NMR spectroscopic study of a DNA duplex with mercury-mediated T-T base pairs

Nucleosides, Nucleotides and Nucleic Acids

Volumn 25, Issue 4-6, 2006, Pages 613-624

  Tanaka, Yoshiyuki ^a   Yamaguchi, Hiroshi ^a   Oda, Shuji ^a   Kondo, Yoshinori ^a   Nomura, Makoto ^b   Kojima, Chojiro ^b   Ono, Akira ^c  

^a TOHOKU UNIVERSITY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^c KANAGAWA UNIVERSITY   (Japan)

Author keywords

1H NMR; Equilibrium; HgII mediated T T base pair; Titration

Indexed keywords

CACODYLIC ACID; DOUBLE STRANDED DNA; MERCURY DERIVATIVE;

ARTICLE; BASE MISPAIRING; BASE PAIRING; BINDING SITE; COMPLEX FORMATION; DNA BINDING; EQUILIBRIUM CONSTANT; METAL BINDING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PROTON NUCLEAR MAGNETIC RESONANCE; SIGNAL TRANSDUCTION; TITRIMETRY;

BASE COMPOSITION; BASE PAIRING; BASE SEQUENCE; DNA; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MERCURY; MODELS, MOLECULAR; THYMINE;

EID: 33747588255     PISSN: 15257770     EISSN: 15322335     Source Type: Journal    
DOI: 10.1080/15257770600686154     Document Type: Article

References (39)

1. Meggers, E.; Holland, P.L.; Tolman, W.B.; Romesberg, F.E.; Schultz, P.G. A novel copper-mediated DNA base pair. Journal of the American Chemical Society 2000, 122, 10714-10715.
2. Atwell, S.; Meggers, E.; Spraggon, G.; Schultz, P.G. Structure of a copper-mediated base pair in DNA. Journal of the American Chemical Society 2001, 123, 12364-12367.
3. Zimmermann, N.; Meggers, E.; Schultz, P.G. A novel silver(I)-mediated DNA base pair. Journal of the American Chemical Society 2002, 124, 13684-13685.
4. Zimmermann, N.; Meggers, E.; Schultz, P.G. Asecond-generation copper(II)-mediated metallo-DNAbase pair. Bioorganic Chemistry 2004, 32, 12-25.
5. Zhang, L.; Meggers E. An extremely stable and orthogonal DNA base pair with a simplified three-carbon backbone. Journal of the American Chemical Society 2005, 127, 74-75.
6. Weizman, H.; Tor, Y. 2,2′-Bipyridine ligandoside: A novel building block for modifying DNA with intra-duplex metal complexes. Journal of the American Chemical Society 2001, 123, 3375-3376.
7. Tanaka, K.; Yamada, Y.; Shionoya, M. Formation of silver(I)-mediated DNA duplex and triplex through an alternative base pair of pyridine nucleobases. Journal of the American Chemical Society 2002, 124, 8802-8803.
8. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shiro, M.; Shionoya, M. Abstract Efficient incorporation of a copper hydroxypyridone base pair in DNA. Journal of the American Chemical Society 2002, 124, 12494-12498.
9. Tanaka, K.; Tengeiji, A.; Kato, T.; Toyama, N.; Shionoya, M. A discrete self-assembled metal array in artificial DNA. Science 2003, 299, 1212-1213.
10. Switzer, C.; Shin D. A pyrimidine-like nickel(II) DNA base pair. Chemical Communications 2005, 1342-1344.
11. Switzer, C.; Sinha, S.; Kim, P.H.; and Heuberger, B.D. A purine-like nickel(II) base pair for DNA. Angewandte Chemie International Edition 2005, 44, 1529-1532.
12. Ono A.; Togashi H. Highly selective oligonucleotide-based sensor for mercury(II) in aqueous solutions. Angewandte Chemie International Edition 2004, 43, 4300-4302.
13. Yamaguchi, H.; Oda, S.; Kondo, Y.; Ono, A.; Tanaka, Y. Spectroscopic analysis of DNA duplexes including T-T mismatches. Nucleic Acids Symposium Series 2004, 48, 113-114.
14. Yamaguchi, H.; Oda, S.; Kojima, C.; Ono, A.; Kondo, Y.; Tanaka, Y. Spectroscopic analyses of DNA duplexes in the presence of mercury ions. Nucleic Acids Symposium Series 2005, 49, 199-200.
15. II/s-thymine base pairs in DNA duplexes. Journal of the American Chemical Society 2006, 128, 2172-2173.
16. Yamane, T.; Davidson, N. 1961. On the Complexing of Desoxyribonucleic Acid (DNA) by Mercuric Ion. Journal of the American Chemical Society 1961, 83, 2599-2607.
17. II: Separation of the strands, Nature 1962, 195, 997-998.
18. Katz, S. The reversible reaction of Hg(II) and double-stranded polynucleotides. A step-function theory and its significance. Biochimica et Biophysica Acta 1963, 68, 240-253.
19. Simpson, R.B. Association Constants of Methylmercuric and Mercuric Ions with Nucleosides. Journal of the American Chemical Society 1964, 86, 2059-2065.
20. 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. Chemical Review 1971, 71, 439-481.
21. Kosturko, L.D.; Folzer, C.; Stewart, R.F. The crystal and molecular structure of a 2:1 complex of 1-methylthymine-mercury(II). Biochemistry 1974, 13, 3949-3952.
22. Gruenwedel, D.W.; Cruikshank M.K. Mercury-induced DNA polymorphism: Probing the conformation of Hg(II)-DNA via staphylococcal nuclease digestion and circular dichroism measurements. Biochemistry 1990, 29, 2110-2116.
23. Gruenwedel, D.W. Effect of Hg(II) on the spectroscopic properties of poly[d(A-T)·d(A-T)] and poly[d(A)·d(T)] and their constituent subunits (deoxyadenosine and thymidine monomers and dimers). Biophysical Chemistry 1994, 52, 115-123.
24. Gruenwedel, D.W. Effect of Hg(II) on the spectroscopic properties of DNA bases: Circular dichroism of deoxyadenosine and thymidine monomers and dimers. Journal of Inorganic Biochemistry 1994, 56, 201-212.
25. Onyido, I.; Norris, A.R.; Buncel, E. Biomolecule-mercury interactions: Modalities of DNA base-mercury binding mechanisms. Remediation strategies. Chemical Reviews 2004, 104, 5911-5929.
26. 13C NMR evidence for the preferred reaction of thymidine over guanosine in exchange and competition reactions with mercury(II) and methylmercury(II). Inorganic Biochemistry 1985, 25, 61-73.
27. Buncel, E.; Boone, C.; Joly, H. Metal ion-biomolecule interactions 13. NMR evidence for the Formation of the mixed-ligand thymidine-mercury-guanosine complex-a model for a putative Hg(II) interstrand cross-linking structure of DNA. Inorganic Chimica Acta 1986, 125, 167-172.
28. Kuklenyik Z.; Marzilli L.G. Mercury(II) Site-Selective Binding to a DNA Hairpin. Relationship of Sequence-Dependent Intra-and Interstrand Cross-Linking to the Hairpin-Duplex Conformational Transition. Inorganic Chemistry 1996, 35, 5654-5662.
29. Seeman, N.C. DNA in a material world. Nature 2003, 421, 427-431.
30. Mao, C.; Sun, W.; Shen, Z.; Seeman, N.C. A nanomechanical device based on the B-Z transition of DNA. Nature 1999, 397, 144-146.
31. Tanaka, Y.; Taira, K. Detection of RNA nucleobase metalation by NMR spectroscopy. Chemical Communications 2005, 2069-2079.
32. Tanaka, Y.; Kasai, Y.; Mochizuki, S.; Wakisaka, A.; Morita, E.H.; Kojima, C.; Toyozawa, A.; Kondo, Y.; Taki, M.; Takagi, Y.; Inoue, A.; Yamasaki, K.; Taira, K. Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes. Journal of the American Chemical Society 2004, 126, 744-752.
33. 15N NMR spectroscopy. Journal of the American Chemical Society 2002, 124, 4595-4601.
34. 31P NMR, of the direct coordination of a metal ion with the phosphoryl oxygen at the cleavage site of a hammerhead ribozyme. Journal of the American Chemical Society 2002, 124, 8230-8236.
35. Tanaka, Y.; Morita, E.H.; Hayashi, Y.; Kasai, Y.; Tanaka T.; Taira, K. Well-conserved tandem G·A pairs and the flanking C·G pair in hammerhead ribozymes are sufficient for capture of structurally and catalytically important metal ions. Journal of the American Chemical Society 2000, 122, 11303-11310.
36. Tanaka, Y.; Kojima, C.; Yamazaki, T.; Kodama, T.S.; Yasuno, K.; Miyashita, S.; Ono, A.; Ono, A.; Kainosho, M.; Kyogoku, Y. Solution structure of an RNA duplex including a C-U base pair. Biochemistry 2000, 39, 7074-7080.
37. Wüthrich, K. NMR of Proteins and Nucleic Acids. John Wiley & Sons: New York 1986.
38. In Figure 4c, unassigned small signals were observed, and there are two possibilities for this result. One is the possibility that the unassigned signals are those from a transient species, and other signals of the transient species are overlapped with those from di-mercurated species. The other is that unassigned signals arise from an unknown minor conformer. Currently, we can not determine which hypothesis is plausible.
39. 2 with Sodium Thymonucleate. Journal of the American Chemical Society 1954, 76, 6032-6034.