temperature on the distribution of supercoiled DNA and its thermal stability

Changes in DNA supercoiling might be essential to generate the response of cellular machinery to temperature stress. The heat-induced structural transition for a topoisomer depends on the value of its specific linking difference. We detect only less negatively supercoiled DNA and an abundance of alternative irregular DNA forms at culture temperatures close to the growth limit of Escherichia coli. We show that the irregular forms are derived from regular plasmid DNAs and their population in the cells is temperature-dependent. Here, we show that it is possible to isolate and characterize individual DNA topoisomers directly from cells without a topoisomerase treatment. Temperature gradient gel electrophoresis (TGGE) and atomic force microscopy (AFM) were used to study the effect of bacteria growth temperature on the distribution of supercoiled DNA and its thermal stability.     

Synergic solvent extraction of divalent cations with decafluoroheptanedione and di-n-butylsulfoxide

The synergic solvent extraction of iron(II), cobalt(II), nickel(II) and lead(II) with l,l,l,2,2,6,6,7,7,7-decafluoro-3,5-heptanedione(H(FHD)) and di-n-butylsulfoxide (DBSO), is described. The divalent cations are extracted with 99.9% efficiency at pH 5.5 in extraction times of less than 15 min. The extracted species was shown to be M(FHD)₂·2 DBSO by mass action studies and elemental analyses. The extraction of copper(II) was also studied. No DBSO adduct was found in the copper extraction.     

Affinity capillary electrophoresis employed for determination of stability constants of antamanide complexes with univalent and divalent cations in methanol

Affinity capillary electrophoresis (ACE) and pressure‐assisted ACE were employed to study the noncovalent molecular interactions of antamanide (AA), cyclic decapeptide from the deadly poisonous fungus Amanita phalloides, with univalent (Li⁺, Na⁺, K⁺, and NH₄⁺) and divalent (Mg²⁺ and Ca²⁺) cations in methanol. The strength of these interactions was quantified by the apparent stability constants of the appropriate AA‐cation complexes. The stability constants were calculated using the nonlinear regression analysis of the dependence of the effective electrophoretic mobility of AA on the concentration of the above ions in the BGE (methanolic solution of 20 mM chloroacetic acid, 10 mM Tris, pH_MeOH 7.8, containing 0–50 mM concentrations of the above ions added in the form of chlorides). Prior to stability constant calculation, the AA effective mobilities measured at actual temperature inside the capillary and at variable ionic strength of the BGEs were corrected to the values corresponding to the reference temperature of 25°C and to the constant ionic strength of 10 mM. From the above ions, sodium cation interacted with AA moderately strong with the stability constant 362 ± 16 L/mol. K⁺, Mg²⁺, and Ca²⁺ cations formed with AA weak complexes with stability constants in the range 37–31 L/mol decreasing in the order K⁺ > Ca²⁺ > Mg²⁺. No interactions were observed between AA and small Li⁺ and large NH₄⁺ cations.     

Interrelations between soil respiration and its thermal stability

Biological transformation of organic matter in soil is a crucial factor affecting the global carbon cycle. In order to understand these complex processes, soils must be investigated by a combination of various methods. This study compares the dynamics of biological mineralization of soil organic matter (SOM) determined via CO₂ evolution during an 80-day laboratory incubation with their thermo-oxidative stability determined by thermogravimetry (TG). Thirty-three soil samples, originating from a wide range of geological and vegetation conditions from various German national parks were studied. The results showed a correlation between the amount and rate of respired CO₂ and thermal mass losses of air-dried, conditioned soils occurring around 100?°C with linear coefficients of determination up to R ²?=?0.85. Further, correlation of soil respiration with thermal mass losses around 260?°C confirmed previous observations. The comparison of TG profiles from incubated and non-incubated soils underlined the importance of thermal mass losses in these two temperature intervals. Incubated soils had reduced thermal mass losses above 240?°C and conversely an increased mass loss at 100?C120?°C. Furthermore, the accurate determination of soil properties by TG such as soil organic carbon content was confirmed, and it was shown that it can be applied to a wider range of carbon contents as was previously thought. It was concluded that results of thermal analysis could be a helpful starting point for estimation of soil respiration and for development of methods revealing processes in soils.     

Selective transport of ATP across a phospholipid bilayer by a molecular umbrella

Acylation of each primary group of spermidine with cholic acid, followed by acylation of the secondary amino group using an activated form of Nalpha,Ndelta,Nomega-tri-CBZ-l-arginine, and subsequent hydrogenolysis, afforded a conjugate (i.e., 1) which readily transports adenosine 5-triphosphate, but not glutathione, across phospholipid bilayers made from 1-palmitoyl-2-oleyol-sn-glycero-3-phosphocholine and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol.     

分子筛稳定的Lewis酸稀土中心在醛自缩合反应中的应用

羟醛缩合是重要的C–C键偶联反应,可以增长碳链,降低O/C比,用于生产很多大宗化学品,在生物质转化和生物油升级中广受关注.本文以丙醛分子自缩合反应作为模型反应,对比研究了稀土分子筛和稀土氧化物在醛自缩合反应中的催化性能,发现稀土分子筛的活性远高于稀土氧化物,其中Y/Beta活性最佳,并且具有良好的循环性能.随后采用程序...     

Probing the mechanical stability of DNA in the presence of monovalent cations

We examine the interaction between monovalent cations and DNA using several different assays that measure the stability of double-stranded DNA (dsDNA). The thermal melting of dsDNA and the mechanical separation of dsDNA into two single strands both depend on the stability of dsDNA with respect to ssDNA and are sensitive to the interstrand phosphate repulsion. We find that the experimentally measured melting temperatures and unzipping forces are approximately the same for all of the ions considered in this study. Likewise, the force required to transform B-DNA into the overstretched form is also similar for all of the ions. In contrast, for a given ion concentration, the force at which the overstretched state fully relaxes back to the canonical B-DNA form depends on the cation; however, for all cations, the overstretching force decreases with decreasing ion concentration, suggesting that this force is sensitive to screening. We observe a general trend for smaller ions to produce more efficient relaxation. Finally, for a given cation, the relaxation can also depend on the anion.