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Effect of Zn2+ 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 Zn2+ 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-Zn2+ system. The phase diagram revealed a region in which ordered single-stranded structures, stabilized by Zn2+-mediated cross-links involving N3 atom of cytosine, are formed. The phase diagram also demonstrated that the behavior of the polyC-Zn2+ system is similar to the effect of retrograde condensation observed in some binary solutions of simple liquids. A dependence of Zn2+-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. [ABSTRACT FROM AUTHOR]

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., (Copyright © 2013 Elsevier B.V. All rights reserved.)

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°С upon formation of m-form in the presence of Zn(2+) ions was observed and rationalized. Furthermore, a strong cooperative decrease (up to 30°С) of the temperature of В→m transition induced by heating in the presence of Zn(2+) was found and its nature was explained., (Copyright © 2013 Elsevier B.V. All rights reserved.)

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., (Copyright © 2011 Elsevier B.V. All rights reserved.)

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., (Copyright © 2011 Elsevier B.V. All rights reserved.)

The methods of UV (DUV) spectroscopy and thermal denaturation were used to study the effect of Cd2+ ions on the conformational equilibrium of three-stranded (A21, A2U) and single-stranded (poly U, poly A and poly I) polynucleotides in aqueous solutions containing 0.1 M Na+ (pH 7). An analysis of the form and intensities of DUV-spectra of poly A, poly I and A2I revealed the presence of two types of complexes: interaction with N7 of purines, resulting in the formation of macrochelates and binding to N1 of poly A and poly I. Cd2+ ions do not bind to heteroatoms of A2U nitrogen bases, and, therefore, the conformation of its structure remains unchanged up to a concentration of Cd2+ 0.01 M. A "critical" concentration (1.5x10(-4) M) of Cd2+ ions exists above which A2I transits cooperatively into a new helical conformation, which has a lower thermostability. It is supposed that, during the formation of metallized A2I, Cd2+ ions form bridges between the adenine and hypoxanthine of its homopolynucleotide circuits, being arranged inside the triple helix.