Two-dimensional packing of short DNA with nonpairing overhangs in cationic liposome-DNA complexes: from Onsager nematics to columnar nematics with finite-length columns

We report the formation of liquid crystalline (LC) phases of short double-stranded DNA with nonpairing (nonsticky) overhangs, confined between two-dimensional (2D) lipid bilayers of cationic liposome-DNA complexes. In a landmark study (Science2007, 318, 1276), Nakata et al. reported on the discovery of strong end-to-end stacking interactions between short DNAs (sDNAs) with blunt ends, leading to the formation of 3D nematic (N) and columnar LC phases. Employing synchrotron small-angle X-ray scattering, we have studied the interplay between shape anisotropy-induced and DNA end-to-end interaction-induced N ordering for 11, 24, and 48 bp sDNA rods with single-stranded oligo-thymine (T) overhangs modulating the end-to-end interactions. For suppressed stacking interactions with 10-T overhangs, the volume fraction of sDNA at which the 2D isotropic (I)-to-N transition occurs for 24 and 48 bp sDNA rods depended on their length-to-width (L/D) shape anisotropy, qualitatively consistent with Onsager's theory for the entropic alignment of rigid rods. As the overhang length is reduced from 10 to 5 and 2 T for 24 and 48 bp sDNA, the N-to-I transition occurs at lower volume fractions, indicating the onset of some degree of end-to-end stacking interactions. The 11 bp sDNA rods with 5- and 10-T overhangs remain in the I phase, consistent with their small shape anisotropy (L/D ≈ 1.9) below the limit for Onsager LC ordering. Unexpectedly, in contrast to the behavior of 24 and 48 bp sDNA, the end-to-end interactions between 11 bp sDNA rods with 2-T overhangs set in dramatically, and a novel 2D columnar N phase (N(C)) with finite-length columns formed. The building blocks of this phase are comprised of 1D stacks of (on average) four 11 bp DNA-2T rods with an effective L(stacked)/D ≈ 8.2. Our findings have implications for the DNA-directed assembly of nanoparticles on 2D platforms via end-to-end interactions and in designing optimally packed LC phases of short anisotropic biomolecules (such as peptides and short-interfering RNAs) on nanoparticle membranes, which are used in gene silencing and chemical delivery.     

Molecular aspects of the interaction between plants sterols and DPPC bilayers: an experimental and theoretical approach

The effect of sterols composition in a lipid bilayer was investigated on membranes of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and mixtures with the plant sterols β-sitosterol and stigmasterol. Differential scanning calorimetry, 1,6-diphenyl-1,3,5-hexatriene (DPH) fluorescence polarization and infrared spectroscopy studies showed that both sterols changed the packing of the membrane and the hydration of the polar headgroup of the phospholipids, disordering the gel phase and, vice versa, ordering the membrane in the liquid crystalline phase. In all cases some differences among β-sitosterol and stigmasterol could be observed, being β-sitosterol slightly more efficient than stigmasterol in ordering a fluid membrane, bringing the membrane to a more packed liquid ordered phase. Molecular dynamic simulations were carried out to better characterize the distinct behavior of both sterols in a DPPC-membrane. The calculated parameters agreed quite well with the experimental results and a molecular model is proposed to explain differences in the sterols molecules and their effect on the DPPC-bilayer.     

Predicting the phase diagram of two-dimensional colloidal systems with long-range interactions

The phase diagram of a two-dimensional model system for colloidal particles at the air-water interface was determined using Monte Carlo computer simulations in the isothermic-isobaric ensemble. The micrometer-range binary colloidal interaction has been modeled by hard disklike particles interacting via a secondary minimum followed by a weaker longer-range repulsive maximum, both of the order of kBT. The repulsive part of the potential drives the clustering of particles at low densities and low temperatures. Pinned voids are formed at higher densities and intermediate values of the surface pressure. The analysis of isotherms, translational and orientational correlation functions as well as structure factor gives clear evidence of the presence of a melting first-order transition. However, the melting process can be also followed by a metastable route through a hexatic phase at low surface pressures and low temperatures, before crystalization occurs at higher surface pressure.     

EDXRF as an analytical tool in art: Case studies from pigment identification and treatment assessment

Energy dispersive X-ray fluorescence (EDXRF) was employed for the identification of pigments decorating Hellenistic figurines, and the assessment of the efficiency of a treatment with barium hydroxide applied to stone. Elements present in the colored areas of the figurines, as well as the treated stone was identified by EDXRF. These data together with complementary information obtained by Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction analysis (XRD) led to the identification of several precious pigments. As far as the treatment efficiency is concerned, EDXRF analysis revealed that barium is unevenly distributed on the treated surface and reaches a maximum depth of 2.5 mm.     

Photoisomerization of azobenzenes and spirocompounds in nematic and in twisted nematic liquid crystals

Samples of a nematic mixture of ZLI1132 and of a twisted nematic mixture composed of ZLI1132 and chiral inductor S811, including 1%-10% (w/w) 4-N,N-dimethylaminoazobenzene (DAB), (4'-nitro)-4-N,N-dimethylaminoazobenzene (NDAB), spiropyran (SP), or spirooxazine (SO) were irradiated to produce the photochromic transformation of the dopant. The changes in the system were monitored by time-resolved transmission spectroscopy, time-resolved birefringence, or polarized Raman scattering. The medium sensitivity of the kinetics and spectroscopy of some of the probes was used to derive information on polarity of the medium. In the systems studied, apart from the changes in absorption spectrum, great changes in birefringence can be photoinduced and the order of the nematic phase can be changed in either direction, depending on the dopant. The open form of SP can discriminate orientation polarity. Although the polarity parallel to the mesogenic director is similar to that for acetone, the perpendicular orientation has a polarity similar to acetonitrile. In agreement with this observation, the kinetics of the Z --> E isomerization of NDAB, oriented parallel to the mesogenic director, also experiences a polarity similar to that for acetone. The decay rate constant of the open form of SP displays a linear relationship between its Arrhenius parameters, which is universal in a great variety of homogeneous solvents, solvent mixtures, and liquid crystals, therefore validating the hypothesis that the same type of transformation is observed in all these cases, namely, the decay of the open form monomer. The dopants used have been proven to be adequate probes of bulklike properties in locally heterogeneous systems as liquid crystals.     

Properties of χ-alumina as related to catalysis

-Alumina was synthesized by thermal decomposition of aluminium(III) isopropoxide, and its properties were investigated. The change in its surface area with increasing calcination temperature resembled that of -alumina. Both aluminas had the same acid strength, and their activities in isomerization of 1-butene were the same. -Alumina as a support for molybdenum catalyst in the epoxidation of allyl alcohol also behavedin the same manner as -alumina. Thus -alumina has almost the same catalytic properties as -alumina.     

Testing the photocatalytic activity of cyanogen-and thiocyanogen-based inorganic polymers

The photocatalytic properties of some cyanogen-and thiocyanogen-based inorganic polymers, such as paracyanogens containing different metals (Hg, Ag, Cu), polythiocyanogens of different iodine contents, polycyanogen and poly (cyanogenthiocyanate), have been tested in two systems. Cu-containing paracyanogen and the iodine-poor polythiocyanogens catalyze the photoreduction of methylviologen under visible light, furthermore the Cu-containing paracyanogen catalyzes the photoreduction of water to hydrogen under UV irradiation.

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Retention of ionisable compounds on high-performance liquid chromatography XVII. Estimation of the pH variation of aqueous buffers with the change of the methanol fraction of the mobile phase

The use of methanol-aqueous buffer mobile phases in HPLC is a common election when performing chromatographic separations of ionisable analytes. The addition of methanol to the aqueous buffer to prepare such a mobile phase changes the buffer capacity and the pH of the solution. In the present work, the variation of these buffer properties is studied for acetic acid-acetate, phosphoric acid-dihydrogenphosphate-hydrogenphosphate, citric acid-dihydrogencitrate-hydrogencitrate-citrate, and ammonium-ammonia buffers. It is well established that the pH change of the buffers depends on the initial concentration and aqueous pH of the buffer, on the percentage of methanol added, and on the particular buffer used. The proposed equations allow the pH estimation of methanol-water buffered mobile phases up to 80% in volume of organic modifier from initial aqueous buffer pH and buffer concentration (before adding methanol) between 0.001 and 0.01 mol L(-1). From both the estimated pH values of the mobile phase and the estimated pKa of the ionisable analytes, it is possible to predict the degree of ionisation of the analytes and therefore, the interpretation of acid-base analytes behaviour in a particular methanol-water buffered mobile phase.     

Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach

Manganese superoxide dismutases catalyze the disproportionation of the superoxide radical anion to molecular oxygen and hydrogen peroxide. Recently, atomic-resolution crystal structures of the reduced and oxidized enzymes have been reported. They show an active site with the manganese ion bound to one aspartate, three histidine residues, and a solvent molecule. In this paper, we combine crystallographic refinement with quantum mechanical methods to show that the solvent ligand is undoubtedly a water molecule in the reduced state. However, the putative oxidized structure is to a large extent reduced during data collection, so that it contains a mixture of the Mn2+ and Mn3+ structure. The crystal structures show that the Mn-bound solvent molecule accepts a hydrogen bond from the side chain of the conserved Gln-146 residue. If the solvent ligand is water, then this could lead to a steric clash, but it is avoided by the plane of water molecule forming an angle of 72 degrees to the Mn-O bond. Such a conformation is also found outside the enzyme, giving a minimal destabilization of the reduced state. We show by molecular dynamics simulations that the suggested Mn2+-H2O and Mn3+-OH- structures are stable. Moreover, we show that the superoxide substrate may bind both in the first coordination sphere of the Mn ion, opposite to the aspartate ligand, or in the second sphere, close to the conserved Tyr-34 and His-30 residues, approximately 5 A from Mn. However, the second-sphere structures are not stable in long molecular dynamics simulations. We see no difference in the coordination between the reduced and the oxidized states of the enzyme.     

Are the mixtures of homologous surfactants ideal?

The interaction between homologous surfactants in mixed micelles was studied by the Regular Solution Theory of mixed micelles. The interaction is independent of the nature of the polar head groups and attractive and the interaction parameter betaM depends linearly on the difference in chain length DeltanC. The interaction becomes ideal at DeltanC=0.75+/-0.06. Above DeltanC approximately 5, the dependence remains linear but the slope increased 2.7 times. The phenomenon is explained as the effect of the reduction of the hydrocarbon/water micelle interface and a better packing of the chains in the micelle core, caused by the inclusion of a shorter homologous surfactants. This reduction can be more effective when DeltanC>or=5.