Effects of monovalent and divalent cations on the rheology of entangled DNA

In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.

Flanking AT base pairs affect the localization of monovalent cations in DNA A-tracts

Capillary electrophoresis has been used to measure the free solution mobilities of a series of 26-base pair (bp) DNA oligomers containing two phased A4T1in-tracts embedded in flanking sequences containing 0 to 11 additional AT bps. A random-sequence 26-bp oligomer with 12 isolated AT bps was used as the reference. Mobility ratios (A-tract/reference) were measured in background electrolytes (BGEs) containing mixtures of small monovalent cations and tetrabutylammonium (TBA+ ) or tetrapropylammonium (TPA+ ) ions. The mobility ratios observed in 0.3 M TBA+ were >1.00, suggesting that the TBA+ ions had formed electrostatic contact pairs with the AT bp in the reference and in the A-tract flanking sequences, decreasing the mobilities of both oligomers. The TBA-AT pairing interactions could be eliminated by increasing the concentration of small monovalent cations in the BGE. In 0.3 M TPA+ , electrostatic contact pairs were formed with the AT bps in the flanking sequences and in the A-tracts. Interestingly, the shapes of the mobility ratio profiles observed for the A4T1in-tract oligomers depended on the total number of A + T residues in the oligomer.

G-Quadruplexes as Sensors of Intracellular Na+/K+ Ratio: Potential Role in Regulation of Transcription and Translation

Data on the structure of G-quadruplexes, noncanonical nucleic acid forms, supporting an idea of their potential participation in regulation of gene expression in response to the change in intracellular Na+i/K+i ratio are considered in the review. Structural variety of G-quadruplexes, role of monovalent cations in formation of this structure, and thermodynamic stability of G-quadruplexes are described. Data on the methods of their identification in the cells and biological functions of these structures are presented. Analysis of information about specific interactions of G-quadruplexes with some proteins was conducted, and their potential participation in the development of some pathological conditions, in particular, cancer and neurodegenerative diseases, is considered. Special attention is given to the plausible role of G-quadruplexes as sensors of intracellular Na+i/K+i ratio, because alteration of this parameter affects folding of G-quadruplexes changing their stability and, thereby, organization of the regulatory elements of nucleic acids. The data presented in the conclusion section demonstrate significant change in the expression of some early response genes under certain physiological conditions of cells and tissues depending on the intracellular Na+i/K+i ratio.

Intricate 3D architecture of a DNA mimic of GFP

Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.

Cation valence dependence of hydrogen bond and stacking potentials in DNA mesoscopic models

Monovalent and divalent cations play a crucial role in living cells and for molecular techniques such as PCR. Here we evaluate DNA melting temperatures in magnesium (Mg²⁺) and magnesium‑potassium (Mg²⁺+ K⁺) buffers with a mesoscopic model that allows us to estimate hydrogen bonds and stacking interaction potentials. The Mg²⁺ and Mg²⁺+ K⁺ results are compared to previous calculations for sodium ions (Na⁺), in terms of equivalent sodium concentration and ionic strength. Morse potentials, related to hydrogen bonding, were found to be essentially constant and unaffected by cation conditions. However, for stacking interactions we find a clear dependence with ionic strength and cation valence. The highest ionic strength variations, for both hydrogen bonds and stacking interactions, was found at the sequence terminals. This suggests that end-to-end interactions in DNA will be strongly dependent on cation valence and ionic strength.

Diffusion NMR-based comparison of electrostatic influences of DNA on various monovalent cations

Counterions are important constituents for the structure and function of nucleic acids. Using 7Li and 133Cs nuclear magnetic resonance (NMR) spectroscopy, we investigated how ionic radii affect the behavior of counterions around DNA through diffusion measurements of Li+ and Cs+ ions around a 15-bp DNA duplex. Together with our previous data on 23Na+ and 15NH4+ ions around the same DNA under the same conditions, we were able to compare the dynamics of four different monovalent ions around DNA. From the apparent diffusion coefficients at varied concentrations of DNA, we determined the diffusion coefficients of these cations inside and outside the ion atmosphere around DNA (Db and Df, respectively). We also analyzed ionic competition with K+ ions for the ion atmosphere and assessed the relative affinities of these cations for DNA. Interestingly, all cations (i.e., Li+, Na+, NH4+, and Cs+) analyzed by diffusion NMR spectroscopy exhibited nearly identical Db/Df ratios despite the differences in their ionic radii, relative affinities, and diffusion coefficients. These results, along with the theoretical relationship between diffusion and entropy, suggest that the entropy change due to the release of counterions from the ion atmosphere around DNA is also similar regardless of the monovalent ion types. These findings and the experimental diffusion data on the monovalent ions are useful for examination of computational models for electrostatic interactions or ion solvation.

Sodium Ions as Regulators of Transcription in Mammalian Cells

The maintenance of an uneven distribution of Na+ and K+ ions between the cytoplasm and extracellular medium is the basis for the functioning of any animal cell. Changes in the intracellular ratio of these cations occur in response to numerous stimuli and are important for the cell activity regulation. Numerous experimental data have shown that gene transcription in mammalian cells can be regulated by changes in the intracellular [Na+]_i/[K+]_i ratio. Here, we discuss possible mechanisms of such regulation in various cell types, with special attention to the [Ca2+]-independent signaling pathways that suggest the presence of an intracellular sensor of monovalent cations. As such sensor, we propose the secondary structures of nucleic acids called G-quadruplexes. They are widely represented in mammalian genomes and are often found in the promoters of genes encoding transcription factors.

Guanine-Based G-Quadruplexes Templated by Various Cations toward Potential Use as Single-Ion Conductors

Inspired by the atomic-sized, shape-regulated features of G-quadruplexes comprising guanine motifs with a monovalent metal cation, the G-quadruplex-forming ability, and properties of a guanine-based π-conjugated Y2 molecule containing bithiophene and peripheral dodecyl chain units in the presence of various cation salts (Li⁺ , Na⁺ , K⁺ , and Mg²⁺ ) were exploited. A series of structural characterization revealed that Y2 yielded desirable G-quadruplexes with all the tested cations as a consequence of the combination of a hydrogen-bonded cyclic G-quartet, π-stacking, and cation-dipole interactions. The radius and nature of the coordinating cations crucially affected the structural characteristics of G-quadruplexes, leading to variations in the ion migration ability inside the cavity of the G-quadruplex (Li⁺ >Na⁺ >K⁺ >Mg²⁺ ), as characterized through theoretical and experimental investigations. These results not only improve the understanding of G-quadruplex self-assemblies based on guanine but also provide an impetus for their diverse potential applications, especially in the field of Li batteries.

A DFT/PCM Study on the Affinity of Salinomycin to Bind Monovalent Metal Cations

The affinity of the polyether ionophore salinomycin to bind IA/IB metal ions was accessed using the Gibbs free energy of the competition reaction between SalNa (taken as a reference) and its rival ions: [M+-solution] + [SalNa] → [SalM] + [Na+-solution] (M = Li, K, Rb, Cs, Cu, Ag, Au). The DFT/PCM computations revealed that the ionic radius, charge density and accepting ability of the competing metal cations, as well as the dielectric properties of the solvent, have an influence upon the selectivity of salinomycin. The optimized structures of the monovalent metal complexes demonstrate the flexibility of the ionophore, allowing the coordination of one or two water ligands in SalM-W1 and SalM-W2, respectively. The metal cations are responsible for the inner coordination sphere geometry, with coordination numbers spread between 2 (Au+), 4 (Li+ and Cu+), 5/6 (Na+, K+, Ag+), 6/7 (Rb+) and 7/8 (Cs+). The metals' affinity to salinomycin in low-polarity media follows the order of Li+ > Cu+ > Na+ > K+ > Au+ > Ag+ > Rb+ > Cs+, whereas some derangement takes place in high-dielectric environment: Li+ ≥ Na+ > K+ > Cu+ > Au+ > Ag+ > Rb+ > Cs+.

pH-dependent sedimentation of DNA in the presence of divalent, but not monovalent, metal ions

Precipitation of DNA is performed frequently in molecular biology laboratories for the purpose of purification and concentration of samples and also for transfer of DNA into cells. Metal ions are used to facilitate these processes, though their precise functions are not well characterized. In the current study we have investigated the precipitation of double-stranded DNA by group 1 and group 2 metal ions. Double-stranded DNAs were not sedimented efficiently by metals alone, even at high concentrations. Increasing the pH to 11 or higher caused strong DNA precipitation in the presence of the divalent group 2 metals magnesium, calcium, strontium and barium, but not group 1 metals. Group 2 sedimentation profiles were distinctly different from that of the transition metal zinc, which caused precipitation at pH 8. Analysis of DNAs recovered from precipitates formed with calcium revealed that structural integrity was retained and that sedimentation efficiency was largely size-independent above 400 bp. Several tests supported a model whereby single-stranded DNA regions formed by denaturation at high pH became bound by the divalent metal cations. Neutralization of negative surface charges reduced the repulsive forces between molecules, leading to formation of insoluble aggregates that could be further stabilized by cation bridging (ionic crosslinking).

Influence of the Nucleophilic Ligand on the Reactivity of Carbonyl Rhenium(I) Complexes towards Methyl Propiolate: A Computational Chemistry Perspective

A comparative theoretical study on the reactivity of the complexes [ReY(CO)₃(bipy)] (Y = NH₂, NHMe, NHpTol, OH, OMe, OPh, PH₂, PHMe, PMe₂, PHPh, PPh₂, PMePh, SH, SMe, SPh; bipy = 2,2′-bipyridine) towards methyl propiolate was carried out to analyze the influence of both the heteroatom (N, O, P, S) and the alkyl and/or aryl substituents of the Y ligand on the nature of the product obtained. The methyl substituent tends to accelerate the reactions. However, an aromatic ring bonded to N and O makes the reaction more difficult, whereas its linkage to P and S favour it. On the whole, ligands with O and S heteroatoms seem to disfavour these processes more than ligands with N and P heteroatoms, respectively. Phosphido and thiolato ligands tend to yield a coupling product with the bipy ligand, which is not the general case for hydroxo, alcoxo or amido ligands. When the Y ligand has an O/N and an H atom the most likely product is the one containing a coupling with the carbonyl ligand, which is not always obtained when Y contains P/S. Only for OMe and OPh, the product resulting from formal insertion into the Re-Y bond is the preferred.

Metal ions confinement defines the architecture of G-quartet, G-quadruplex fibrils and their assembly into nematic tactoids

G-quadruplex, assembled from a square array of guanine (G) molecules, is an important structure with crucial biological roles in vivo but also a versatile template for ordered functional materials. Although the understanding of G-quadruplex structures is the focus of numerous studies, little is known regarding the control of G-quartet stacking modes and the spontaneous orientation of G-quadruplex fibrils. Here, the effects of different metal ions and their concentrations on stacking modes of G-quartets are elucidated. Monovalent cations (typically K+) facilitate the formation of G-quadruplex hydrogels with both heteropolar and homopolar stacking modes, showing weak mechanical strength. In contrast, divalent metal ions (Ca2+, Sr2+, and Ba2+) at given concentrations can control G-quartet stacking modes and increase the mechanical rigidity of the resulting hydrogels through ionic bridge effects between divalent ions and borate. We show that for Ca2+ and Ba2+ at suitable concentrations, the assembly of G-quadruplexes results in the establishment of a mesoscopic chirality of the fibrils with a regular left-handed twist. Finally, we report the discovery of nematic tactoids self-assembled from G-quadruplex fibrils characterized by homeotropic fibril alignment with respect to the interface. We use the Frank-Oseen elastic energy and the Rapini-Papoular anisotropic surface energy to rationalize two different configurations of the tactoids. These results deepen our understanding of G-quadruplex structures and G-quadruplex fibrils, paving the way for their use in self-assembly and biomaterials.

Influence of the Compensating Cation Nature on the Water Adsorption Properties of Zeolites

The influence of the compensating cation (Na⁺, Li⁺, Mg²⁺) nature on the water adsorption properties of LTA and FAU-type zeolites was investigated. Cation exchanges were performed at 80 °C for 2 h using 1 M aqueous solutions of lithium chloride (LiCl) or magnesium chloride (MgCl₂). XRF and ICP-OES analyses indicate that the cation exchange yields reach values between 59 to 89% depending on the number of exchange cycles and the nature of the zeolite and cation, while both zeolites structures are preserved during the process, as shown by XRD and solid state NMR analyses. Nitrogen adsorption-desorption experiments indicate a higher available microporous volume when sodium cations are replaced by smaller monovalent lithium cations or by divalent magnesium cations because twice less cations are needed compared to monovalent cations. Up to 15% of gain in the available microporous volume is obtained for FAU-type zeolites exchanged with magnesium cation. This improvement facilitates the adsorption of water with an increase in the water uptake up to 30% for the LTA and FAU type zeolites exchanged with magnesium. These exchanged zeolites are promising for uses in water decontamination because a smaller amount is needed to trap the same amount of water compared to their sodium counterparts.

C-terminal Cysteines of CueR Act as Auxiliary Metal Site Ligands upon HgII Binding-A Mechanism To Prevent Transcriptional Activation by Divalent Metal Ions?

Intracellular CuI is controlled by the transcriptional regulator CueR, which effectively discriminates between monovalent and divalent metal ions. It is intriguing that HgII does not activate transcription, as bis-thiolate metal sites exhibit high affinity for HgII . Here the binding of HgII to CueR and a truncated variant, ΔC7-CueR, without the last 7 amino acids at the C-terminus including a conserved CCHH motif is explored. ESI-MS demonstrates that up to two HgII bind to CueR, while ΔC7-CueR accommodates only one HgII . 199m Hg PAC and UV absorption spectroscopy indicate HgS2 structure at both the functional and the CCHH metal site. However, at sub-equimolar concentrations of HgII at pH 8.0, the metal binding site displays an equilibrium between HgS2 and HgS3 , involving cysteines from both sites. We hypothesize that the C-terminal CCHH motif provides auxiliary ligands that coordinate to HgII and thereby prevents activation of transcription.

Harnessing Ion-Binding Sites for GPCR Pharmacology

Endogenous ions play important roles in the function and pharmacology of G-protein coupled receptors (GPCRs). Historically the evidence for ionic modulation of GPCR function dates to 1973 with studies of opioid receptors, where it was demonstrated that physiologic concentrations of sodium allosterically attenuated agonist binding. This Na+-selective effect was distinct from effects of other monovalent and divalent cations, with the latter usually counteracting sodium's negative allosteric modulation of binding. Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na+ site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophysical, and structural characterization of ions bound to GPCRs. Taken together, these findings provide a molecular understanding of the unique roles of Na+ and other ions as GPCR allosteric modulators. We will also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacological profiles. SIGNIFICANCE STATEMENT: The function and pharmacology of GPCRs strongly depend on the presence of mono and divalent ions in experimental assays and in living organisms. Recent insights into the molecular mechanism of this ion-dependent allosterism from structural, biophysical, biochemical, and computational studies provide quantitative understandings of the pharmacological effects of drugs in vitro and in vivo and open new avenues for the rational design of chemical probes and drug candidates with improved properties.

Impact of Sodium Cationization on Gas-Phase Conformations of DNA and RNA Cytidine Mononucleotides

Gas-phase conformations of the sodium-cationized forms of the 2'-deoxycytidine and cytidine mononucleotides, [pdCyd+Na]⁺ and [pCyd+Na]⁺, are examined by infrared multiple photon dissociation action spectroscopy. Complimentary electronic structure calculations at the B3LYP/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory provide candidate conformations and their respective predicted IR spectra for comparison across the IR fingerprint and hydrogen-stretching regions. Comparisons of the predicted IR spectra and the measured infrared multiple photon dissociation action spectra provide insight into the impact of sodium cationization on intrinsic mononucleotide structure. Further, comparison of present results with those reported for the sodium-cationized cytidine nucleoside analogues elucidates the impact of the phosphate moiety on gas-phase structure. Across the neutral, protonated, and sodium-cationized cytidine mononucleotides, a preference for stabilization of the phosphate moiety and nucleobase orientation is observed, although the details of this stabilization differ with the state of cationization. Several low-energy conformations of [pdCyd+Na]⁺ and [pCyd+Na]⁺ involving several different orientations of the phosphate moiety and sugar puckering modes are observed experimentally.

Specific Ion Effects of Dodecyl Sulfate Surfactants with Alkali Ions at the Air-Water Interface

The influence of Li⁺, Na⁺ and Cs⁺ cations on the surface excess and structure of dodecyl sulfate (DS⁻) anions at the air–water interface was investigated with the vibrational sum-frequency generation (SFG) and surface tensiometry. Particularly, we have addressed the change in amplitude and frequency of the symmetric S-O stretching vibrations as a function of electrolyte and DS⁻ concentration in the presence of Li⁺, Na⁺ and Cs⁺ cations. For the Li⁺ and Na⁺ ions, we show that the resonance frequency is shifted noticeably from 1055 cm⁻¹ to 1063 cm⁻¹ as a function of the surfactants’ surfaces excess, which we attribute to the vibrational Stark effect within the static electric field at the air–water interface. For Cs⁺ ions the resonance frequency is independent of the surfactant concentration with the S-O stretching band centered at 1063 cm⁻¹. This frequency is identical to the frequency at the maximum surface excess when Li⁺ and Na⁺ ions are present and points to the ion pair formation between the sulfate headgroup and Cs⁺ counterions, which reduces the local electric field. In addition, SFG experiments of the O-H stretching bands of interfacial H₂O molecules are used in order to calculate the apparent double layer potential and the degree of dissociation between the surfactant head group and the investigated cations. The latter was found to be 12.0%, 10.4% and 7.7% for lithium dodecyl sulfate (LiDS), sodium dodecyl sulfate (SDS) and cesium dodecyl sulfate (CsDS) surfactants, which is in agreement with Collins ‘rule of matching water affinities’.

Effects of Metal Ions, Temperature, and a Denaturant on the Oxidative Folding Pathways of Bovine α-Lactalbumin

Bovine α-lactalbumin (αLA) has four disulfide (SS) bonds in the native form (N). On the oxidative folding pathways of this protein, two specific SS folding intermediates, i.e., (61–77, 73–91) and des[6–120], which have two and three native SS bonds, respectively, accumulate predominantly in the presence of Ca²⁺. In this study, we reinvestigated the pathways using a water-soluble cyclic selenoxide reagent, trans-3,4-dihydroxyselenolane oxide (DHS^ox), as a strong and quantitative oxidant to oxidize the fully reduced form (R). In the presence of ethylenediaminetetraacetic acid (EDTA) (under a metal-free condition), SS formation randomly proceeded, and N did not regenerate. On the other hand, two specific SS intermediates transiently generated in the presence of Ca²⁺. These intermediates could be assigned to (61–77, 73–91) and des[6–120] having two common SS bonds, i.e., Cys61-Cys77 and Cys73-Cys91, near the calcium binding pocket of the β-sheet domain. Much faster folding to N was observed in the presence of Mn²⁺, whereas Na⁺, K⁺, Mg²⁺, and Zn²⁺ did not affect the pathways. The two key intermediates were susceptible to temperature and a denaturant. The oxidative folding pathways revealed were significantly different from those of hen egg white lysozyme, which has the same SS-bonding pattern as αLA, suggesting that the folding pathways of SS-containing proteins can alter depending on the amino acid sequence and other factors, even when the SS-bond topologies are similar to each other.

Mg2+ ions: do they bind to nucleobase nitrogens?

Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg2+ coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg2+ assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na+, K+, NH4+ ions, water molecules or spurious density peaks. Consequently, apart from few documented exceptions, Mg2+ ions do not bind to N7 atoms. Without much of a surprise, Mn2+, Zn2+ and Cd2+, which have a higher affinity for nitrogens, may contact N7 atoms when present in crystallization buffers. In this respect, we describe for the first time a potential Zn2+ ribosomal binding site involving two purine N7 atoms. Further, we provide a set of guidelines to help in the assignment of Mg2+ in crystallographic, cryo-EM, NMR and model building practices and discuss implications of our findings related to ion substitution experiments.

The influence of Na+ and Ca2+ on the migration of colloids or/and ammonia nitrogen in an unsaturated zone medium

This experiment was conducted with an indoor sand-column device, the migration of colloids with the presence of Na⁺ and Ca²⁺ and the migration of ammonia nitrogen with the presence of Na⁺, Ca²⁺ or/and colloids was studied. The results showed that the migration of colloids was influenced by the ion valence state, different ions with different valence could block the migration of colloids. In addition, the blocking effect of bivalent ions was more obvious than that of monovalent ions. In the presence of Na⁺ and Ca²⁺, the R_d value of the ammonia-nitrogen migration process were 1.01 and 1.41, respectively, which indicated that bivalent ions have a greater blocking effect on ammonia-nitrogen migration than monovalent ions. Colloids could also block the ammonia-nitrogen migration, and R_d value in the ammonia-nitrogen migration process was 1.17. Moreover, the presence of Na⁺/colloids and Ca²⁺/colloids could enhance the blocking effect on the ammonia-nitrogen migration, and resulting the R_d values at 1.20 and 1.52, respectively. The cohesion of colloids caused by the compaction of its electric double layer with those ions added maybe the key causes of those blocking.

Dynamics of Water Associated with Lithium Ions Distributed in Polyethylene Oxide

The dynamics of water in polyethylene oxide (PEO)/LiCl solution has been studied with quasielastic neutron scattering experiments and molecular dynamics (MD) simulations. Two different time scales of water diffusion representing interfacial water and bulk water dynamics have been identified. The measured diffusion coefficient of interfacial water remained 5-10 times smaller than that of bulk water, but both were slowed by approximately 50% in the presence of Li(+). Detailed analysis of MD trajectories suggests that Li(+) is favorably found at the surface of the hydration layer, and the probability to find the caged Li(+) configuration formed by the PEO is lower than for the noncaged Li(+)-PEO configuration. In both configurations, however, the slowing down of water molecules is driven by reorienting water molecules and creating water-Li(+) hydration complexes. Performing the MD simulation with different ions (Na(+) and K(+)) revealed that smaller ionic radius of the ions is a key factor in disrupting the formation of PEO cages by allowing spaces for water molecules to come in between the ion and PEO.

Generalized Manning Condensation Model Captures the RNA Ion Atmosphere

RNA is highly sensitive to the ionic environment and typically requires Mg(2+) to form compact structures. There is a need for models capable of describing the ion atmosphere surrounding RNA with quantitative accuracy. We present a model of RNA electrostatics and apply it within coarse-grained molecular dynamics simulation. The model treats Mg(2+) ions explicitly to account for ion-ion correlations neglected by mean-field theories. Since mean-field theories capture KCl well, it is treated implicitly by a generalized Manning counterion condensation model. The model extends Manning condensation to deal with arbitrary RNA conformations, nonlimiting KCl concentrations, and the ion inaccessible volume of RNA. The model is tested against experimental measurements of the excess Mg(2+) associated with the RNA, Γ(2+), because Γ(2+) is directly related to the Mg(2+)-RNA interaction free energy. The excellent agreement with experiment demonstrates that the model captures the ionic dependence of the RNA free energy landscape.

Chabazite: stable cation-exchanger in hyper alkaline concrete pore water

To avoid impact on the environment, facilities for permanent disposal of hazardous waste adopt multibarrier design schemes. As the primary barrier very often consists of cement-based materials, two distinct aspects are essential for the selection of suitable complementary barriers: (1) selective sorption of the contaminants in the repository and (2) long-term chemical stability in hyperalkaline concrete-derived media. A multidisciplinary approach combining experimental strategies from environmental chemistry and materials science is therefore essential to provide a reliable assessment of potential candidate materials. Chabazite is typically synthesized in 1 M KOH solutions but also crystallizes in simulated young cement pore water, a pH 13 aqueous solution mainly containing K(+) and Na(+) cations. Its formation and stability in this medium was evaluated as a function of temperature (60 and 85 °C) over a timeframe of more than 2 years and was also asessed from a mechanistic point of view. Chabazite demonstrates excellent cation-exchange properties in simulated young cement pore water. Comparison of its Cs(+) cation exchange properties at pH 8 and pH 13 unexpectedly demonstrated an increase of the KD with increasing pH. The combined results identify chabazite as a valid candidate for inclusion in engineered barriers for concrete-based waste disposal.

Ion distributions around left- and right-handed DNA and RNA duplexes: a comparative study

The ion atmosphere around nucleic acids is an integral part of their solvated structure. However, detailed aspects of the ionic distribution are difficult to probe experimentally, and comparative studies for different structures of the same sequence are almost non-existent. Here, we have used large-scale molecular dynamics simulations to perform a comparative study of the ion distribution around (5'-CGCGCGCGCGCG-3')2 dodecamers in solution in B-DNA, A-RNA, Z-DNA and Z-RNA forms. The CG sequence is very sensitive to ionic strength and it allows the comparison with the rare but important left-handed forms. The ions investigated include Na(+), K(+) and Mg(2 +), with various concentrations of their chloride salts. Our results quantitatively describe the characteristics of the ionic distributions for different structures at varying ionic strengths, tracing these differences to nucleic acid structure and ion type. Several binding pockets with rather long ion residence times are described, both for the monovalent ions and for the hexahydrated Mg[(H2O)6](2+) ion. The conformations of these binding pockets include direct binding through desolvated ion bridges in the GpC steps in B-DNA and A-RNA; direct binding to backbone oxygens; binding of Mg[(H2O)6](2+) to distant phosphates, resulting in acute bending of A-RNA; tight 'ion traps' in Z-RNA between C-O2 and the C-O2' atoms in GpC steps; and others.

Impedance spectroscopic characterization of Sm2O3 containing lithium borate glasses

27.5 Li2O-(72.5-X) B2O3-X Sm2O3 (X=0.5, 1, 1.5 and 2) were prepared by conventional melt quench technique. Impedance spectroscopy (IS) is used to study the electrical properties of these prepared glasses. Modulus formalism is introduced to study relaxation behaviour of these glasses. Scaling model shows the good overlap of data on single master curve which suggests that conduction mechanism in these glasses is compositional dependent. Variation of dielectric constant and dielectric loss with the addition of Sm2O3 and frequency are discussed here.

G-triplex structure and formation propensity

The occurrence of a G-triplex folding intermediate of thrombin binding aptamer (TBA) has been recently predicted by metadynamics calculations, and experimentally supported by Nuclear Magnetic Resonance (NMR), Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) data collected on a 3' end TBA-truncated 11-mer oligonucleotide (11-mer-3'-t-TBA). Here we present the solution structure of 11-mer-3'-t-TBA in the presence of potassium ions. This structure is the first experimental example of a G-triplex folding, where a network of Hoogsteen-like hydrogen bonds stabilizes six guanines to form two G:G:G triad planes. The G-triplex folding of 11-mer-3'-t-TBA is stabilized by the potassium ion and destabilized by increasing the temperature. The superimposition of the experimental structure with that predicted by metadynamics shows a great similarity, with only significant differences involving two loops. These new structural data show that 11-mer-3'-t-TBA assumes a G-triplex DNA conformation as its stable form, reinforcing the idea that G-triplex folding intermediates may occur in vivo in human guanine-rich sequences. NMR and CD screening of eight different constructs obtained by removing from one to four bases at either the 3' and the 5' ends show that only the 11-mer-3'-t-TBA yields a relatively stable G-triplex.

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions

Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.

Extensive calculations on 12 Λ-S and 27 Ω states of PCl+ cation including spin-orbit coupling

The potential energy curves (PECs) of 27 Ω states generated from the 12 Λ-S states (X(2)Π, A(2)Π, 1(4)Π, 2(4)Π, 1(2)Σ(-), 2(2)Σ(-), 1(4)Σ(-), 2(4)Σ(-), 1(2)Σ(+), 1(4)Σ(+), 1(2)Δ and 1(4)Δ) of PCl(+) cation are studied for the first time for internuclear separations from about 0.10 to 1.10nm using an ab initio quantum chemical method. All the 12 Λ-S states correlate to the first dissociation channel of PCl(+) cation. Of these Λ-S states, the 2(4)Π is found to be the repulsive one. The 1(4)Σ(+), 1(2)Δ and 1(4)Δ are found to be the inverted ones. And the 1(2)Δ is found to possess the double wells. The PECs are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction in combination with the correlation-consistent basis sets, aug-cc-pV(n+d)Z. The effect of core-valence correlation and scalar relativistic corrections on the spectroscopic parameters is briefly discussed. Scalar relativistic corrections are included by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. Core-valence correlation corrections are included with a cc-pCVTZ basis set. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling is accounted for by the state interaction method with the Breit-Pauli Hamiltonian using the all-electron cc-pCVTZ basis set. All the PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated for the 11 Λ-S bound states and for the 23 Ω bound states, and are compared with available experimental and other theoretical results. Fair agreement has been found between the present spectroscopic parameters and the measurements. The energy splitting in the X(2)Π Λ-S state is calculated to be 346.11 cm(-1), close to the estimated measurements of 370 cm(-1). It demonstrates that the spectroscopic parameters reported here can be expected to be reliably predicted ones.

Li+ transport in poly(ethylene oxide) based electrolytes: neutron scattering, dielectric spectroscopy, and molecular dynamics simulations

The dynamics of Li(+) transport in polyethylene oxide (PEO) and lithium bis(trifluoromethanesulfonyl)imde mixtures are investigated by combining neutron spin-echo (NSE) and dielectric spectroscopy with molecular dynamics (MD) simulations. The results are summarized in a relaxation time map covering wide ranges of temperature and time. The temperature dependence of the dc conductivity and the dielectric α relaxation time is found to be identical, indicating a strong coupling between both. The relaxation times obtained from the NSE measurements at 0.05 Å(-1)<q<0.2 Å(-1) are of similar magnitude as the relaxation time of Li(+) predicted by MD simulation. Our results suggest that the characteristic live times of the ions within the oxygen cages are mainly determined by the α relaxation that corresponds to local segmental motions of polymers, to a much lesser extent by the main chain relaxation, and not at all by the β relaxation or other faster processes. It is the first time decisive experimental evidence for a microscopic picture of the Li ion transportation process is shown in which the PEO chain forms EO cages over several monomer units and the Li ion "jump" from cage to cage. The role of the backbone of the polymer is discussed and contributes signifcantly to the Li ion transportation process. Moreover, detailed characteristic length and time scales of the Li(+) transport process in this polymer electrolyte are identified and interpreted.

[Physico-chemical properties of Bacillus thuringiensis IMV B-7324 fibrinolytic peptidase]

Investigations of physico-chemical properties of the Bacillus thuringiensis IMV B-7324 fibrinolytic peptidase showed that optimal activity of enzyme displayed at pH 10.0 and temperature 60 degrees C. Stability of peptidase retained in the range of pH from 6.0 to 11.0 and temperature from 20 to 50 degrees C over 1 h. Inhibition of fibrinolytic peptidase activity by ethylene glycol tetraacetic acid (EGTA) and tetrasodium salt of ethylenediaminetetraacetic acid (trilon B) indicates the belonging of this enzyme to the group of metallopeptidases. It was established that cations Ag+, Mg2+ and Ba2+ increased the fibrinolytic activity by 40 %, 25 % and 30 %, respectively, but Ca2+, Zn2+, Cu2+, Pb2+ and Hg2+ reduced it by 30-60%. Several of studied anions (F-, Br-, SO2-, S2O(2-)3, AsO(3-)4, NO-(3) and NO2(-) inhibit the activity of B. thuringiensis IMV B-7324 fibrinolytic peptidase by 25-100%.

DNA A-tracts are not curved in solutions containing high concentrations of monovalent cations

The intrinsic curvature of seven 98 bp DNA molecules containing up to four centrally located A6-tracts has been measured by gel and capillary electrophoresis as a function of the number and arrangement of the A-tracts. At low cation concentrations, the electrophoretic mobility observed in polyacrylamide gels and in free solution decreases progressively with the increasing number of phased A-tracts, as expected for DNA molecules with increasingly curved backbone structures. Anomalously slow electrophoretic mobilities are also observed for DNA molecules containing two pairs of phased A-tracts that are out of phase with each other, suggesting that out-of-phase distortions of the helix backbone do not cancel each other out. The mobility decreases observed for the A-tract samples are due to curvature, not cation binding in the A-tract minor groove, because identical free solution mobilities are observed for a molecule with four out-of-phase A-tracts and one with no A-tracts. Surprisingly, the curvature of DNA A-tracts is gradually lost when the monovalent cation concentration is increased to ∼200 mM, regardless of whether the cation is a hydrophilic ion like Na+, NH4+, or Tris+ or a hydrophobic ion like tetrabutylammonium. The decrease in A-tract curvature with increasing ionic strength, along with the known decrease in A-tract curvature with increasing temperature, suggests that DNA A-tracts are not significantly curved under physiological conditions.

FT-IR, 1H, 13C NMR, ESI-MS and semiempirical investigation of the structures of Monensin phenyl urethane complexes with the sodium cation

In this paper three forms of phenyl urethane of Monensin i.e. its acid form (H-MU) and its 1:1 complex with NaClO4 (H-MU-Na) and its sodium salt (Na-MU) were obtained and their structures were studied by FT-IR, (1)H and (13)C NMR, ESI MS and PM5 methods. The FT-IR data of Na-MU complexes demonstrate that the C=O urethane group is not engaged in the complexation of the sodium cation. However spectroscopic studies of H-MU-Na complex show that the structure in which this C=O urethane groups participate in the complexation is also present, but it is in the minority. The PM5 semiempirical calculations allow visualisation of all structures and determination of the hydrogen bond parameters.

Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure

We have obtained a 1.55-Å crystal structure of a hammerhead ribozyme derived from Schistosoma mansoni under conditions that permit detailed observations of Na(+) ion binding in the ribozyme's active site. At least two such Na(+) ions are observed. The first Na(+) ion binds to the N7 of G10.1 and the adjacent A9 phosphate in a manner identical with that previously observed for divalent cations. A second Na(+) ion binds to the Hoogsteen face of G12, the general base in the hammerhead cleavage reaction, thereby potentially dissipating the negative charge of the catalytically active enolate form of the nucleotide base. A potential but more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of previous predictions. Hammerhead ribozymes have been observed to be active in the presence of high concentrations of monovalent cations, including Na(+), but the mechanism by which monovalent cations substitute for divalent cations in hammerhead catalysis remains unclear. Our results enable us to suggest that Na(+) directly and specifically substitutes for divalent cations in the hammerhead active site. The detailed geometry of the pre-catalytic active-site complex is also revealed with a new level of precision, thanks to the quality of the electron density maps obtained from what is currently the highest-resolution ribozyme structure in the Protein Data Bank.

Influence of competing inorganic cations on the ion exchange equilibrium of the monovalent organic cation metoprolol on natural sediment

The aim of this study was to systematically investigate the influence of the mono- and divalent inorganic ions Na(+) and Ca(2+) on the sorption behavior of the monovalent organic cation metoprolol on a natural sandy sediment at pH=7. Isotherms for the beta-blocker metoprolol were obtained by sediment-water batch tests over a wide concentration range (1-100000 μg L(-1)). Concentrations of the competing inorganic ions were varied within freshwater relevant ranges. Data fitted well with the Freundlich sorption model and resulted in very similar Freundlich exponents (n=0.9), indicating slightly non-linear behavior. Results show that the influence of Ca(2+) compared to Na(+) is more pronounced. A logarithmic correlation between the Freundlich coefficient K(Fr) and the concentration or activity of the competing inorganic ions was found allowing the prediction of metoprolol sorption on the investigated sediment at different electrolyte concentrations. Additionally, the organic carbon of the sediment was completely removed for investigating the influence of organic matter on the sorption of metoprolol. The comparison between the experiments with and without organic carbon removal revealed no significant contribution of the organic carbon fraction (0.1%) to the sorption of metoprolol on the in this study investigated sediment. Results of this study will contribute to the development of predictive models for the transport of organic cations in the subsurface.

Selective bond cleavage in potassium collisions with pyrimidine bases of DNA

Electron transfer in alkali-molecule collisions to gas phase thymine and uracil yielding H- formation is selectively controlled in the energy range between 5.3 and 66.1 eV. By tuning the collision energy, electron transfer from the alkali to partly deuterated thymine, methylated thymine at the N1 and methylated uracil at the N3 positions, H- loss proceeds not only through the breaking of the (C-H) against (N-H) bonds but also through N1 against N3 sites. Such selectivity, as far as bond and site are concerned, is here reported for the first time by electron transfer induced dissociation experiments in alkali-molecule collisions.

Gas phase chemistry of Li+ with amides: the observation of LiOH loss in mass spectrometry

Collision-induced dissociation (CID) of Li(+) adducts of three sets of compounds that contains an amide bond, including 2-(4, 6-dimethoxypyrimidin-2-ylsulfanyl)-N-phenylbenzamide, its derivatives and simpler structures was investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Observed fragment ions include those that reflect loss of LiOH. Other product ions result from the Smiles rearrangement and direct C-S bond cleavage. MS/MS of H/D exchange products demonstrated occurrence of a 1,3-H shift from the amide nitrogen atom to the phenyl ring of these compounds. The LiOH loss from Li(+) adducts of amides was further examined by CID of [M + Li](+) ions of N-phenylbenzamide and N-phenylcinnamide. Loss of LiOH was essentially the sole fragmentation reaction observed for the former. For the latter, both losses of LiOH and H(2)O were discovered. The presence of electron-donating substituents of the phenyl ring of these compounds was found to facilitate elimination of LiOH, while that loss was retarded by electron-withdrawing substituents. Proposed fragment ion structures were supported by elemental compositions deduced from ultrahigh resolution Fourier transform ion cyclotron resonance tandem mass spectrometry (FTICR-MS/MS) m/z value determinations. Density functional theory-based (DFT) calculations were performed to evaluate potential mechanisms for these reactions.

Is ryanodine receptor a calcium or magnesium channel? Roles of K+ and Mg2+ during Ca2+ release

The ryanodine receptor (RyR) is a poorly selective channel that mediates Ca(2+) release from intracellular Ca(2+) stores. How RyR's selectivity between the physiological cations K(+), Mg(2+), and Ca(2+) affects single-channel Ca(2+) current amplitude is examined using a recent model of RyR permeation. It is found that K(+) provides the vast majority of the countercurrent (through RyR itself) that is needed to prevent the sarcoplasmic reticulum (SR) membrane potential from changing and stopping Ca(2+) release. Moreover, intra-pore competition between Ca(2+) and Mg(2+) defines single RyR Ca(2+) current amplitude. Since both [Mg(2+)] and [Ca(2+)](SR) can change during pathophysiological conditions, the RyR unitary Ca(2+) current amplitude during Ca(2+) release may change significantly due to this Ca(2+)/Mg(2+) competition. Compared to the classic action of Mg(2+) on RyR open probability, these Ca(2+) current amplitude changes have as large or larger effects on overall RyR Ca(2+) mobilization. A new aspect of RyR divalent versus monovalent selectivity is also identified where this kind of selectivity decreases as divalent concentration increases.

Effects of monovalent cations on the competitive adsorption of perfluoroalkyl acids by kaolinite: experimental studies and modeling

Our hypothesis that longer-chained perfluoroalkyl acids (PFAAs) outcompete shorter-chained PFAAs during adsorption was tested in this study, wherein the adsorption interactions of six frequently detected PFAAs with kaolinite clay were modeled and examined experimentally using various suspension compositions. Competitive adsorption of PFAAs on the kaolinite surface was observed for the first time, and longer-chained PFAAs outcompeted those with a shorter chain. The electrostatic repulsion between adsorbed PFAA molecules is a primary inhibitory factor in PFAA adsorption. An increase in aqueous sodium or hydrogen ion concentration weakened electrostatic repulsions and changed the adsorption free energy. Therefore, the adsorption of a shorter-chained PFAA with weaker hydrophobicity could occur at high sodium or hydrogen ion concentrations. The experimental and modeling data suggest that the adsorption of shorter-chained PFAAs (≤4 perfluorinated carbons) in freshwater with a typical ionic strength of 10(-2.5) is not thermodynamically favorable. Furthermore, by measuring the electrokinetic potential of kaolinite suspension in the presence of PFAAs, we found that the kaolinite surface became more negatively charged because of the adsorption of PFAAs. This observation indicates that the adsorbed PFAA molecules were within the electrical double layer of the kaolinite surface and that they contributed to the potential at the slipping plane. The possible alignments of adsorbed PFAA molecules on the kaolinite surface were then proposed.

Excess sludge reduction by biological way: from experimental experience to a real full scale application

The aim of this study was to investigate the ability of a biological process applied in the sludge line and based on the alternation of oxic and anoxic phases, to minimize the waste sludge production. After some tests in pilot scale, the process was applied in a real municipal wastewater treatment plant of 35,000 PE trying out one setting of working experimental conditions. A rate of the recycle flow was conditioned in a treatment basin, maintaining an HRT of 10 days. The control device operated for the 50% of time in the ORP range between -400 and -200 mV, and for the 50% in the ORP range between -200 and +50 mV. The mass balance defined an actual observed growth yield equal to 0.09 kgTVSkgCODr(-1), and the heterotrophic yield values, assessed by batch tests, seemed to be a suitable marker for the sludge reduction and for the energy uncoupling.

Adsorption of chitosan onto carbonaceous surfaces and its application: atomic force microscopy study

The adsorption of chitosan onto highly ordered pyrolytic graphite(HOPG) surfaces and its applications have been studied by atomic force microscopy (AFM). The results indicated that chitosan topography formed on the HOPG surface significantly depends on the pH conditions and its concentration for the incubation. Under strongly acidic conditions (pH < 3.5) and at a concentration of 1 mg ml⁻¹, chitosan formed into uniform network structures composed of fine chains. When the solution pH was changed from 3.5 to 6.5, chitosan tends to form a thicker film. Under neutral and basic conditions, chitosan changed into spherical nanoparticles, and their sizes were increased with increasing pH. Dendritic structures have been observed when the chitosan concentration was increased up to 5 mg ml⁻¹. In addition, the chitosan topography can also be influenced by ionic strength and the addition of different metal ions. When 0.1 M metal ions Na+, Mg²+, Ca²+ and Cu²+ were added into the chitosan solution at pH 3.0 for the incubation, network structures, branched chains, block structures and dense networks attached with many small particles were observed, respectively. The potential applications of these chitosan structures on HOPG have been explored. Preliminary results characterized by AFM and XPS indicated that the chitosan network formed on the HOPG surface can be used for AFM lithography, selective adsorption of gold nanoparticles and DNA molecules.

Sorption of thallium(I) onto geological materials: influence of pH and humic matter

The sorption behaviour of the severely toxic heavy metal thallium (Tl) as a monovalent cation onto three representative materials (goethite, pyrolusite and a natural sediment sampled from a field site) was examined as a function of pH in the absence and presence of two natural humic acids (HAs), using 204Tl(I) as a radiotracer. In order to obtain a basic understanding of trends in the pH dependence of Tl(I) sorption with and without HA, sorption of HAs and humate complexation of Tl(I) as a function of pH were investigated as well. In spite of the low complexation between Tl(I) and HAs, the presence of HAs results in obvious alterations of Tl(I) sorption onto pyrolusite and sediment. An influence on Tl(I) sorption onto goethite was not observed. Predictions of Kd (distribution coefficient) for Tl(I) on goethite in the presence of HAs, based on a linear additive model, agree well with the experimental data, while a notable disagreement occurs for the pyrolusite and sediment systems. Accordingly, it is suggested that HAs and goethite may act as a non-interacting sorbent mixture under the given conditions, but more complex interactions may take place between the HAs and the mineral phases of pyrolusite or sediment.

Bridging interactions and selective nanoparticle aggregation mediated by monovalent cations

Selective aggregation and precipitation of like-charged nanoparticles (NPs) covered with carboxylate ligands can be induced by different monovalent cations. The ordering of critical concentrations required for NP precipitation is Cs(+) ≫ K(+) > Li(+) > Na(+) > Rb(+) and does not correlate with the size of hydrated cations M(+), nor can it be predicted by the Hofmeister series. On the other hand, different anions have no effect on the precipitation trends. These observations are rationalized by a theoretical model combining the elements of the DLVO theory with molecular-level calculations. The key component of the model is the cation-specific binding of various metal cations to the carboxylate ligands.

Silver nanoparticles compromise neurodevelopment in PC12 cells: critical contributions of silver ion, particle size, coating, and composition

BACKGROUND

Silver exposures are rising because of the increased use of silver nanoparticles (AgNPs) in consumer products. The monovalent silver ion (Ag+) impairs neurodevelopment in PC12 cells and zebrafish.

OBJECTIVES AND METHODS

We compared the effects of AgNPs with Ag+ in PC12 cells for neurodevelopmental end points including cell replication, oxidative stress, cell viability, and differentiation. First, we compared citrate-coated AgNPs (AgNP-Cs) with Ag+, and then we assessed the roles of particle size, coating, and composition by comparing AgNP-C with two different sizes of polyvinylpyrrolidone-coated AgNPs (AgNP-PVPs) or silica nanoparticles.

RESULTS

In undifferentiated cells, AgNP-C impaired DNA synthesis, but to a lesser extent than an equivalent nominal concentration of Ag+, whereas AgNP-C and Ag+ were equally effective against protein synthesis; there was little or no oxidative stress or loss of viability due to AgNP-C. In contrast, in differentiating cells, AgNP-C evoked robust oxidative stress and impaired differentiation into the acetylcholine phenotype. Although the effects of AgNP-PVP showed similarities to those of AgNP-C, we also found significant differences in potencies and differentiation outcomes that depended both on particle size and coating. None of the effects reflected simple physical attributes of nanoparticles, separate from composition or coating, as equivalent concentrations of silica nanoparticles had no detectable effects.

CONCLUSIONS

AgNP exposure impairs neurodevelopment in PC12 cells. Further, AgNP effects are distinct from those of Ag+ alone and depend on size and coating, indicating that AgNP effects are not due simply to the release of Ag+ into the surrounding environment.

Direct imaging of salt effects on lipid bilayer ordering at sub-molecular resolution

The interactions of salts with lipid bilayers are known to alter the properties of membranes and therefore influence their structure and dynamics. Sodium and calcium cations penetrate deeply into the headgroup region and bind to the lipids, whereas potassium ions only loosely associate with lipid molecules and mostly remain outside of the headgroup region. We investigated a dipalmitoylphosphatidylcholine (DPPC) bilayer in the gel phase in the presence of all three cations with a concentration of Ca²+ ions an order of magnitude smaller than the Na+ and K+ ions. Our findings indicate that the area per unit cell does not significantly change in these three salt solutions. However the lipid molecules do re-order non-isotropically under the influence of the three different cations. We attribute this reordering to a change in the highly directional intermolecular interactions caused by a variation in the dipole-dipole bonding arising from a tilt of the headgroup out of the membrane plane. Measurements in different NaCl concentrations also show a non-isotropic re-ordering of the lipid molecules.

Decameric uracil complexes around Li+

Electrospray ionization (ESI) in combination with mass spectrometry (MS) experiments were carried out to study decameric uracil complexes cationized with Li(+) ion. A previous study has shown that, under specific experimental conditions, a particularly intense peak of the decamer U(10)Li(+) is formed, which was referred to as an indication for so-called 'magic number' cluster. In order to gain more insight on the structure of this decameric complex, here, we report experimental studies concerning the kinetics of the fragmentation. In accordance with the new experimental data, structural models were constructed and fully optimized using ab initio and density functional theory quantum chemistry calculations. The theoretical study allowed us to propose a stable gas-phase structure which is compatible with all experimental findings.

Selective monovalent cation association and exchange around Keplerate polyoxometalate macroanions in dilute aqueous solutions

The interaction between water-soluble Keplerate polyoxometalate {Mo(72)Fe(30)} macroions and small countercations is explored by laser light scattering, anomalous small-angle X-ray scattering (ASAXS), and isothermal titration calorimetry (ITC) techniques. The macroions are found to be able to select the type of associated counterions based upon the counterions' valence state and hydrated size, when multiple types of additional cations are present in solution (even among different monovalent cations). The preference goes to the cations with higher valences or smaller hydrated sizes if the valences are identical. This counterion exchange process changes the magnitude of the macroion-counterion interaction and, thus, is reflected in the dimension of the self-assembled {Mo(72)Fe(30)} blackberry supramolecular structures. The hydrophilic macroions exhibit a competitive recognition of various monovalent counterions in dilute solutions. A critical salt concentration (CSC) for each type of cation exists for the blackberry formation of {Mo(72)Fe(30)} macroions, above which the blackberry size increases significantly with the increasing total ionic strength in solution. The CSC values are much smaller for cations with higher valences and also decrease with the cations' hydrated size for various monovalent cations. The change of blackberry size corresponding to the change of ionic strength in solution is reversible.

Influence of salts and natural organic matter on the stability of bacteriophage MS2

The stability of functionalized nanoparticles generally results from both steric and electrostatic interactions. Viruses like bacteriophage MS2 have adopted similar strategies for stability against aggregation, including a net negative charge under natural water conditions and using polypeptides that form loops extending from the surface of the protein capsid for stabilization. In natural systems, dissolved organic matter can adsorb to and effectively functionalize nanoparticle surfaces, affecting the fate and transport of these nanoparticles. We used time-resolved dynamic light scattering to measure the aggregation kinetics of a model virus, bacteriophage MS2, across a range of solution chemistries to determine what factors might destabilize viruses in aquatic systems. In monovalent electrolytes (LiCl, NaCl, and KCl), aggregation of MS2 could not be induced within a reasonable kinetic time frame, and MS2 was stable even at salt concentrations greater than 1.0 M. Aggregation of MS2 could be induced in divalent electrolytes when we employed Ca(2+). This trend was also observed in solutions containing 10 mg/L Suwannee River organic matter (SROM) reference material. Even at Ca(2+) concentrations as high 200 mM, diffusion-controlled aggregation was never achieved, demonstrating an additional barrier to aggregation. These results were confirmed by small-angle X-ray scattering experiments, which indicate a transition from repulsive to attractive interactions between MS2 virus particles as monovalent salts are replaced by divalent salts.

[Role of hydrogen ions in the regulation of the redox state of erythrocytes]

The parameters of the acid-base state and redox state of erythrocytes have been studied with the use of the fluorescent probes 2',7'-bis(2-carboxyethyl)-5(6)-carboxyfluorescein and 2',7'-dichlorodihydrofluorescein. It has been found that the value of redox state parameters in erythrocytes depends both on the extracellular and intracellular concentrations of hydrogen ions. It has been shown that hydrogen peroxide induces a decrease in the value of the intracellular pH. The interrelation of cellular homeostasis parameters characterizing the acid-base and redox states of erythrocytes has been theoretically and experimentally substantiated.

The influence of monovalent cation size on the stability of RNA tertiary structures

Many RNA tertiary structures are stable in the presence of monovalent ions alone. To evaluate the degree to which ions at or near the surfaces of such RNAs contribute to stability, the salt-dependent stability of a variety of RNA structures was measured with each of the five group I cations. The stability of hairpin secondary structures and a pseudoknot tertiary structure are insensitive to the ion identity, but the tertiary structures of two other RNAs, an adenine riboswitch and a kissing loop complex, become more stable by 2-3 kcal/mol as ion size decreases. This "default" trend is attributed to the ability of smaller ions to approach the RNA surface more closely. The degree of cation accumulation around the kissing loop complex was also inversely proportional to ion radius, perhaps because of the presence of sterically restricted pockets that can be accessed only by smaller ions. An RNA containing the tetraloop-receptor motif shows a strong (up to approximately 3 kcal/mol) preference for Na(+) or K(+) over other group I ions, consistent with the chelation of K(+) by this motif in some crystal structures. This RNA reverts to the default dependence on ion size when a base forming part of the chelation site is mutated. Lastly, an RNA aptamer for cobinamide, which was originally selected in the presence of high concentrations of LiCl, binds ligand more strongly in the presence of Li(+) than other monovalent ions. On the basis of these trends in RNA stability with group I ion size, it is argued that two features of RNA tertiary structures may promote strong interactions with ions at or near the RNA surface: negative charge densities that are higher than that in secondary structures, and the occasional presence of chelation sites, which are electronegative pockets that selectively bind ions of an optimum size.