Monovalent cations affect the free solution mobility of DNA by perturbing the hydrogen-bonded structure of water

The free solution mobilities of single- and double-stranded DNA molecules of various molecular weights have been measured by capillary electrophoresis in solutions of constant ionic strength containing a common anion and fifteen different monovalent cations. In solutions with the same ionic composition, the mobilities of different DNA molecules can vary by up to 20%, depending on molecular weight, the number of strands, and the presence or absence of A-tracts, runs of four or more contiguous adenine residues. Importantly, the mobilities observed for the same DNA sample can vary by up to 40% in solutions containing different cations. The mobility differences observed for the same DNA in solutions containing different cations cannot be rationalized by differences in the anhydrous radii or intrinsic conductivities of the various cations, or by the sequence-dependent binding of certain cations to A-tracts. Instead, the observed mobilities are linearly correlated with the average number of water-water hydrogen bonds that are present in solutions containing different cations. The mobilities are also correlated with the viscosity B coefficients of the various cations and with the rotational correlation times frictional coefficients observed for water molecules in solutions containing different cations. Hence, monovalent cations modify the free solution mobility of DNA primarily by perturbing the hydrogen-bonded structure of water, affecting the friction experienced by the migrating DNA molecules during electrophoresis.     

Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations

Accurate predictions of DNA stability in physiological and enzyme buffers are important for the design of many biological and biochemical assays. We therefore investigated the effects of magnesium, potassium, sodium, Tris ions, and deoxynucleoside triphosphates on melting profiles of duplex DNA oligomers and collected large melting data sets. An empirical correction function was developed that predicts melting temperatures, transition enthalpies, entropies, and free energies in buffers containing magnesium and monovalent cations. The new correction function significantly improves the accuracy of predictions and accounts for ion concentration, G-C base pair content, and length of the oligonucleotides. The competitive effects of potassium and magnesium ions were characterized. If the concentration ratio of [Mg (2+)] (0.5)/[Mon (+)] is less than 0.22 M (-1/2), monovalent ions (K (+), Na (+)) are dominant. Effects of magnesium ions dominate and determine duplex stability at higher ratios. Typical reaction conditions for PCR and DNA sequencing (1.5-5 mM magnesium and 20-100 mM monovalent cations) fall within this range. Conditions were identified where monovalent and divalent cations compete and their stability effects are more complex. When duplexes denature, some of the Mg (2+) ions associated with the DNA are released. The number of released magnesium ions per phosphate charge is sequence dependent and decreases surprisingly with increasing oligonucleotide length.     

Detection for folding of the thrombin binding aptamer using label-free electrochemical methods

The folding of aptamer immobilized on an Au electrode was successfully detected using label-free electrochemical methods. A thrombin binding DNA aptamer was used as a model system in the presence of various monovalent cations. Impedance spectra showed that the extent to which monovalent cations assist in folding of aptamer is ordered as K(+) > NH(4)(+) > Na(+) > Cs(+). Our XPS analysis also showed that K(+) and NH(4)(+) caused a conformational change of the aptamer in which it forms a stable complex with these monovalent ions. Impedance results for the interaction between aptamer and thrombin indicated that thrombin interacts more with folded aptamer than with unfolded aptamer. The EQCM technique provided a quantitative analysis of these results. In particular, the present impedance results showed that thrombin participates a folding of aptamer to some extent, and XPS analysis confirmed that thrombin stabilizes and induces the folding of aptamer.     

Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation.

The binding of a 19-mer guanosine-rich oligodeoxyribonucleotide, TG3TG4TG4TG3T (ODN 1), to a complementary polypurine DNA target was investigated by DNase I footprinting and restriction endonuclease protection assays. Monovalent cations inhibited intermolecular purine-purine-pyrimidine triple-helical DNA formation, with K+ and Rb+ being most effective, followed by NH4+ and Na+. Li+ and Cs+ had little to no effect. Similar results were observed with the G/A-rich oligonucleotide AG3AG4AG4AG3AGCT. Kinetic studies indicated that monovalent cations interfered with oligonucleotide-duplex DNA association but did not significantly promote triplex dissociation. The observed order of monovalent cation inhibition of triplex formation is reminiscent of their effect on tetraplex formation with G/T-rich oligonucleotides. However, using electrophoretic mobility shift assays we found that the oligonucleotide ODN 1 did not appear to form a four-stranded species under conditions promoting tetraplex formation. Taken together, our data suggest that processes other than the self-association of oligonucleotides into tetraplexes might be involved in the inhibitory effect of monovalent cations on purine-pyrimidine-purine triplex formation.     

Activation by monovalent cations of dissimilatory nitrate reductase in the cells of Pseudomonas denitrificans

Cellular activity of nitrate reductase in Pseudomonas denitrificans which had been grown under denitrifying conditions was increased several times upon incubation of cell suspension with monovalent cations. The enhancement of nitrate reductase activity caused by monovalent cations was ascribed to the activation of the enzyme, since the membrane fraction isolated from the cells after the cation treatment retained the elevated levels of enzyme activity. However, monovalent cations had no effect when added directly to cell-free homogenate, suggesting an important role of some definite structure of membrane in the expression of the effect of monovalent cations.     

Atomic force microscopy study of the effects of Mg(2+) and other divalent cations on the end-to-end DNA interactions

Atomic force microscopy (AFM) was applied to directly visualize the end-to-end DNA interaction mediated by magnesium cations. We took advantage of the APS-mica, allowing the preparation of samples in a broad range of monovalent and divalent cations to separate the effects of Mg(2+) and Na(+) cations on the interaction of restriction DNA fragments with cohesive end. The AFM data clearly show that DNA restriction fragments with cohesive ends form substantial amount of circles in the presence of Mg(2+) cations, suggesting that Mg(2+) cations stabilize the interaction of cohesive ends. This effect depends on the MgCl(2) concentration, so that the yield of circles approaches 18% in the presence of 50 mM MgCl(2). Furthermore, we demonstrate that this conferred cohesive end stability is specific for divalent cations, as substitution of MgCl(2) with NaCl leads to a near complete loss of cohesive end stability. We further demonstrate that cohesive end stabilization is achieved by substituting Mg(2+) with Ca(2+), Mn(2+), or Zn(2+). The data obtained suggest that the end stabilization mediated by divalent cations is primarily the result of inter-base interactions rather than bridging of phosphate moieties.     

Locating monovalent cations in the grooves of B-DNA

Here we demonstrate that monovalent cations can localize around B-DNA in geometrically regular, sequence-specific sites in oligonucleotide crystals. Positions of monovalent ions were determined from high-resolution X-ray diffraction of DNA crystals grown in the presence of thallium(I) cations (Tl(+)). Tl(+) has previously been shown to be a useful K(+) mimic. Tl(+) positions determined by refinement of model to data are consistent with positions determined using isomorphous F(Tl) - F(K) difference Fouriers and anomalous difference Fouriers. None of the observed Tl(+) sites surrounding CGCGAATTCGCG are fully occupied by Tl(+) ions. The most highly occupied sites, located within the G-tract major groove, have estimated occupancies ranging from 20% to 35%. The occupancies of the minor groove sites are estimated to be around 10%. The Tl(+) positions in general are not in direct proximity to phosphate groups. The A-tract major groove appears devoid of localized cations. The majority of the observed Tl(+) ions interact with a single duplex and so are not engaged in lattice interactions or crystal packing. The locations of the cation sites are dictated by coordination geometry, electronegative potential, avoidance of electropositive amino groups, and cation-pi interactions. It appears that partially dehydrated monovalent cations, hydrated divalent cations, and polyamines compete for a common binding region on the floor of the G-tract major groove.     

Some characteristics of the uptake of glutamine by corn scutellum

Slices of corn scutellum were used to study amino acid uptake, a natural function of this tissue. The uptake of glutamine was found to be inhibited by several monovalent cations. The accompanying anion did not affect the inhibition. Divalent cations stimulated glutamine uptake, particularly at high glutamine concentrations. The inhibition by monovalent cations was reversed by divalent cations.     

Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method

A variation of affinity capillary electrophoresis, called the replacement ion (RI) method, has been developed to measure the binding of monovalent cations to random sequence, double-stranded (ds) DNA. In this method, the ionic strength is kept constant by gradually replacing a non-binding ion in the solution with a binding ion and measuring the mobility of binding and non-binding analytes as a function of binding ion concentration. The method was validated by measuring the binding of Li+ ions to adenosine nucleotides; the apparent dissociation constants obtained by the RI method are comparable to literature values obtained by other methods. The binding of Tris+, NH4+, Li+, Na+, and K+ to dsDNA was then investigated. The apparent dissociation constants observed for counterion binding to a random-sequence 26-base pair (bp) oligomer ranged from 71 mM for Tris+ to 173 mM for Na+ and K+. Hence, positively charged Tris buffer ions will compete with other monovalent cations in Tris-buffered solutions. The bound cations identified in this study may correspond to the strongly correlated, tightly bound ions recently postulated to exist as a class of ions near the surface of dsDNA (Tan, Z.-J., and Chen, S.-J. (2006) Biophys. J. 91, 518-536). Monovalent cation binding to random-sequence dsDNA would be expected to occur in addition to any site-specific binding of cations to A-tracts or other DNA sequence motifs. Single-stranded DNA oligomers do not bind the five tested cations under the conditions investigated here.     

Na+ shows a markedly higher potential than K+ in DNA compaction in a crowded environment

Whereas many physicochemical investigations have shown that among monovalent cations Na(+) ion possesses minimal potential for DNA binding, biological assays have shown that Na(+) ion (in contrast to K(+) ion) plays a primary role in chromatin compaction and related processes. It is difficult to explain this inverse relationship between the compaction potentials of Na(+) and K(+) and their binding abilities. In this study we sought to resolve this contradiction and emphasize the phenomenological distinction between DNA compaction and DNA binding processes in the case of DNA compaction by monocations. Using polyethylene glycol solutions as a model of a crowded cell environment, we studied DNA compaction by alkali metal salts LiCl, NaCl, KCl, RbCl, and CsCl, and found that all of these monocations promote DNA compaction. Among these monovalent cations Na(+) produces the greatest compaction and the ratio of K(+) cand Na(+) oncentrations for DNA compaction is approximately 1.5-2. A comparative analysis of recent experimental results indicates that a higher binding activity of monocation generally corresponds to a low compaction potential of the corresponding monovalent ion. This inverse relation is explained as a result of partial dehydration of monocations in the compact state.     

Regulation of inter- and intramolecular ligation with T4 DNA ligase in the presence of polyethylene glycol.

Polyethylene glycol (PEG) stimulates ligation with T4 DNA ligase. In 10% (w/v) PEG 6,000 solutions, only intermolecular ligation is enhanced by monovalent cations, while both inter- and intramolecular ligation occur without their presence. Similar stimulation was also caused by divalent cations or polyamines in the PEG 6,000 solutions. Such properties of the ligase could be applied to control the extent of inter- and intramolecular ligation. Ligation with cations or polyamines in 10% PEG 6,000 solutions was effective for intermolecular ligation. Ligation without cations or polyamines in 6.0% to 10% PEG 6,000 solutions was effective for intramolecular ligation.     

A relationship between potassium and proline accumulation in salt-stressed Sorghum bicolor

The amount of total monovalent cations in leaves of Sorghum bicolor , L. Moench, RS 610, which were exposed to salinity stress, was a function of both the osmotic potential and the concentration of K⁺ of growth media. The plants have a Na⁺ exclusion mechanism that keeps the level of Na⁺ in leaves low. Thus, most of the osmotic adjustment in leaves was due to K⁺. Proline did not start to accumulate in leaves until the concentration of total monovalent cations in leaves reached a threshold of approximately 200 μmol/g fresh weight. Above this threshold, the contents of prolioe and monovalent cations in leaves increased with increasing salinity of the medium. The ratio of proline to monovalent cation was 5% of that amount of monovalent cation in excess of the threshold concentration. Therefore, if the cations are located in the vacuoles and proline accumulates in the cytoplasm, then the amount of accumulated proline is sufficient to act as a balancing osmoticum across the tonoplast. Very little proline accumulated in roots because this tissue contained much less total monovalent cations than leaves from the same salt-stressed plants. The same threshold of 200 μmol/g fresh weight of total monovalent cations was required in roots as in leaves to initiate proline accumulation.     

Size-dependent allosteric effects of monovalent cations on rabbit liver fructose-1,6-bisphosphatase.

Effects of monovalent cations on the neutral rabbit liver fructose-1,6-bisphosphatase are multifunctional and dependent on their nonhydrated ionic size. (a) The maximal velocity is increased by addition of monovalent cations with the optimum stimulation occurring with a nonhydrated ionic radius of 1.2 A in the presence of a chelating agent such as EDTA. (B) Activation curves are sigmoidal with n values varying from 1.5 to 2.3 as ionic radius of monovalent cation increases. The apparent Ka values from 16.0 to 180 mM, obtained for various monovalent cations, have a linear relationship to ionic radii of cations. (c) At lower concentrations of fructose 1,6-bisphosphate monovalent cations show the inhibitory effect and the apparent Km for fructose 1,6-bisphosphate is increased as the concentration of monovalent cation is increased. A linear relationship is obtained between the slopes of increase in the Km and the reciprocals of ionic volume of monovalent cations. (d) The apparent Ka for Mg2+ is also increased as the concentration of monovalent cation is increased, and a linear relationship is obtained again between the increases in Ka and the reciprocals of ionic volume of monovalent cations. The cooperative nature for Mg2+ saturation is decreased as the Ka increases. (e) The apparent Ki for AMP is also linearly altered as the concentration of monovalent cation is varied. However, the alteration of the Ki is unusual, that is, the smaller cations than K+ increase the Ki (Li+ greater than Na+ greater than NH4+), whereas the larger cations decrease the value ((CH2CH2OH)3N+ greater than Cs+ greater than Rb+). The effect of K+ is insignificant. Alterations in the Ki are also linearly related to the reciprocals of ionic volume of monovalent cations. The cooperative nature for AMP inhibition is decreased or increased as the Ki increased or decreased. (f) In the absence of the chelating agent, the curves for Mg2+ saturation and AMP inhibition were hyperbolic without monovalent cations. By addition of monovalent cation the Ka for Mg+2+ or Ki for AMP is increased and cooperative natures for binding of both ligands are induced. For nonspherical monovalent cations, the application of "functional ionic radius" is proposed. Functional ionic radii of NH4+, (CH2OH)3CNH3+, and (CH2CH2OH)3N+ are estimated to be 1.17, 2.55, and 2.87 A, respectively. The presence of two distinct sites for the actions of monovalent cations is suggested.     

Salt and base sequence specific changes in the chiroptical properties of DNA

Chiroptical properties of natural DNA molecules differing in base composition were studied in solutions with high concentrations of monovalent sodium and caesium salts. It was found that the properties were dependent on the DNA base sequence and nature of both cations and anions. A comparison with the behaviour of the synthetic molecules of DNA demonstrated that the salt-induced changes in the natural molecules of DNA could not be accounted for by the appearance of the left-handed Z conformation. On the other hand, the tendency of the alternating A--T sequence to assume the novel X--DNA conformation seems to play a role even in the conformational properties of natural DNA.     

An energy dependent divalent cation-hydrogen ion binding in the outer membranes of rat liver mitochondria and its dependence on monovalent cation-hydrogen ion binding

Intact mitochondria are able to bind monovalent and divalent metal cations and to release protons in an energy-independent exchange process. Directly accessible binding sites exist in the outer membrane. They seem to be identical for monovalent and divalent metal ions. The inner membrane-matrix-fraction possesses exchange sites after ultrasonic disruption only for monovalent cations, but not for divalent cations.     

Using light scattering measurements to study the effects of monovalent and divalent cations on alginate aggregates

Light scattering measurements were used to assess the effectsof selected divalent and monovalent cations on alginate aggregationin vitro. Alginate, formed with either strontium, calcium orcobalt was partially dissolved with sodium. Calcium-alginatewas also partially dissolved with two other monovalent cations,lithium and potassium. Phosphate, when added to a solution containingcalcium-alginate, scrubbed algin-ate-bound calcium as well asfree calcium in solution. These findings provide an explanationfor an alternative approach for breaking down cell wall alginate. Key words: Alginate aggregates, monovalent cations, divalent cations, light scattering     

9-Amino-acridine as a probe of the electrical double layer associated with the chloroplast thylakoid membranes

Chloroplasts washed with monovalent cations are found to quench 9-amino-acridine fluorescence after resuspension in a cation-free medium. This quenching occurs in the absence of a high energy state and can be reversed by the addition of salts. The effectiveness of these salts is related to the charge carried by the cations and appears to be essentially independent of the associated anions. The order of effectiveness is polyvalent > divalent > monovalent, and virtually no variation is found within the groups of monovalent cations and divalent cations tested. Furthermore, choline and lysine are as effective as alkali metal cations, and lysyl-lysine is almost as effective as alkaline earth metal cations. These results are consistent with an effect mediated by the electrical double layer at the membrane surface rather than chemical bonding, and can be qualitatively explained in terms of the Gouy-Chapman theory.It appears that 9-amino-acridine acts as a diffusible monovalent cation which increases its fluorescence when displaced from the diffuse layer adjacent to the negatively charged membrane surface. The 9-amino-acridine fluorescence changes have been experimentally correlated with the cation-induced chlorophyll a fluorescence changes also observed with isolated chloroplasts.     

Cooperativity and specificity in the interactions between DNA and the glucocorticoid receptor DNA-binding domain

We have employed fluorescence spectroscopy to study the chemical equilibrium between a 115 amino acid protein fragment containing the DNA-binding domain of the human glucocorticoid receptor (DBDr) and a 24-base-pair DNA oligomer containing the glucocorticoid response element (GRE) from the mouse mammary tumor virus promoter region and compared it with the binding to nonspecific DNA at various ionic conditions. We find that binding to both DNAs is cooperative but that DBDr shows a higher affinity for the GRE than for nonspecific DNA and that this difference is more pronounced at increased salt concentrations. Sequence-specific binding to the GRE sequence at 570 mM monovalent cations can be described by a two-site cooperative model, and this supports the notion that DBDr binding to the GRE is enhanced by dimer formation at the recognition site. The product between the (average) association constant for binding to a GRE half-site and the cooperativity parameter was estimated to be K omega = (1-4) x 10(7) M-1 at this salt concentration and 20 degrees C. The sequence-specific binding is not very sensitive to salt concentration in the interval 270-570 mM monovalent cations. However, at lower salt (70 mM) additional binding takes place, presumably nonspecific (cooperative) association to DNA adjacent to the GRE sequence. DBDr binding to nonspecific DNA can be described by the McGhee-von Hippel model for cooperative binding to a chain polymer and is very sensitive to ionic conditions.(ABSTRACT TRUNCATED AT 250 WORDS)     

The effect of monovalent cations on calcium efflux in yeasts

The properties of the calcium efflux system in the yeast Saccharomyces cerevisiae were investigated. After growing the cells overnight in medium containing ⁴⁵Ca, the cells were transferred to medium containing glucose, Hepes buffer (pH 5.2) and monovalent cations. The presence of potassium or sodium in the medium induced efflux of calcium from the cells. The magnitude of the efflux was dependent on the concentration of these cations in the medium. The time course of calcium efflux was analyzed, and two types of exchangeable calcium pools, which turned over at different rates, were detected: ‘Fast turnover’ and ‘slow turnover’. Increase in the concentration of monovalent cations in the medium caused an increase in the fraction of cellular calcium which turned over at a fast rate, and activation of calcium efflux from the ‘slow turnover’ calcium pool. The specific changes in the parameters of calcium efflux induced by monovalent cations were different from those reported previously to be induced by divalent cations. Both processes, i.e. activation of calcium efflux by monovalent and by divalent cations, were found to be additive, indicating that they operate via different mechanisms. Experiments using the respiratory inhibitor Antimycin A, showed that stimulation of calcium efflux by monovalent cations is energy dependent. Lanthanum ions which are known to inhibit calcium influx into yeast cells, inhibitted the activation of calcium efflux by both divalent and monovalent cations. Determination of the cationic composition of the cells indicated that the stimulation of calcium efflux was accompanied by influx of potassium or sodium into the cells.     

Channel permeant cations compete selectively with noncompetitive inhibitors of the nicotinic acetylcholine receptor.

Previous work suggests that noncompetitive inhibitor (NCI) ligands and channel permeant cations bind to sites within the nicotinic acetylcholine receptor ion channel. We have used ethidium as a fluorescent probe of the NCI site to investigate interactions between NCI ligands and channel permeant cations. We found that ethidium can be completely displaced from the receptor by a variety of inorganic monovalent and divalent cations. The rank order of monovalent cation affinities was found to be Tl+ greater than Rb+ greater than or equal to K+ greater than Cs+ greater than Na+ greater than Li+. The monovalent cation Kd values vary markedly over a 40-fold range, from 3 to 121 mM. The Kd values and rank order correspond to values determined previously from electrophysiological data. Hill plots of the back titrations yield slopes of 1.0 for all monovalent cations, indicating a single class of independent sites, as shown previously for NCI ligands. Scatchard analysis of ethidium binding in the presence of Tl+ reveals a reduction in affinity and no changes in the maximal number of sites. In the presence of agonist the kinetics of ethidium dissociation induced by the addition of phencyclidine or cations alone or the simultaneous addition of both are nearly identical. The ethidium dissociation rate induced by either phencyclidine or cations is regulated by the occupation of the agonist sites in a similar manner. These results indicate that the effect of cations on NCI ligand binding occurs by mutually exclusive competition. We suggest that NCIs can regulate cation binding at a physiological cation recognition site that is likely part of the cation permeation path through the receptor channel.