Thermodynamic properties of the specific binding between Ag+ ions and C:C mismatched base pairs in duplex DNA

Nucleosides, Nucleotides and Nucleic Acids

Volumn 30, Issue 2, 2011, Pages 149-167

  Torigoe, Hidetaka ^a   Miyakawa, Yukako ^a   Ono, Akira ^b   Kozasa, Tetsuo ^a  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

^b KANAGAWA UNIVERSITY   (Japan)

Author keywords

Ag+ ion; C:C mismatched base pair; circular dichroism; isothermal titration calorimetry; thermodynamics

Indexed keywords

DNA; SILVER;

ARTICLE; BASE MISPAIRING; CIRCULAR DICHROISM; DNA BINDING; DNA SEQUENCE; ISOTHERMAL TITRATION CALORIMETRY; THERMODYNAMICS;

BASE PAIR MISMATCH; BASE SEQUENCE; BINDING SITES; DNA; IONS; MOLECULAR SEQUENCE DATA; NANOTECHNOLOGY; SILVER; THERMODYNAMICS;

EID: 79952143816     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770.2011.553210     Document Type: Article

References (43)

1. Draper, D. E. RNA folding: Thermodynamic and molecular descriptions of the roles of ions. Biophys. J. 2008, 95, 5489-5495.
2. Aleman, E. A.; Lamichhane, R.; Rueda, D. Exploring RNA folding one molecule at a time. Curr. Opin. Chem. Biol. 2008, 12, 647-654.
3. Frederiksen, J. K.; Piccirilli, J. A. Identification of catalytic metal ion ligands in ribozymes. Methods 2009, 49, 148-166.
4. Schnabl, J.; Sigel, R. K. Controlling ribozyme activity by metal ions. Curr. Opin. Chem. Biol. 2010, 14, 269-275.
5. Gazit, E. Use of biomolecular templates for the fabrication of metal nanowires. FEBS J. 2007, 274, 317-322. (Pubitemid 46046642)
6. Aldaye, F. A.; Palmer, A. L.; Sleiman, H. F. Assembling materials with DNA as the guide. Science 2008, 321, 1795-1799.
7. Meggers, E.; Holland, P.; Tolman, W.; Romesberg, F.; Schultz, P. A Novel Copper-Mediated DNA Base Pair. J. Am. Chem. Soc. 2000, 122, 10714-10715.
8. Weizman, H.; Tor, Y. 2,2́-Bipyridine ligandoside: A novel building block for modifying DNA with intra-duplex metal complexes. J. Am. Chem. Soc. 2001, 123, 3375-3376. (Pubitemid 32884630)
9. Atwell, S.;Meggers, E.; Spraggon, G.; Schultz, P.G. Structure of a copper-mediated base pair in DNA. J. Am. Chem. Soc. 2001, 123, 12364-12367. (Pubitemid 33136073)
10. Tanaka, K.; Yamada, Y.; Shionoya, M. Formation of silver(I)-mediated DNA duplex and triplex through an alternative base pair of pyridine nucleobases. J. Am. Chem. Soc. 2002, 124, 8802-8803. (Pubitemid 34809618)
11. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shiro, M.; Shionoya, M. Efficient incorporation of a copper hydroxypyridone base pair in DNA. J. Am. Chem. Soc. 2002, 124, 12494-12498. (Pubitemid 35204574)
12. Zimmermann, N.; Meggers, E.; Schultz, P. G. A novel silver(i)-mediated DNA base pair. J. Am. Chem. Soc. 2002, 124, 13684-13685. (Pubitemid 35378976)
13. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shionoya, M. A discrete self-assembled metal array in artificial DNA. Science 2003, 299, 1212-1213. (Pubitemid 36237458)
14. Shionoya, M.; Tanaka, K. Artificial metallo-DNA: A bio-inspired approach to metal array programming. Curr. Opin. Chem. Biol. 2004, 8, 592-597. (Pubitemid 39535719)
15. Clever, G. H.; Kaul, C.; Carell, T. DNA-metal base pairs, Angew Chem. Int. Ed. Engl. 2007, 46, 6226-6236. (Pubitemid 47329411)
16. Polonius, F. A.; Muller, J. An artificial base pair, mediated by hydrogen bonding and metal-ion binding. Angew Chem. Int. Ed. Engl. 2007, 46, 5602-5604. (Pubitemid 47121639)
17. Schlegel, M. K.; Essen, L. O.; Meggers, E. Duplex structure of a minimal nucleic acid. J. Am. Chem. Soc. 2008, 130, 8158-8159. (Pubitemid 351898529)
18. Ono, A.; Togashi, H. Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions. Angew Chem. Int. Ed. 2004, 43, 4300-4302. (Pubitemid 39257405)
19. Miyake, Y.; Togashi, H.; Tashiro, M.; Yamaguchi, H.; Oda, S.; Kudo, M.; Tanaka, Y.; Kondo, Y.; Sawa, R.; Fujimoto, T.; Machinami, T.; Ono, A. MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes. J. Am. Chem. Soc. 2006, 128, 2172-2173.
20. Okamoto, I.; Iwamoto, K.; Watanabe, Y.; Miyake, Y.; Ono, A. Metal-ion selectivity of chemically modified uracil pairs in DNA duplexes. Angew Chem. Int. Ed. Engl. 2009, 48, 1648-1651.
21. Ono, A.; Cao, S.; Togashi, H.; Tashiro, M.; Fujimoto, T.; Machinami, T.; Oda, S.;Miyake, Y.; Okamoto, I.; Tanaka, Y. Specific interactions between silver(I) ions and cytosine-cytosine pairs inDNA duplexes. Chem. Commun. (Camb.) 2008, 4825-4827.
22. Torigoe, H.; Kawahashi, K.; Takamori, A.; Ono, A. Novel strategy for single nucleotide polymorphism (SNP) genotyping by heteroduplex analysis: specific stabilization of TT mismatch base pair by mercury (II) cation and CC mismatch base pair by silver (I) cation. Nucleosides, Nucleotides Nucleic Acids 2005, 24, 915-917. (Pubitemid 41440719)
23. Wiseman, T.; Williston, S.; Brandts, J. F.; Lin, L. N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 1989, 179, 131-137. (Pubitemid 19149635)
24. Arakawa, H.; Ahmad, R.; Naoui, M.; Tajmir-Riahi, H. A. A comparative study of calf thymus DNA binding to Cr(III) and Cr(VI) ions. Evidence for the guanine N-7-chromium-phosphate chelate formation. J. Biol. Chem. 2000, 275, 10150-10153. (Pubitemid 30202068)
25. Ouameur, A. A.; Nafisi, S.; Mohajerani, N.; Tajmir-Riahi, H. A. Thallium-DNA complexes in aqueous solution. Major or minor groove binding. J. Biomol. Struct. Dyn. 2003, 20, 561-565. (Pubitemid 36206099)
26. Ouameur, A. A.; Arakawa, H.; Ahmad, R.; Naoui, M.; Tajmir-Riahi, H. A. A comparative study of Fe(II) and Fe(III) interactions with DNA duplex: major and minor grooves bindings. DNA Cell Biol. 2005, 24, 394-401. (Pubitemid 40840348)
27. Wu, J.; Du, F.; Zhang, P.; Khan, I. A.; Chen, J.; Liang, Y. Thermodynamics of the interaction of aluminum ions with DNA: implications for the biological function of aluminum. J. Inorg. Biochem. 2005, 99, 1145-1154. (Pubitemid 40514424)
28. Stellwagen, E.; Dong, Q.; Stellwagen, N. C. Quantitative analysis of monovalent counterion binding to random-sequence, double-stranded DNA using the replacement ion method. Biochemistry 2007, 46, 2050-2058.
29. 2+ binding. Chem. Pharm. Bull. (Tokyo) 2008, 56, 247-249. (Pubitemid 351463231)
30. Li, Y.; Xia, Y. L.; Jiang, Y.; Yan, X. P. Extracting stoichiometry, thermodynamics, and kinetics for the interaction of DNA with cadmium ion by capillary electrophoresis on-line coupled with electrothermal atomic absorption spectrometry. Electrophoresis 2008, 29, 1173-1179. (Pubitemid 351404692)
31. Yamane, T.; Davidson, N. None on the spectra of the mercury (II) and silver (I) complexes of some polyribonucleotides and ribonucleic acid. Biochim. Biophys. Acta 1962, 55, 780-782.
32. Izatt, R. M.; Christensen, J. J.; Rytting, J. H. Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides. Chem. Rev. 1971, 71, 439-481.
33. Yamane, T.; Davidson, N. On the complexing of deoxyribonucleic acid by silver (I). Biochim. Biophys. Acta 1962, 55, 609-621.
34. Daune, M.; Dekker, C. A.; Schachman, H. K. Complexes of silver ion with natural and synthetic polynucleotides. Biopolymers 1966, 4, 51-76.
35. Jensen, R. H.; Davidson, N. Spectrophotometric, potentiometric, and density gradient ultracentrifugation studies of the binding of silver ion by DNA. Biopolymers 1966, 4, 17-32.
36. Eichhorn, G. L.; Butzow, J. J.; Clark, P.; Tarien, E. Interaction of metal ions with polynucleotides and related compounds. X. Studies on the reaction of silver (I) with the nucleosides and polynucleotides, and the effect of silver(I) on the zinc(II) degradation of polynucleotides. Biopolymers 1967, 5, 283-296.
37. Marzilli, L. G.; Kistenmacher, T. J.; Rossi, M. An extension of the role of O(2) of cytosine residues in the binding of metal ions. Synthesis and structure of 1-methylcytosine. J. Am. Chem. Soc. 1977, 99, 2797-2798.
38. Tanaka, Y.; Oda, S.; Yamaguchi,H.; Kondo, Y.; Kojima, C.;Ono, A. 15N-15N J-coupling acrossHg(II): direct observation of Hg(II)-mediated T-T base pairs in a DNA duplex. J. Am. Chem. Soc. 2007, 129, 244-245. (Pubitemid 46106604)
39. Tanaka, Y.; Ono, A. Nitrogen-15 NMR spectroscopy of N-metallated nucleic acids: insights into 15N NMR parameters and N-metal bonds. Dalton Trans. 2008, 4965-4974.
40. Tanaka, Y.; Kojima, C.; Morita, E. H.; Kasai, Y.; Yamasaki, K.; Ono, A.; Kainosho, M.; Taira, K. Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using (15)N NMR spectroscopy. J. Am. Chem. Soc. 2002, 124, 4595-4601. (Pubitemid 34464997)
41. Rau, D. C.; Parsegian, V. A. Direct measurement of temperature-dependent solvation forces between DNA double helices. Biophys. J. 1992, 61, 260-271.
42. Rosseinsky, D. R. Electrode potentials and hydration energies-theories and correlations. Chem. Rev. 1965, 65, 467-490.
43. Rashin, A. A.; Honig, B. Reevaluation of the Born model of ion hydration. J. Phys. Chem. 1985, 89, 5588-5593.