Effect of ethanol on structural transitions of DNA and polyphosphates under Ca2+ ions action in mixed solutions

In the present work using the IR spectroscopy method the effect of ethanol on structural transitions of DNA and polyphosphates under the action of Ca2+ ions in mixed solutions containing ethanol (0-25 vol.%) was studied. It was shown that, on its interaction with Ca2+ ions, in aqueous and mixed solutions DNA becomes transformed into compact form. With the increase of concentration of ethanol the degree of Ca2+-induced DNA compactisation rises. It was found that, in mixed solutions containing ethanol, Ca2+-induced DNA compactisation depends not only on the solution's dielectric permeability but also on the solution structure. On stabilisation of the water structure in the presence of low ethanol concentrations a stabilisation of the DNA macromolecule occurs that leads to the increase of the Ca2+ ion concentration necessary for DNA compactisation. Comparison of the effects of ethanol on Ca2+-induced structural transitions in DNA and polyphosphates in mixed solvents permits to suppose that at alcohol concentrations in solution resulting in disruption of the water spatial structure, some peculiarities are observed in the behavior of those molecules whose hydrophobic interactions are essential.     

Vibrational circular dichroism and IR absorption of DNA complexes with Cu2+ ions

Vibrational circular dichroism (VCD) spectroscopy and simultaneous IR absorption measurements are applied to study the interaction of natural calf thymus DNA with Cu2+ ions at room temperature in a Cu2+ concentration range of 0-0.4M (a Cu2+/phosphate molar ratio [Cu]/[P] of 0-0.7). In some important instances, VCD provides more detailed insights than previous IR investigations whereas in several others it leads to the same interpretations. The Cu2+ ions bind to phosphate groups at a low metal concentration. Upon increasing the ion concentration, chelates are formed in which Cu2+ binds to the N7 of guanine (G) and a phosphate group. Detectable only by VCD, significant distortion of most guanine-cytosine (GC) base pairs occurs at a [Cu]/[P] ratio of 0.5 with only a minor affect on adenine-thymine (AT) base pairs, which favors a "sandwich" complex in which a Cu2+ ion is inserted between two adjacent guanines in a GpG sequence. The AT base pairs become significantly distorted when the metal concentration is increased to 0.7 [Cu]/[P]. A number of GC base pairs, which are possibly involved in sandwich complexes, remain stacked and paired even at 0.7 [Cu]/[P], preventing complete strand separation. The DNA secondary structure changes considerably from the standard B-form geometry at a [Cu]/[P] ratio of 0.4 and higher. A further transition to some intermediate conformation that is inconsistent with either the A- or Z-form or a completely denatured state is suggested in agreement with other works. In general, VCD proves to be a reliable indicator of the 3-dimensional structure of the DNA-metal ion complexes, which reveals structural details that cannot be deduced from the IR absorption spectra alone.     

The role of Ca ions in changes induced by excess Cu2+ in bean plants. Growth parameters

The effect of Ca on Cu toxicity in runner bean plants (Phaseolus coccineus L. cv. Piěkny Jaś) grown hydroponically in nutrient solution was studied. The toxic effect of excess Cu on plants depends on their age and Ca content in the medium. Copper applied in excess to the plants at the early phase of leaf development strongly limits the uptake of Ca ions from the nutrient solution, particularly their translocation to leaves. Increased Ca content limits the inhibitory effect of Cu on leaf growth and decreases the content of chloroplast pigments to the level approximate to that of control. At this growth stage the effect of excess Cu is at least partially connected with limited Ca transport to leaves. At the intermediate leaf phase Cu-treated plants react slightly to changed Ca content. At the end of the primary leaf development increased Ca concentration in the medium intensifies senescence processes induced by excess Cu. The changes are partially connected with intensified water deficit. Increased Ca content in the nutrient solution limits Cu accumulation in the individual organs of Cu-treated plants. However, Cu accumulation in leaves is not decreased at a high level of Ca. Copper generally decreases Ca content in the youngest plants, whereas in the oldest ones only in the case of a low level of Ca in the nutrient solution.     

Ca2+ and Cu2+ supplementation augments vancomycin production by Amycolatopsis orientalis

Supplementation with CaCl₂2H₂O (40 mg l^–1) or CuSO₄5H₂O (10 mg l^–1) improved vancomycin production by Amycolatopsis orientalis by 12 and 11%, respectively; used in combination, they acted synergistically. Ca²⁺ decreased the intracellular concentration of vancomycin 36%, whereas Cu²⁺ increased the intracellular activity of TDP-glucose:aglycosylvancomycin glucosyltransferase 3 times more than control. Ca²⁺ probably works by altering the permeability of cells to vancomycin, whereas Cu²⁺ increases the activity of an enzyme responsible for vancomycin biosynthesis.     

Influence of Ca2+ cations on low pH-induced DNA structural transitions

A confocal Raman microspectrometer was used to investigate the influence of Ca2+ cations on low pH-induced DNA structural changes. The effects of Ca2+ cations on the protonation mechanism of opening AT and changing the protonation of GC base pairs in DNA are discussed. Based on the observation that the midpoint of the transition of Watson-Crick GC base pairs to protonated GC base pairs lies at around pH 3 (analyzing the 681 cm(-1) line), measurements were carried out on calf thymus DNA at neutral pH and pH 3 in the presence of low and high concentrations of Ca2+ cations. Raman spectra show that low concentrations of Ca2+ cations partially protect DNA against protonation of cytosine (characteristic line at 1262 cm(-1)) and do not protect adenine (characteristic line at 1304 cm(-1)) and the N(7) of guanine (line at 1488 cm(-1)) against binding of H+. High Ca2+ concentrations can prevent protonation of cytosine and protonation of adenine (little disruption of AT pairs). Analyzing the line at 1488 cm(-1), which obtains most of its intensity from a guanine vibration, high salt was also found to protect the N(7) of guanine against protonation.     

Interaction of Cu2+ and Ca2+ ions with DNA immobilized in polyacrylamide gel

Interaction of cupric and calcium ions with DNA entrapped in acrylamide gel was studied by means of ion-exchange method. Ion-exchangers on the basis of DNA were obtained by polymerization of acrylamide with and without warming-up. Samples of DNA with different degrees of denaturation were also used for preparation of ion-exchangers. It was demonstrated that ion-exchange capacity is determined by the number of phosphate groups of DNA entrapped in gel. Cu2+ and Ca2+ ion-exchange equilibrium on the macromolecules of immobilized DNA was studied at different temperatures. Ion-exchange equilibrium constant alpha Cu2+ Ca2+ was shown to vary from 1,9 to 8,2 an increase of selectivity for Cu2+ ions taking place under conditions favouring denaturation of DNA. Stoichiometric ratio between the quantity of the phosphate groups and the number of equivalents of Cu2+ and Ca2+ was observed in all the experiments. Lack of over-equivalent absorption of CuCl2 on the DNA molecules indicates that chloride ions do not participate in charge neutralization within the Cu2+.DNA complex. It means that Cu2+ ions interact with phosphate groups of DNA coordinate simultaneously with DNA bases only.     

Intramolecular and intermolecular guanine quadruplexes of DNA in aqueous salt and ethanol solutions

DNA guanine quadruplexes are all based on stacks of guanine tetrads, but they can be of many types differing by mutual strand orientation, topology, position and structure of loops, and the number of DNA molecules constituting their structure. Here we have studied a series of nine DNA fragments (G(3)Xn)(3)G(3), where X = A, C or T, and n = 1, 2 or 3, to find how the particular bases and their numbers enable folding of the molecule into quadruplex and what type of quadruplex is formed. We show that any single base between G(3) blocks gives rise to only four-molecular parallel-stranded quadruplexes in water solutions. In contrast to previous models, even two Ts in potential loops lead to tetramolecular parallel quadruplexes and only three consecutive Ts lead to an intramolecular quadruplex, which is antiparallel. Adenines make the DNA less prone to quadruplex formation. (G(3)A(2))(3)G(3) folds into an intramolecular antiparallel quadruplex. The same is true with (G(3)A(3))(3)G(3) but only in KCl. In NaCl or LiCl, (G(3)A(3))(3)G(3) prefers to generate homoduplexes. Cytosine still more interferes with the quadruplex, which only is generated by (G(3)C)(3)G(3), whereas (G(3)C(2))(3)G(3) and (G(3)C(3))(3)G(3) generate hairpins and/or homoduplexes. Ethanol is a more potent DNA guanine quadruplex inducer than are ions in water solutions. It promotes intramolecular folding and parallel orientation of quadruplex strands, which rather corresponds to quadruplex structures observed in crystals.     

Urea effect on Cu(2+)-induced DNA structural transitions in solution

Cu(2+) ion interaction with DNA in aqueous solutions containing urea (0-5 M) was studied by IR spectroscopy. It was shown that upon the Cu(2+) ion binding DNA transition into a compact form occurs. This transition is of positive cooperativity. We suppose that the mechanism of Cu(2+)-induced DNA compaction in solutions containing urea is not completely electrostatic. Urea addition to the DNA solution decreases the Cu(2+) ion concentration required to induce DNA compaction. As the urea content in solution rises, the binding constant of Cu(2+) ions interacting with DNA increases, going through the maximum in the case of 2 M solution; further increase of the urea content in solutions leads to decrease of the binding constant. DNA transition into the compact form under the Cu(2+) ion action is determined not only by the effects of the solution dielectric permeability but by the solvation effects; when changes of the dielectric permeability are small the solvation effects may prevail. Urea addition to the DNA solution also decreases cooperativity of the DNA compaction process. Perhaps, cooperativity of the DNA transition into the compact state depends on the ordered spatial structure of water adjacent to the macromolecule and decreases on the structure destruction.     

菲咯啉铜配合物与DNA作用机制研究进展

综述了菲咯啉铜配合物与ＤＮＡ作用机制的研究进展,主要阐述了菲咯啉铜配合物与ＤＮＡ结合的主要方式及切割ＤＮＡ的反应机理。     

Conformational transitions in the Ca2+ + Mg2+-activated ATPase and the binding of Ca2+ ions.

We have studied the fluorescence of the Ca2+ + Mg2+-activated ATPase of sarcoplasmic reticulum labelled with fluorescein isothiocyanate. The change in intensity of fluorescein fluorescence caused by addition of Ca2+ to the labelled ATPase can be interpreted in terms of a two-conformation model for the ATPase, one conformation (E1) having a high affinity for Ca2+, the other (E2) a low affinity. Effects of Ca2+ as a function of pH allow an estimate of the effect of pH on the E1/E2 ratio, consistent with kinetic studies. A model is presented for binding of Ca2+ to the ATPase as a function of pH that is consistent both with the data on the E1/E2 equilibrium and with literature data on Ca2+ binding.     

Effect of nuclear Ca2+ uptake inhibitors on Ca2+-activated DNA fragmentation in rat liver nuclei

The effect of nuclear Ca²⁺ uptake inhibitors on the Ca²⁺-activated DNA fragmentation in rat liver nuclei was investigated. The addition of Ca²⁺ (40 M) into the reaction mixture containing liver nuclei in the presence of 2.0 mM ATP caused a remarkable increase in nuclear DNA fragmentation. This Ca²⁺-activated DNA fragmentation was not seen in the absence of ATP, because nuclear Ca²⁺ uptake is not initiated without ATP addition. Moreover, the presence of various reagents (10 M arachidonic acid, 2.0 mM NAD⁺, 10 M zinc sulfate and 0.2 mM N-ethylmaleimide), which could inhibit Ca²⁺-ATPase activity and Ca²⁺ uptake in the nuclei, produced a significant inhibition of the Ca²⁺-activated DNA fragmentation in the nuclei. The results show that the Ca²⁺-activated DNA fragmentation is involved in the uptake of Ca²⁺ by the nuclei, suggesting a role of Ca²⁺ transport system in the regulation of liver nuclear functions.     

DNA aggregation induced by Mg2+ ions under different conditions

Cations‐induced DNA aggregation can modify the local structure of oligonucleotides and has potential applications in medicine and biotechnology. Here, we used atomic force microscopy to investigate λ‐DNA aggregation on Mg²⁺‐treated glass (Mg²⁺/glass) and in Mg²⁺ solution. Atomic force microscopy topography images showed that some DNA fragments were slightly stacked together on 10 mM Mg²⁺/glass and stacked stronger on ≥50 mM Mg²⁺/glass. They also showed that DNA aggregated stronger in Mg²⁺ solution than on Mg²⁺/glass, ie, DNAs are strongly stacked and twisted at 10 mM Mg²⁺, rolled together at 50 mM Mg²⁺, and slightly aggregated to form small particles at 100 mM Mg²⁺. At a specific condition, ie, heating λ‐DNA to 92°C, cooling down to 75°C, adding Mg²⁺, and vortexing the resulting solution, DNA strongly aggregated and formed pancake‐like shapes at 10 and 50 mM or a large aggregate at 100 mM Mg²⁺ solutions. Our results may be helpful for medical applications and gene therapy using cation‐DNA technology.     

低温胁迫下龙眼(Dimocarpus longana Lour.)幼叶细胞内Ca2+水平及细胞超微结构

用焦锑酸钾沉淀的电镜细胞化学方法研究低温胁迫下龙眼幼叶细胞内Ｃａ＾２＋水平的变化。未经低温处理的幼叶,细胞壁,细胞间隙,质膜和液泡存在大量的Ｃａ＾２＋沉淀颗粒,叶绿体,细胞质和细胞核中也有一些Ｃａ＾２＋沉淀颗粒分布,表明液泡和细胞间隙是植物细胞的钙库。     

Modelling the effect of specific inositol 1,4,5-trisphosphate receptor isoforms on cellular Ca2+ signals

BACKGROUND INFORMATION: Oscillations of cytosolic Ca2+ are well-known to rely on the regulatory properties of the InsP3R (inositol 1,4,5-trisphosphate receptor). Three isoforms of this channel have been identified. They differ in their regulatory properties by Ca2+ and InsP3. Experiments in different cell types clearly indicate that the relative amounts of each isoform affect the time course of Ca2+ changes after agonist stimulation. In the present study, we investigate whether different steady-state curves for the open probability of the InsP3Rs as a function of Ca2+ imply different dynamical behaviours when these receptors are present in a cellular environment. We therefore describe by a specific phenomenological model the three main types of curves that have been reported: (i) the classical bell-shaped curve, (ii) the bell-shaped curve that is shifted towards higher Ca2+ concentrations when InsP3 is increased, and (iii) a monotonous increasing function of cytosolic Ca2+. RESULTS: We show that, although these types of curves can be ascribed to slight differences in the channel regulation by Ca2+ and InsP3, they can indicate important variations as to the receptor role in cellular Ca2+ control. Thus the receptor associated with the classical bell-shaped curve appears to be the most robust Ca2+ oscillator. If the steady-state curve is supposed to be a monotonous increasing function of cytosolic Ca2+, the modelled receptor cannot sustain Ca2+ oscillations in the absence of Ca2+ exchanges with the extracellular medium. When the bell-shaped curve is shifted towards higher Ca2+ concentrations with increasing InsP3 levels, the model predicts that the receptor is less robust to changes in density; this receptor, however, provides a finer control of the steady-state level of Ca2+ when varying the InsP3 concentration. CONCLUSIONS: Our model allows us to propose an explanation for the experimental observations about the effect of selectively expressing or down-regulating InsP3R isoforms, as well as to make theoretical predictions.     

Auxiliary Ca2+ binding sites can influence the structure of CIB1

Recent X-ray crystal structures and solution NMR spectroscopy data for calcium- and integrin-binding protein 1 (CIB1) have all revealed a common EF-hand domain structure for the protein. However, the orientation of the two protein domains, the oligomerization state, and the conformations of the N- and C-terminal extensions differ among the structures. In this study, we examine whether the binding of glutathione or auxiliary Ca²⁺ ions as observed in the crystal structures, occur in solution, and whether these interactions can influence the structure or dimerization of CIB1. In addition, we test the potential phosphatase activity of CIB1, which was hypothesized based on the glutathione binding site geometry observed in one of the crystal structures of the protein. Biophysical and biochemical experiments failed to detect glutathione binding, protein dimerization, or phosphatase activity for CIB1 under several solution conditions. However, our data identify low affinity (K_d, 10⁻²M) Ca²⁺ binding events that influence the structures of the N- and C-terminal extensions of CIB1 under high (300 mM) Ca²⁺ crystallization conditions. In addition to providing a rationale for differences amongst the various solution and crystal structures of CIB1, our results show that the impact of low affinity Ca²⁺ binding events should be considered when analyzing and interpreting protein crystallographic structures determined in the presence of very high Ca²⁺ concentrations.     

The effect of Ca2+ ions on DNA compaction in the complex with non-histone chromosomal protein HMGB1

The analysis of absorption and circular dichroism spectra in UV and IR regions showed that Ca2+ ions interact both with the phosphate groups of DNA and with the HMGB1 protein. Not only negatively charged C-terminal part of the protein molecule participates in interaction with metal ions but also its DNA-binding domains. The latter fact leads to the change of the mode of protein-DNA interaction. The presence of Ca2+ ions prevents formation of ordered supramolecular structures, specific for the HMGB1-DNA complexes, though promotes intermolecular aggregation. The structure of the complexes between DNA and the protein HMGB1 lacking C-terminal tail appears to be the most sensitive to the presence of Ca2+ ions. The data obtained allow to conclude that Ca2+ ions do not play a structural role in the HMGB1/DNA complexes and the presence of these ions is not necessary to DNA compaction in such systems.     

The role of Ca2+ and hemodynamics in the action of diltiazem on hepatic energy metabolism

Diltiazem causes vasoconstriction in the liver when present at high concentrations, an action that is strictly Ca²⁺-dependent. Diltiazem is also active on energy metabolism. This toxic action could be partly a consequence of hemodynamic effects. In the absence of Ca²⁺, the hemodynamic effects are no longer present and, consequently, Ca²⁺-free experiments are useful for distinguishing between hemodynamics-dependent and hemodynamics-independent effects. The experimental system used was the hemoglobin-free perfused rat liver from fed and fasted rats. Diltiazem was infused at various concentrations in the presence and absence of Ca²⁺. Several metabolic parameters were measured: lactate and pyruvate production (glycolysis), glycogenolysis, oxygen uptake, gluconeogenesis, and the cellular levels of lactate, pyruvate, glucose, AMP, ADP, and ATP. The effects of diltiazem can be divided into three groups: (1) Effects that are strictly dependent on the Ca²⁺-mediated hemodynamic action. This group comprises inhibition of oxygen uptake at all concentrations (50–500 mol/L) inhibition of lactate, pyruvate, and glucose release at high concentrations; the decrease in cellular ATP; the increase in cellular AMP; and the cellular accumulation of glucose and lactate. (2) Effects that are independent of the hemodynamic action. The most relevant effect of this type is inhibition of gluconeogenesis. (3) Effects that are influenced by Ca²⁺ but are independent of the hemodynamic effects. This is the typical case of lactate and glucose release from endogenous glycogen, whose stimulation by low diltiazem concentrations is more pronounced in the presence of Ca²⁺ than in its absence.     

Structural changes of low density lipoproteins with Cu2+ and glucose induced oxidation

The compositional and structural changes of lipids and apolipoproteins during in vitro oxidation of low density lipoprotein (LDL) are investigated in this study by IR spectroscopy. For comparison, LDL samples containing either copper or glucose at physiological or pathological concentrations are considered in order to know the separate affects of these chemical factors on LDL oxidation. The results show that the initial steps of lipid oxidation proceed through hydrogen atom loss from methylene groups, as well as loss of cholesteryl ester molecules, and later a recovering of carbonyl compounds resulting from aldehyde formation that generally occurs in autooxidation processes. Lipid oxidation is induced by copper ions, and glucose enhances metal ion induced LDL oxidation as determined by conjugated diene formation. As to the protein conformational changes, IR spectroscopy reveals for the first time that LDL oxidation involves formation of beta-sheet structures, these being more abundant in LDL samples with pathological concentrations of glucose or copper. Consequently, the LDL structural changes may contribute to the recognition of oxidized LDL particles by scavenger receptors.     

The effect of spermine on transport of Ca2+ ions in brain mitochondria

The effect of spermine (50-400 microM) on the Ca-transporting system of brain mitochondria was studied. In a medium containing Mg2+ and ATP, spermine facilitates the accumulation of Ca2+ by decreasing Km of the uniporter. Spermine inhibits Na-stimulated Ca2+ efflux; this effect is dependent on the ionic strength of the medium--it is decreased when KCl concentration is increased from 20 to 120 mM. Spermine (200 microM) decreases (by 50%) the steady state concentration of Ca2+ maintained by mitochondria. The importance of spermine as a regulator of Ca2+-transport in brain mitochondria is discussed.     

Protein phosphorylation and the role of Ca2+ in planarian turbellarian regeneration

During planarian regeneration, relationships in timing were established between variations of calcium and calmodulin contents on one hand, and protein phosphorylation and stimulation of DNA and RNA synthesis on the other. Special attention was paid to changes in histone phosphorylation in regenerating fragments. Using in vitro experiments on dissociated planarian cells, we demonstrated causal relationships between these events. In particular, the key role of Ca²⁺ in the activation of protein kinases and in the initiation of DNA synthesis was emphasized.