Interaction of Zn(2+) ions with single-stranded polyU and polyC in neutral solutions.

Effect of Zn(2+) ions on the conformation of single-stranded polynucleotides polyU and polyC in a wide temperature range at pH 7 was studied by differential UV spectroscopy and by thermal denaturation. The atoms coordinating Zn(2+) ions were determined (O4 and N3 in polyU and N3 in polyC). A three-dimensional phase diagram and its two-dimensional components were constructed for a polyC-Zn(2+) system. The phase diagram revealed a region in which ordered single-stranded structures, stabilized by Zn(2+)-mediated cross-links involving N3 atom of cytosine, are formed. The phase diagram also demonstrated that the behavior of the polyC-Zn(2+) system is similar to the effect of retrograde condensation observed in some binary solutions of simple liquids. A dependence of Zn(2+)-polyC binding constant on the metal ion concentration was obtained. The reason why zinc-induced transition of the sequences with adenine-uracil (AU) base pairs from A-form geometry to a metallized m-form requires higher pH compared to the sequences comprised of guanine-cytosine (GC) base pairs is explained. This information can be useful for the development of possible technological applications based on m-DNA.

Effect of Zn2+ and temperature on the conformational equilibrium of single-stranded polyA in neutral solutions.

Effect of Zn(2+) ions on the conformation of polyA in cacodilic buffer at pH 7 was investigated by differential UV spectroscopy (DUV) and by thermal denaturation. The shapes of the DUV spectra and melting curves suggest a transition of polyA into a more ordered "metallized", possibly double-helical conformation at Zn(2+) concentrations above 3×10(-5) M. A phase diagram of polyA complexes with Zn(2+) was constructed for the temperature range from 20 °C to 95 °C and Zn(2+) concentrations between 10(-5) M and 5×10(-4) M. It was found that the transition of a single strand into the "metallized" form is possible only if the length of the disordered single-stranded region becomes larger than a certain critical value, ranging between 98% and 78% as the metal concentration increases from 3×10(-5) to 5×10(-4) M.

Specific features of Zn²âº, Co²âº and Ni²âº ion binding to DNA in alkaline solutions.

Dependence of DNA metallization degree during B-DNA transition into the metallized (m) form on DNA concentration has been studied by visible and differential UV-spectroscopy in the presence of Zn(2+), Co(2+) and Ni(2+) ions in tetraborate buffer (pH 8.5) with and without ethidium bromide. Constants of Mt(2+) binding to double stranded DNA were calculated. The obtained binding constants corresponded to the formation of inter-strand metal bridges stabilizing m-form. Thermodynamic origin of higher efficiency of Zn(2+) ions in DNA metallization compared to Co(2+) and Ni(2+) was revealed. Increase of the DNA helix-coil transition temperature by up to 10°Ð¡ upon formation of m-form in the presence of Zn(2+) ions was observed and rationalized. Furthermore, a strong cooperative decrease (up to 30°Ð¡) of the temperature of В→m transition induced by heating in the presence of Zn(2+) was found and its nature was explained.

DNA conformational equilibrium in the presence of Zn2+ ions in neutral and alkaline solutions.

Effect of Zn(2+) ions on DNA transition from B-form to a metallized form (m-DNA) in Tris and tetraborate buffers at pH 8.5 has been studied by visible and differential UV-spectroscopy and by thermal denaturation. The results have been compared to those obtained at pH 6.5 in cacodylate buffer. It was found that in alkaline solutions Zn(2+) ions induced a hypochromicity of the DNA absorption in the whole spectral range monitored, which was attributed to DNA transition from B- to the m-form. Complete metallization occurred only upon heating the DNA solutions containing more than ~2×10(-4) M of Zn(2+) ions. Phase diagrams of the DNA-zinc complexes at pH 6.5 and 8.5 have been obtained for the first time. The m-DNA form showed higher thermal stability compared to B-DNA.

Divalent metal ion effect on helix-coil transition of high molecular weight DNA in neutral and alkaline solutions.

Effect of Mg(2+), Ca(2+), Ni(2+) and Cd(2+) ions on parameters of DNA helix-coil transition in sodium cacodylate (pH 6.5), Tris (pH 8.5) and sodium tetraborate (pH 9.0) buffers have been studied by differential UV-visible spectroscopy and by thermal denaturation. Anomalous behavior of the melting temperature T(m) and the melting interval ΔT in the presence of MgCl(2) was observed in Tris, but not in cacodylate or tetraborate buffers. Changes in the buffer type and pH did not influence T(m) and ΔT dependence on Ca(2+) and Cd(2+) concentrations. Decrease of the T(m) and ΔT of DNA in the presence of Ni(2+) and Cd(2+) was caused by preferential ion interaction with N7 of guanine. This type of interaction was also found for Mg(2+) in Tris buffer. The anomalous decrease in the T(m) and ΔT values was connected to formation of complexes between metal ions and Tris molecules. Transition of DNA single-stranded regions into a compact form with the effective radius of the particles of 300±100 Å was induced by Mg(2+) ions in Tris buffer.

A spectroscopic method to estimate the binding potency of amphiphile assemblies.

A fast and convenient spectroscopic methodology to determine the water uptake capacity of amphiphile assemblies studied in multilayer films is presented. This method was developed to provide a reliable but relatively simple tool for estimating the binding potency of such complex systems. The water-binding potency represents a general propensity of higher-order systems to bind or embed relevant ligands, such as various non-lipid effectors in the case of artificial lipid membranes. In this sense, the binding potency might contribute to a specific functional role of certain lipids. The essence of the new method is that the calibration of data measured by infrared (IR) spectroscopy against those directly obtained by Karl-Fischer titration (KFT) enables one to replace the expensive chemical-analytical technique by a more comfortable and efficient IR-spectroscopic protocol. This approach combines the easy handling, versatility, and availability of IR spectroscopy with the high accuracy of KFT. The usefulness of the procedure is demonstrated on an example set of six amphiphiles with a common chain length of 18 carbon atoms. Despite this similarity, the binding potency data differ tremendously in a way which can be correlated with the systematic variations introduced into the amphiphile structure. Going further beyond the methodical aspect, the scientific relevance of the data is comprehensively discussed especially in terms of the structural factors that govern the binding potency of amphiphiles. That is favored mainly by fluidity and disfavored mainly by inter-amphiphile binding networks. For phosphatidylcholine, our data are strongly in favor of a particular hydration model that involves primary water binding to phosphate as well as the formation of water semi-clathrates hosting the trimethylammonium moiety. Interestingly, stearylamine and diolein assemblies did not take up any water at all. This unexpected hydrophobicity is due to the unusual structures formed in these latter cases: rigid ammonium amide with a strong hydrogen-bonding/salt bridge network in stearylamine, and patches of inverted micelles in diolein, as revealed by molecular dynamics simulations.

The effect of manganese(II) on the structure of DNA/HMGB1/H1 complexes: electronic and vibrational circular dichroism studies.

The interactions were studied of DNA with the nonhistone chromatin protein HMGB1 and histone H1 in the presence of manganese(II) ions at different protein to DNA and manganese to DNA phosphate ratios by using absorption and optical activity spectroscopy in the electronic [ultraviolet (UV) and electronic circular dichroism ECD)] and vibrational [infrared (IR) and vibrational circular dichroism (VCD)] regions. In the presence of Mn2+, the protein-DNA interactions differ from those without the ions and cause prominent DNA compaction and formation of large intermolecular complexes. At the same time, the presence of HMGB1 and H1 also changed the mode of interaction of Mn2+ with DNA, which now takes place mostly in the major groove of DNA involving N7(G), whereas interactions between Mn2+ and DNA phosphate groups are weakened by histone molecules. Considerable interactions were also detected of Mn2+ ions with aspartic and glutamic amino acid residues of the proteins.

[The effect of Ca2+ ions on DNA compaction in the complex with non-histone chromosomal protein HMGB1]. / Vliianie ionov Ca2+ na kompaktizatsiiu DNK v komplekse s negistonovym khromosomnym belkov 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 effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies.

The interaction of DNA with Mn2+ was studied in absorbance and optical activity in the electronic and vibrational regions. Based on the data, several stages of the interaction were identified. Con formational transition towards the C-form of DNA was observed in solution at the molar ratio Mn2+/DNA-phosphates between 0.1 and 1.5. The exact ratio depended on the ionic strength and increased with increasing NaCl concentration. Although manganese interacted with the phosphates and bases of DNA at higher metal concentrations, it is unlikely that direct chelation occurred. A model for the interaction between manganese ions and DNA mediated by water is suggested destabilizing the double helix and partially breaking the hydrogen bonds between the base pairs. At high Mn2+ concentrations DNA aggregation was observed.

Complexes of (dG-dC)20 with Mn2+ ions: a study by vibrational circular dichroism and infrared absorption spectroscopy.

The B-Z transition of the synthetic oligonucleotide, (dG-dC)20, induced by Mn2+ ions at room temperature, was investigated by absorption and Vibrational Circular Dichroism (VCD) spectroscopy in the range of 1800-800 cm(-1). Metal ion concentration was varied from 0 to 0.73 M Mn2+ (0 to 8.5 moles of Mn2+ per mole of oligonucleotide phosphate, [Mn]/[P]). While both types of spectra showed considerable changes as the Mn2+ concentrations were raised, differences between the two were often complementary in their expression and extent, those displayed by VCD being more clearly evident due to the inversion of the opposite helical sense from the right-handed to the left-handed conformation. The main phase of the transition occurred in the metal ion concentration between 0.8-1.1 [Mn]/[P]. Gradual changes that took place in the spectra were interpreted in terms of simultaneous processes that depended on metal ion concentration, namely B-Z transformation, binding of Mn2+ to phosphates and to nitrogen bases, and partial denaturation. Below approximately 0.6 [Mn]/[P], only a small portion of the oligonucleotide adopted the Z conformation within a 3 hour period, whereas conversion was completed in the same time interval for concentrations between 0.9-1.2 [Mn]/[P]. At [Mn]/[P] >1.7, complete transition to the Z-form took place immediately on adding Mn2+. Applying VCD spectroscopy in combination with conventional infrared absorption proved most useful for corroborating changes in the absorption spectra, and for detecting in an unique manner, not attainable by absorption methods, conformational changes that lead to the inversion of the helical sense of the oligonucleotide.