Interaction of surfactants with DNA. Role of hydrophobicity and surface charge on intercalation and DNA melting

A probe, 9-(anthrylmethyl)trimethylammonium chloride, 1, was prepared. 1 binds to calf-thymus DNA or Escherichia coli genomic DNA with high affinity, as evidenced from the absorption titration. Strong hypochromism, spectral broadening and red-shifts in the absorption spectra were observed. Half-reciprocal plot constructed from this experiment gave binding constant of 5±0.5×104 M−1 in base molarity. We employed this anthryl probe-DNA complex for studying the effects of addition of various surfactant to DNA. Surfactants of different charge types and chain lengths were used in this study and the effects of surfactant addition to such probe-DNA complex were compared with that of small organic cations or salts. Addition of either salts or cationic surfactants led to structural changes in DNA and under these conditions, the probe from the DNA-bound complex appeared to get released. However, the cationic surfactants could induce such release of the probe from the probe-DNA complex at a much lower concentration than that of the small organic cations or salts. In contrast the anionic surfactants failed to promote any destabilization of such probe-DNA complexes. The effects of additives on the probe-DNA complexes were also examined by using a different technique (fluorescence spectroscopy) using a different probe ethidium bromide. The association complexes formed between the cationic surfactants and the plasmid DNA pTZ19R, were further examined under agarose gel electrophoresis and could not be visualized by ethidium bromide staining presumably due to cationic surfactant-induced condensation of DNA. Most of the DNA from such association complexes can be recovered by extraction of surfactants with phenol-chloroform. Inclusion of surfactants and other additives into the DNA generally enhanced the DNA melting temperatures by a few °C and at high [surfactant], the corresponding melting profiles got broadened.

On the relationship of thermodynamic parameters with the buried surface area in protein-ligand complex formation

Prediction of thermodynamic parameters of protein-protein and antigen-antibody complex formation from high resolution structural parameters has recently received much attention, since an understanding of the contributions of different fundamental processes like hydrophobic interactions, hydrogen bonding, salt bridge formation, solvent reorganization etc. to the overall thermodynamic parameters and their relations with the structural parameters would lead to rational drug design. Using the results of the dissolution of hydrocarbons and other model compounds the changes in heat capacity (DeltaCp), enthalpy (DeltaH) and entropy (DeltaS) have been empirically correlated with the polar and apolar surface areas buried during the process of protein folding/unfolding and protein-ligand complex formation. In this regard, the polar and apolar surfaces removed from the solvent in a protein-ligand complex have been calculated from the experimentally observed values of changes in heat capacity (DeltaCp) and enthalpy (DeltaH) for protein-ligand complexes for which accurate thermodynamic and high resolution structural data are available, and the results have been compared with the x-ray crystallographic observations. Analyses of the available results show poor correlation between the thermodynamic and structural parameters. Probable reasons for this discrepancy are mostly related with the reorganization of water accompanying the reaction which is indeed proven by the analyses of the energetics of the binding of the wheat germ agglutinin to oligosaccharides.

Underwater Sustainability of the ``Cassie'' State of Wetting

A rough hydrophobic surface when immersed in water can result in a ``Cassie'' state of wetting in which the water is in contact with both the solid surface and the entrapped air. The sustainability of the entrapped air on such surfaces is important for underwater applications such as reduction of flow resistance in microchannels and drag reduction of submerged bodies such as hydrofoils. We utilize an optical technique based oil total internal reflection of light at the water-air interface to quantify the spatial distribution of trapped air oil such a surface and its variation with immersion time. With this technique, we evaluate the sustainability of the Cassie state on hydrophobic surfaces with four different kinds of textures. The textures studied are regular arrays of pillars, ridges, and holes that were created in silicon by a wet etching technique, and also a texture of random craters that was obtained through electrodischarge machining of aluminum. These surfaces were rendered hydrophobic with a self-assembled layer Of fluorooctyl trichlorosilane. Depending on the texture, the size and shape of the trapped air pockets were found to vary. However, irrespective of the texture, both the size and the number of air pockets were found to decrease with time gradually and eventually disappear, suggesting that the sustainability of the ``Cassie'' state is finite for all the microstructures Studied. This is possibly due to diffusion of air from the trapped air pockets into the water. The time scale for disappearance of air pockets was found to depend on the kind of microstructure and the hydrostatic pressure at the water-air interface. For the surface with a regular array of pillars, the air pockets were found to be in the form of a thin layer perched on top of the pillars with a large lateral extent compared to the spacing between pillars. For other surfaces studied, the air pockets are smaller and are of the same order as the characteristic length scale of the texture. Measurements for the surface with holes indicate that the time for air-pocket disappearance reduces as the hydrostatic pressure is increased.

Influence of Hydrophilic Surface Specificity on the Structural Properties of Confined Water

The influence of chemical specificity of hydrophilic surfaces on the structure of confined water in the subnanometer regime is investigated using grand canonical Monte Carlo Simulations. The structural variations for water confined between hydroxylated silica surfaces are contrasted with water confined between mica surfaces. Although both surfaces are hydrophilic, our Study shows that hydration of potassium ions on the mica surface has a strong influence on the water Structure and solvation force response of confined water. In contrast to the disrupted hydrogen bond network observed for water confined between Mica Surfaces, water between silica surfaces retains its hydrogen bond network displaying bulklike structural features down to surface separations as small as 0.45 nm. Hydrogen bonding of all invariant contact water layer with the surface silanol groups aids in maintaining a constant number of hydrogen bonds per water molecule for the silica surfaces. As a consequence water depletion and rearrangement upon decreasing confinement is a strong function of the hydrophilic surface specificity, particularly at smaller separations. An oscillatory solvation force response is only observed for water confined between Silica surfaces, and bulklike features are observed for both Surfaces above a surface separation of about 1.2 nm. We evaluate and contrast the water density, dipole moment distributions, pi pair correlation functions, and solvation forces as a function of the surface separation.

Analysis of microstructure and texture evolution in pure magnesium during symmetric and asymmetric rolling

Asymmetric rolling of commercially pure magnesium was carried out at three different temperatures: room temperature, 200 degrees C and 350 degrees C. Systematic analysis of microstructures, grain size distributions, texture and misorientation distributions were performed using electron backscattered diffraction in a field emission gun scanning electron microscope. The results were compared with conventional (symmetric) rolling carried out under the same conditions of temperature and strain rate. Simulations of deformation texture evolution were performed using the viscoplastic self-consistent polycrystal plasticity model. The main trends of texture evolution are faithfully reproduced by the simulations for the tests at room temperature. The deviations that appear for the textures obtained at high temperature can be explained by the occurrence of dynamic recrystallization. Finally, the mechanisms of texture evolution in magnesium during asymmetric and symmetric rolling are explained with the help of ideal orientations, grain velocity fields and divergence maps displayed in orientation space.

On Multi-Dimensional Packets of Surface Waves

By using the method of operators of multiple scales, two coupled nonlinear equations are derived, which govern the slow amplitude modulation of surface gravity waves in two space dimensions. The equations of Davey and Stewartson, which also govern the two-dimensional modulation of the amplitude of gravity waves, are derived as a special case of our equations. For a fully dispersed wave, symmetric about a point which moves with the group velocity, the coupled equations reduce to a nonlinear Schrödinger equation with extra terms representing the effect of the curvature of the wavefront.

ERAP2 functional knockout in humans does not alter surface heavy chains or HLA-B27, inflammatory cytokines or endoplasmic reticulum stress markers

Introduction Single nucleotide polymorphisms in ERAP2 are strongly associated with ankylosing spondylitis (AS). One AS-associated single nucleotide polymorphism, rs2248374, causes a truncated ERAP2 protein that is degraded by nonsense-mediated decay. Approximately 25% of the populations of European ancestry are therefore natural ERAP2 knockouts. We investigated the effect of this associated variant on HLA class I allele presentation, surface heavy chains, endoplasmic reticulum (ER) stress markers and cytokine gene transcription in AS. Methods Patients with AS and healthy controls with either AA or GG homozygous status for rs2248374 were studied. Antibodies to CD14, CD19-ECD, HLA-A-B-C, Valpha7.2, CD161, anti-HC10 and anti-HLA-B27 were used to analyse peripheral blood mononuclear cells. Expression levels of ER stress markers (GRP78 and CHOP) and proinflammatory genes (tumour necrosis factor (TNF), IL6, IL17 and IL22) were assessed by qPCR. Results There was no significant difference in HLAclass I allele presentation or major histocompatibility class I heavy chains or ER stress markers GRP78 and CHOP or proinflammatory gene expression between genotypes for rs2248374 either between cases, between cases and controls, and between controls. Discussion Large differences were not seen in HLAB27 expression or cytokine levels between subjects with and without ERAP2 in AS cases and controls. This suggests that ERAP2 is more likely to influence AS risk through other mechanisms.

Surface Proteins of Lactobacillus crispatus: Adhesive Properties and Cell Wall Anchoring

Bacterial surface-associated proteins are important in communication with the environment and bacteria-host interactions. In this thesis work, surface molecules of Lactobacillus crispatus important in host interaction were studied. The L. crispatus strains of the study were known from previous studies to be efficient in adhesion to intestinal tract and ECM. L. crispatus JCM 5810 possess an adhesive surface layer (S-layer) protein, whose functions and domain structure was characterized. We cloned two S-layer protein genes (cbsA; collagen-binding S-layer protein A and silent cbsB) and identified the protein region in CbsA important for adhesion to host tissues, for polymerization into a periodic layer as well as for attachment to the bacterial cell surface. The analysis was done by extensive mutation analysis and by testing His6-tagged fusion proteins from recombinant Escherichia coli as well as by expressing truncated CbsA peptides on the surface of Lactobacillus casei. The N-terminal region (31-274) of CbsA showed efficient and specific binding to collagens, laminin and extracellular matrix on tissue sections of chicken intestine. The N-terminal region also contained the information for formation of periodic S-layer polymer. This region is bordered at both ends by a conserved short region rich in valines, whose substitution to leucines drastically affected the periodic polymer structure. The mutated CbsA proteins that failed to form a periodic polymer, did not bind collagens, which indicates that the polymerized structure of CbsA is needed for collagen-binding ability. The C-terminal region, which is highly identical in S-layer proteins of L. crispatus, Lactobacillus acidophilus and Lactobacillus helveticus, was shown to anchor the protein to the bacterial cell wall. The C-terminal CbsA peptide specifically bound to bacterial teichoic acid and lipoteichoic acids. In conclusion, the N-terminal domain of the S-layer protein of L. crispatus is important for polymerization and adhesion to host tissues, whereas the C-terminal domain anchors the protein to bacterial cell-wall teichoic acids. Lactobacilli are fermentative organisms that effectively lower the surrounding pH. While this study was in progress, plasminogen-binding proteins enolase and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were identified in the extracellular proteome of L. crispatus ST1. In this work, the cell-wall association of enolase and GAPDH were shown to rely on pH-reversible binding to the cell-wall lipoteichoic acids. Enolase from L. crispatus was functionally compared with enolase from L. johnsonii as well as from pathogenic streptococci (Streptococcus pneumoniae, Streptococcus pyogenes) and Staphylococcus aureus. His6-enolases from commensal lactobacilli bound human plasminogen and enhanced its activation by human plasminogen activators similarly to, or even better than, the enolases from pathogens. Similarly, the His6-enolases from lactobacilli exhibited adhesive characteristics previously assigned to pathogens. The results call for more detailed analyses of the role of the host plasminogen system in bacterial pathogenesis and commensalism as well of the biological role and potential health risk of the extracellular proteome in lactobacilli.

Spinodal Decomposition in Tellurite-Based Glasses Induced by Excimer Laser Irradiation

Tellurite-based glasses in the TeO2-K3Li2Nb5O15, TeO2-Ba5Li2Ti2Nb8O30, and V2Te2O9 were fabricated by the conventional melt-quenching technique. Amorphous and glassy characteristics of the as-quenched samples were established via the X-ray powder diffraction technique and differential thermal analysis, respectively. The as-quenched samples were irradiated by an excimer laser (248 nm). The effect of laser power, duration of irradiation, and the frequency of the laser pulses on the surface features of the above glasses were studied. The optical microscopic studies carried out on the above systems revealed the presence of quasi-periodic and periodic structures on their surfaces. The local compositional variations of these structures were confirmed by back-scattered electron imaging using scanning electron microscope accompanied by energy-dispersive X-ray analysis. These results were convincing enough to state that the glasses in the present investigations had undergone spinodal decomposition on laser irradiation. The incidence of the interconnected texture of two different phases was observed owing to the quenching effect produced by the heating and cooling cycle of the successive laser pulses. Ring- and line-shaped patterns were also observed, respectively, when the pulse frequency of the laser and the duration of irradiation were increased.

Influence of surface chemistry of mesoporous alumina with wide pore distribution on controlled drug release

The crucial role of the drug carrier surface chemical moeities on the uptake and in vitro release of drug is discussed here in a systematic manner. Mesoporous alumina with a wide pore size distribution (2-7 nm) functionalized with various hydrophilic and hydrophobic surface chemical groups was employed as the carrier for delivery of the model drug ibuprofen. Surface functionalization with hydrophobic groups resulted in low degree of drug loading (approximately 20%) and fast rate of release (85% over a period of 5 h) whereas hydrophilic groups resulted in a significantly higher drug payloads (21%-45%) and slower rate of release (12%-40% over a period of 5 h). Depending on the chemical moiety, the diffusion controlled (proportional to time(-0.5)) drug release was additionally observed to be dependent on the mode of arrangement of the functional groups on the alumina surface as well as on the pore characteristics of the matrix. For all mesoporous alumina systems the drug dosages were far lower than the maximum recommended therapeutic dosages (MRTD) for oral delivery. We envisage that the present study would aid in the design of delivery systems capable of sustained release of multiple drugs.

Effect of surface radiation on conjugate natural convection in a horizontal annulus driven by inner heat generating solid cylinder

This paper reports a numerical study of the laminar conjugate natural convection heat transfer with and without the interaction of the surface radiation in a horizontal cylindrical annulus formed between an inner heat generating solid circular cylinder and an outer isothermal circular boundary. Numerical solutions are obtained by solving the governing equations with a pressure correction method on a collocated (non-staggered) mesh. Steady-state results are presented for the flow and temperature distributions and Nusselt numbers for the heat generation based Grashof number ranging from 10(7) to 10(10), solid-to-fluid thermal conductivity ratios of 1, 5, 10, 50 and 100, radius ratios of 0.226 and 0.452 and surface emissivities of 0-0.8 with air as the working medium. It is observed that surface radiation reduces the convective heat transfer in the annulus compared to the pure natural convection case and enhances the overall Nusselt number.

Surface-mediated selective photocatalytic aerobic oxidation reactions on TiO2 nanofibres

N-doped TiO2 nanofibres were observed to possess lower aerobic oxidation activity than undoped TiO2 nanofibres in the selective photocatalytic aerobic oxidation of enzylamine and 4-methoxybenzyl alcohol. This was attributed to the reduction free energy of O2 adsorption in the vicinity of nitrogen dopant sites, as indicated by density functional theory (DFT) calculations when three-coordinated oxygen atoms are substituted by nitrogen atoms. It was found that the activity recovered following a controlled calcination of the N-doped NFs in air. The dependence of the conversion of benzylamine and 4-methoxybenzyl alcohol on the intensity of light irradiation confirmed that these reactions were driven by light. Action spectra showed that the two oxidation reactions are responsive to light from the UV region through to the visible light irradiation range. The extended light absorption wavelength range in these systems compared to pure TiO2 materials was found to result from the formation of surface complex species following adsorption of reactants onto the catalysts' surface, evidenced by the in situ IR experiment. Both catalytic and in situ IR results reveal that benzaldehyde is the intermediate in the aerobic oxidation of benzylamine to N-benzylidenebenzylamine process.