Biopolym. Cell. 2007; 23(5):433-440.
Molecular Biophysics
Effect of Cd2+ ions on conformational equilibrium of three-stranded polyU·polyA·polyU polynucleotide under near-physiological conditions
1Sorokin V. A., 1Valeev V. A., 1Usenko E. L., 1Blagoi Yu. P.
- B. I. Verkin Institute for Low Temperature Physics and Engineering, NAS of Ukraine
47, Prospekt Lenina, Kharkiv, Ukraine, 61103
Abstract
Cd2+ ions effect on the conformational equilibrium of three-stranded polyU·polyA·polyU polynucleotide (0.1M Na+, pH 7) has been studied by the method of differential UV spectroscopy. It has been revealed that Cd2+ ions do not bind heteroatoms of nitrogen bases of polyA and polyU being in triple (A2U) and double (AU) helices and do not change their conformation. The heating of A2U results in two subsequent processes: the first one represents separation of one strand of poly U from A2U i. e. A2U AU + U transition (3 → 2 transition) is realized, and the second one corresponds to more cooperative melting of AU, i. e. 2 → 1 (U + A U + A + U) transition. The concentration dependences of melting temperatures for these processes have some intersection point (Tm = 60 °C; [Cd2+] ~ 3.5·10–4 M) at which thermal stability of A2U and AU become identical. The theoretical calculations of concentration dependences (Tm)3→2 revealed that the best agreement between experiment and theory is observed at the enthalpy of transitionΔH3→2 = 5 kcal/mol·triplet.
Keywords: metal ions, three-stranded polynucleotides, conformational transitions
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References
[1]
Moore JW, Ramamoorthy S. Heavy Metals in Natural Waters. Applied Monitoring and Impact Assessment. Springer-Verlag New York. 1984; 268 p
[2]
Durlach J, Bara M, Guiet-Bara A. Metal ions in biological systems. Eds H. Sigel, A. Sigel. New York: Marcel Dekker, 1990. Vol. 26. 243 p.
[3]
Hartwig A, Asmuss M, Ehleben I, Herzer U, Kostelac D, Pelzer A, et al. Interference by Toxic Metal Ions with DNA Repair Processes and Cell Cycle Control: Molecular Mechanisms. Environmental Health Perspectives. 2002;110(s5):797–9.
[4]
Hartwig A. Recent advances in metal carcinogenicity. Pure Appl Chem. 2000;72(6):1007-14.
[5]
Aoki K. Nucleosides, nucleotides and metal ions. Metalloproteins: Chemical properties and biological effects. Eds S. Otsuka, T. Yamanaka. Amsterdam etc.: Elsevier, 1988;457-4\90.
[6]
Sirover MA, Loeb LA. Infidelity of DNA synthesis in vitro: screening for potential metal mutagens or carcinogens. Science. 1976;194(4272):1434-6.
[7]
Andronikashvili EL. [Malignant transformation and changes in various physico-chemical properties of macromolecules and supramolecular structures. I. Nucleic acids]. Biofizika. 1987;32(5):782-99.
[8]
Mills M, V?lker J, Klump HH. Triple helical structures involving inosine: there is a penalty for promiscuity. Biochemistry. 1996;35(41):13338-44.
[9]
Field AK. Oligonucleotides as inhibitors of human immunodeficiency virus. Curr Opin Mol Ther. 1999;1(3):323-31.
[10]
Giovannang?li C, Roug?e M, Garestier T, Thuong NT, H?l?ne C. Triple-helix formation by oligonucleotides containing the three bases thymine, cytosine, and guanine. Proc Natl Acad Sci U S A. 1992;89(18):8631-5.
[11]
Sorokin VA, Valeev VA, Gladchenko GO, Degtyar MV, Andrus EA, Karachevtsev VA, et al. Mg2+ and Ni2+ ion effect on stability and structure of triple poly I·poly A·poly I helix. Int J Biol Macromolecul. 2005;35(3-4):201–10.
[12]
Sorokin VA, Valeev VA, Gladchenko GO, Degtyar MV, Blagoi YuP. Ni2+ ion effect on conformations of single-, double-and three-stranded homopolynucleotides containing adenine and uracil. Macromol Biosci. 2001; 1(5): 191-203.
[13]
Lurie YuYu. Handbook of Analytical Chemistry. Moscow: Khimiya, 1971. 454.
[14]
Sigel H, Massoud SS, Corfu NA. Comparison of the Extent of Macrochelate Formation in Complexes of Divalent Metal Ions with Guanosine (GMP2-), Inosine (IMP2-), and Adenosine 5'-Monophosphate (AMP2-). The Crucial Role of N-7 Basicity in Metal Ion-Nucleic Base Recognition J Am Chem Soc. 1994; 116(7): 2958-71.
[15]
Hellert R, Bau R, Martin RB, Mariam JH. Nucleotides and derivatives: their ligating ambivalency. Metal ions in biological systems. Ed. H. Sigel. New York: Marcel Dekker, 1979. 8: 102-14.
[16]
Massoud SS, Sigel H. Metal ion coordinating properties of pyrimidine-nucleoside 5'-monophosphates (CMP, UMP, TMP) and of simple phosphate monoesters, including D-ribose 5'-monophosphate. Establishment of relations between complex stability and phosphate basicity. Inorg Chem. 1988; 27(8): 1447-53.
[17]
Kotowycz G. A Carbon-13 Nuclear Magnetic Resonance Study of Binding of Copper(II) to Pyrimidine Nucleotides and Nucleosides. Can J Chem. 1974;52(6):924–9.
[18]
Blagoi Y, Gladchenko G, Nafie LA, Freedman TB, Sorokin V, Valeev V, He Y. Phase equilibrium in poly(rA).poly(rU) complexes with Cd2+ and Mg2+ ions, studied by ultraviolet, infrared, and vibrational circular dichroism spectroscopy. Biopolymers. 2005;78(5):275-86.
[19]
Andrushchenko V, Blagoi Y, van de Sande JH, Wieser H. Poly(rA) • Poly(rU) with Ni 2+ Ions at Different Temperatures: Infrared Absorption and Vibrational Circular Dichroism Spectroscopy . J Biomol Struct Dyn. 2002;19(5):889–906.
[20]
Rifkind JM, Shin YA, Heim JM, Eichhorn GL. Cooperative disordering of single-stranded polynucleotides through copper crosslinking. Biopolymers. 1976;15(10):1879-1902.
[21]
Yamada A, Akasaka K, Hatano H. Proton and phosphorus-31 magnetic relaxation studies on the interaction of polyriboadenylic acid with Mn2+. Biopolymers. 1976;15(7):1315-31.
[22]
Enmanji K. Proton, phosphorus and carbon nuclear magnetic relaxation studies on the interaction of poly(riboadenylic acid) with Cu2. Journal of Polymer Science Part A: Polymer Chemistry . 1987;25(3):883–95.
[23]
Sorokin VA, Spol'nik AI, Karachevtsev VA. The interaction of single-walled carbon nanotubes with polynucleotides. Dopovidi Nats Akad Nauk Ukrainy. 2006; (3):68-73.
[24]
Kim S-H, Martin RB. Binding sites and stabilities of transition metal ions with nucleosides and related ligands. Inorg Chim Acta. 1984;91(1):19–24.
[25]
Krakauer H. A thermodynamic analysis of the influence of simple mono-and divalent cations on the conformational transitions of polynucleotide complexes. Biochemistry. 1974;13(12):2579-89.
[26]
Klump HH. Energetics of order/order transitions in nucleic acids. Can J Chem. 1988;66(4):804–11.
[27]
Krakauer H, Sturtevant JM. Heats of the helix-coil transitions of the poly A-poly U complexes. Biopolymers. 1968;6(4):491-512.
[28]
Karapetyan AT, Vardevanyan PO, Terzikyan GA, Frank-Kamenetskii MD. The effect of two types of binding of the ligands on the parameters of the DNA helix-coil transition. Biopolym Cell. 1989; 5(5):38-43.
[29]
Sorokin VA, Valeev VA, Gladchenko GO, Degtiar MV, Karachevtsev VA, Blagoi YP. Mg2+ ion effect on conformational equilibrium of poly A · 2 poly U and poly A poly U in aqueous solutions. Int J Biol Macromol. 2003;31(4-5):223–33.
[30]
Plum GE, Pilch DS, Singleton SF, Breslauer KJ. Nucleic acid hybridization: triplex stability and energetics. Annu Rev Biophys Biomol Struct. 1995;24:319-50.
[31]
Blagoi YuP, Galkin VL, Gladchenko GO, Kornilova SV, Sorokin VA, Shkorbatov A.G. Metal complexes of nucleic acids in solutions Kiev: Naukova dumka, 1991 272 p
[32]
Porschke D. Cooperative nonenzymic base recognition II. thermodynamics of the helix-coil transition of oligoadenylic + oligouridylic acids. Biopolymers. 1971;10(10):1989–2013.
[33]
Kamiya M, Torigoe H, Shindo H, Sarai A. Temperature Dependence and Sequence Specificity of DNA Triplex Formation: An Analysis Using Isothermal Titration Calorimetry. J Am Chem Soc. 1996;118(19):4532–8.
[34]
Blagoi YuP, Zozulya VN, Egupov SA, Ryazanova OA, Shcherbakova AS. Thermodynamic analysis of 32 transition in oligonucleotide triple-helix complexes dAn-2dTm. Biofiz Visn. 2002; 10: 5-10.
[35]
Hynes MJ, Diebler H. The binding of Ni2+ to adenylyl-3',5'-adenosine and to poly(adenylic acid). Biophys Chem. 1982;16(1):79-88.
