pH-induced intramolecular folding dynamics of i-motif DNA

Using the combination of fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) technique, we investigate the mechanism and dynamics of the pH-induced conformational change of i-motif DNA in the bulk phases and at the single-molecule level. Despite numerous studies on i-motif that is formed from cytosine (C)-rich strand at slightly acidic pH, its detailed conformational dynamics have been rarely reported. Using the FRET technique to provide valuable information on the structure of biomolecules such as a protein and DNA, we clearly show that the partially folded species as well as the single-stranded structure coexist at neutral pH, supporting that the partially folded species may exist substantially in vivo and play an important role in a process of gene expression. By measuring the FCS curves of i-motif, we observed the gradual decrease of the diffusion coefficient of i-motif with increasing pH. The quantitative analysis of FCS curves supports that the gradual decrease of diffusion coefficient (D) associated with the conformational change of i-motif is not only due to the change in the intermolecular interaction between i-motif and solvent accompanied by the increase of pH but also due to the change of the shape of DNA. Furthermore, FCS analysis showed that the intrachain contact formation and dissociation for i-motif are 5-10 times faster than that for the open form. The fast dynamics of i-motif with a compact tetraplex is due to the intrinsic conformational changes at the fluorescent site including the motion of alkyl chain connecting the dye to DNA, whereas the slow intrachain contact formation observed from the open form is due to the DNA motion corresponding to an early stage interaction in the folding process of the unstructured open form.     

Effects of cationic and anionic nanoparticles on the stability of the secondary structure of DNA

The effects of anionic and cationic nanoparticles (15 and 100 nm in diameter) on the stability of the secondary structure of DNA were studied in DNA denaturation and renaturation processes. The results showed that DNA denaturation is greatly inhibited in the presence of cationic nanoparticles. In contrast, in the presence of even large amounts of anionic nanoparticles, the DNA melting transition occurs at the original melting temperature. The effects of the size and concentration of nanoparticles on DNA denaturation are discussed.     

The effect of 2'-fluorine substitutions on DNA i-motif conformation and stability

(1)H and (19)F NMR, and UV thermal melting studies have established that the stability of d(TCCCCC) is enhanced by the inclusion of a single 2'-fluorine-modified deoxycytidine residue; the results support the notion of the importance of sugar-sugar contacts in stabilising i-motifs in general and reveal that solvation is the cause of the instability of RNA equivalents.     

Investigation of the influence on conformational transition of DNA induced by cationic lipid vesicles

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper we take nile blue A (NBA) as a probe molecule to study the influence of the conformational transition of DNA induced by didodecyldimethylammonium bromide (DDAB) cationic vesicles to the interaction between DNA and the probe molecules. We find that upon binding to DNA, a secondary conformational transition of DNA induced by the cationic liposome from the native B-form to the C-form resulted in the change of binding modes of NBA to DNA and different complexes are formed between DNA, DDAB and NBA.     

The influence of ionic strength, nutrients and pH on bacterial adhesion to metals

Bacteria-metal interactions in aqueous solutions are important in biofilm formation, biofouling and biocorrosion problems in the natural environment and engineered systems. In this study, the adhesion forces of two anaerobes (Desulfovibrio desulfuricans and Desulfovibrio singaporenus) and an aerobe (Pseudomonas sp.) to stainless steel 316 in various aqueous systems were quantified using atomic force microscopy (AFM) with a cell probe. Results show that the nutrient and ionic strength of the solutions influence the bacteria-metal interactions. The bacteria-metal adhesion force was reduced in the presence of the nutrients in the solution, because a trace organic film was formed and thus decreased the metal surface wettability. Stronger ionic strength in the solution results in a larger bacteria-metal adhesion force, which is due to the stronger electrostatic attraction force between the positively charged metal surface and negatively charged bacterial surface. Solution pH also influences the interaction between the bacterial cells and the metal surface; the bacteria-metal adhesion force reached its highest value when the pH of the solution was near the isoelectric point of the bacteria, i.e. at the zero point charge. The adhesion forces at pH 9 were higher than at pH 7 due to the increase in the attraction between Fe ions and negative carboxylate groups.     

Influence of biological media on the structure and behavior of ferrocene-containing cationic lipid/DNA complexes used for DNA delivery

Biological media affect the physicochemical properties of cationic lipid-DNA complexes (lipoplexes) and can influence their ability to transfect cells. To develop new lipids for efficient DNA delivery, the influence of serum-containing media on the structures and properties of the resulting lipoplexes must be understood. To date, however, a clear and general picture of how serum-containing media influences the structures of lipoplexes has not been established. Some studies suggest that serum can disintegrate lipoplexes formed using certain types of cationic lipids, resulting in the inhibition of transfection. Other studies have demonstrated that lipoplexes formulated from other lipids are stable in the presence of serum and are able to transfect cells efficiently. In this article, we describe the influence of serum-containing media on lipoplexes formed using the redox-active cationic lipid bis(n-ferrocenylundecyl)dimethylammonium bromide (BFDMA). This lipoplex system promotes markedly decreased levels of transgene expression in COS-7 cells as serum concentrations are increased from 0 to 2, 5, 10, and 50% (v/v). To understand the cause of this decrease in transfection efficiency, we used cryogenic transmission electron microscopy (cryo-TEM) and measurements of zeta potential to characterize lipoplexes in cell culture media supplemented with 0, 2, 5, 10, and 50% serum. Cryo-TEM revealed that in serum-free media BFDMA lipoplexes form onionlike, multilamellar nanostructures. However, the presence of serum in the media caused disassociation of the intact multilamellar lipoplexes. At low serum concentrations (2 and 5%), DNA threads appeared to separate from the complex, leaving the nanostructure of the lipoplexes disrupted. At higher serum concentration (10%), disassociation increased and bundles of multilamellae were discharged from the main multilamellar complex. In contrast, lipoplexes characterized in serum-free aqueous salt (Li(2)SO(4)) medium and in OptiMEM cell culture medium (no serum) did not exhibit significant structural changes. The zeta potentials of lipoplexes in serum-free media (salt medium and cell culture medium) were similar (e.g., approximately -35 mV). Interestingly, the presence of serum caused the zeta potentials to become less negative (about -20 mV in OptiMEM and -10 mV in Li(2)SO(4)), even though serum contains negatively charged entities that have been demonstrated to lead to more negative zeta potentials in other lipoplex systems. The combined measurements of zeta potential and cryo-TEM are consistent with the proposition that DNA threads separate from the lipoplex in the presence of serum, resulting in a decrease in the net negative charge of the surface of the lipoplex.     

PNA C-C+ i-motif: superior stability of PNA TC8 tetraplexes compared to DNA TC8 tetraplexes at low pH

Study of self-assembly of PNA TC8 monitored by UV thermal transition at 295 nm indicates formation of a C-C+ tetraplex (i-motif) in acidic pH, with higher stability than the analogous dTC8.     

Secondary structure of DNA is recognized by slightly cross-linked cationic hydrogel

Interaction of salmon sperm DNA (300-500 bp) and ultrahigh molecular mass DNA (166 kbp) from bacteriophage T4dC with linear poly(N-diallyl-N-dimethylammonium chloride) (PDADMAC) and slightly cross-linked (#) PDADMAC (#PDADMAC) hydrogel in water has been studied by means of UV-spectroscopy, ultracentrifugation, atomic force, and fluorescence microscopy (FM). It is found that the linear polycation induced compaction of either native (double-stranded) or denatured (single-stranded) DNA by forming PDADMAC-DNA interpolyelectrolyte complexes (IPEC)s. At the same time, #PDADMAC hydrogel is able to distinguish between native and denatured DNA. Native DNA is adsorbed and captured in the hydrogel surface layer, while denatured DNA diffuses to the hydrogel interior until the whole hydrogel sample is transformed into the cross-linked IPEC. Both native and denatured DNA can be completely released from the hydrogel in appropriate conditions with no degradation by adding a low molecular salt. The data observed using conventional physicochemical methods with respect to DNA of a moderate molecular mass remarkably correlate with the pictures directly observed for ultrahigh molecular mass DNA in dynamics by using FM.     

Interaction of diquat and paraquat with humic acid and the influence of salt concentration and pH on the strength of interaction

Summary The interaction of the herbicides diquat and paraquat with humic acid and the influence of various salts and pH on the strength of interaction was studied by charge-transfer chromatography. Interactions between humic acids and both herbicides, probably by complex formation, were confirmed; they were stronger with paraquat than with diquat. The complex formation makes the herbicides more hydrophilic, facilitating their movement on cellulose surface. Salts in the environment significantly decreased the strength of interaction, indicating the hydrophilic character of the interactive forces. The charge of the cation also influenced the strength of interaction whereas the effect of ion radii was negligible. The effect of pH was lower than that of salt concentration.     

Imidazolium-based ionic liquids formed with dicyanamide anion: influence of cationic structure on ionic conductivity

Ionic liquids composed of dicyanamide anion and various imidazolium-based cations were prepared, and the influence of structural variations such as substituting a hydrogen at 2-position and changing the sort of alkyl group at 1-position of imidazolium cations on their thermal behavior, density, solvatochromic effects, viscosity, ionic conductivity, and surface tension was characterized. The substitution of the 2-hydrogen for methyl group or N-methylimidazole decreases the fluidity and ionic conductivity, mainly caused by the increased cohesive energy associated with the increasing cation size. Chain branching at 1-position also gives rise to the pronounced depression of the fluidity and ionic conductivity, presumably as a consequence of the increased pi-pi interactions between imidazolium rings. We found that the surface tension of the present ionic liquids is in inverse proportion to the molar concentration, which can be originally rationalized on the basis of the hole theory.     

pH-driven conformational switch of "i-motif" DNA for the reversible assembly of gold nanoparticles

Herein we demonstrate that gold nanoparticles conjugated to "i-motif" DNA behave like a pH dependent switch that undergoes reversible aggregations which can be easily visualized by the naked eye.     

Effect of ionic strength, pH and polymer concentration on the separation of DNA fragments in the presence of electroosmotic flow

DNA separations in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solutions have been demonstrated. During the separations, PEO entered capillaries filled with Tris-borate (TB) free buffers by EOF and acted as sieving matrices. We have found that ionic strength and pH of polymer and free solutions affect the bulk EOF and resolution differently from that in capillary zone electrophoresis. The EOF coefficient increases with increasing ionic strength of the free TB buffers as a result of decreases in the adsorption of PEO molecules. In contrast, the bulk EOF decreases with increasing the ionic strength of polymer solutions using capillaries filled with high concentrations of free TB buffers. Although resolution values are high due to larger differential migration times between any two DNA fragments in a small bulk EOF using 10 mM TB buffers, use of a capillary filled with at least 100 mM TB free buffers is suggested for high-speed separations. On the side of PEO solutions, 1.5% PEO solutions prepared in 100 to 200 mM TB buffers are more proper in terms of resolution and speed. The separation of DNA markers V and VI was accomplished less than 29 min in 1.5% PEO solutions prepared in 100 mM TB buffers, pH 7.0 at 500 V/cm using a capillary filled with 10 mM free TB buffers, pH 7.0.     

The porous structure of pulp fibres with different yields and its influence on paper strength

The porous structure of the interior of papermaking fibres is a well-known important property of the fibres. Changes of this structure will influence tensile and burst strength of paper formed from the fibres and a change in pore size of the pores within the fibre wall is also important for the ability of molecules to diffuse in and out of the fibre wall. Relevant examples of this latter effect are the removal of lignin during cooking and the addition of performance chemicals during papermaking. In this paper, pore sizes and the pore size distribution of unbleached softwood fibres have been studied. A well-characterised fibre material consisting of laboratory cooked spruce and pine pulp of various lignin contents was used. Pore size and pore size distribution were measured by studies of the relaxation behaviour of ²H in fibres saturated with ²H₂O. Beside this the total and surface charge of the fibres were also measured together with strength properties of papers from unbeaten fibres. For both pulps, there is a maximum in pore radius at a yield around 46%. Calculations of fibre wall volume from water retention values and yield levels show that there is a discontinuity in pore radius as a function of the fibre wall volume around a yield of 51%. It is suggested that this discontinuity is caused by the breakdown of the hemicellulose/lignin matrix within the fibre wall at this yield level. The strength of the papers formed from the fibres shows a correlation with the surface charge of the fibres. Based on the change in surface charge with yield and the change in total charge with yield, this correlation is suggested to be due to an opening up of the external part of the fibre wall. This stresses the importance of the chemical composition and physical structure of the outer layer of the fibre wall.     

Research on the influence of cationic tenside on silver iodide sols

Summary Colloid properties of silver iodide sols formed in statu nascendi are dependent on various factors. Ionic surface active substances influence a series of colloid chemical properties of these sols. The results of radiometry (heterogeneous exchange processes), adsorption-desorption equilibria, tyndallometry, electronmicroscopy, microelectrophoresis, tensiometry and X-ray diffractometry too are presented for negative silver iodide sols in the presence of a cationic tenside. The results are of importance in a radionuclide separation. A good fixation of radionuclides can be obtained by adding an adequate amount and type of surfactant to a radionuclide solution.

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Zusammenfassung Die Kolloideigenschaften von in statu nascendi gebildeten AgJ Solen sind von verschiedenen Faktoren abhängig. Besonders ausgeprägt ist der Einfluß von ionischen oberflächenaktiven Verbindungen auf viele kolloidal-chemische Eigenschaften von Silberjodidsolen. Die Untersuchungsergebnisse des Einflusses von kationischen Tensiden auf unterschiedlich gebildete AgJ-NaJ-Tensid-Sole werden beschrieben. Radiometrische (heterogene Austauschprozesse), Adsorption-Desorptionsgleichgewichts-, tyndallometrische, elektronenmikroskopische, tensometrische und röntgendiffraktometrische Ergebnisse weisen auf eine Verbindung zwischen Messergebnissen und den Eigenschaften von AgJ-NaJ-Tensid-Solen hin. Sie zeigen, wie durch Anwendung von Tensiden die Trennungswirkung von Radionukliden in einem kolloiden System erhöht werden kann.

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With 3 figures and 2 tables     

The influence of the multi-level structure under high drawing on the preparation of high strength Lyocell fiber

Cellulose - In order to research the multi-level structure of Lyocell fiber at different draw ratios and to reveal the limiting factors for preparing the high strength Lyocell fiber, the paper...     

Electrophoretic behavior of peptides in capillary electrophoresis influence of ionic strength and pH in aqueous-organic media.

Through correct pH, pKa and activity coefficients values, a model describing the effect of pH on electrophoretic mobility of substances has been applied to a series of peptides in water and in acetonitrile-water mixtures. The derived equations permit prediction of the optimum pH for the electrophoretic separation from only a few experimental values and they also permit determination of pKa values of analytes in the aqueous-organic media employed. Furthermore, the electrophoretic resolution between pairs of substances can be predicted, in order to evaluate electrophoretic separations of the studied peptides.