Metal-mediated Base Pairs Research Articles

Spectroscopic analysis of AgI-DNA complex

It has recently been reported that C-C mismatches were able to recognize Ag(I) specifically, and form Ag(I)-mediated cytosine-cytosine base pairs (C-Ag(I)-C pair). In this study, we explored DNA sequences, which are appropriate for structural studies of this new type of metal-mediated base pairs. For this experiments, we synthesized four kinds of DNA duplexes including a single C-C mismatch. By using UV spectra, we performed titration experiments of DNA duplexes with AgNO(3). Within the sequences we tested, it was found that the DNA duplex: 5'-CGCGCGTCC-3' x 5'-GGACCCGCG-3' showed 1:1 complexation of this DNA duplex and Ag(I). In addition, a DNA duplex: 5'-TAAATCTAATA-3' x 5'-TATTACATTTA-3' also exhibited a similar character. Therefore, these two DNA duplexes are interesting candidates for structural analyses.

Electronic Coupling Mediated by Stacked [Thymine-Hg-Thymine] Base Pairs

Very recently it has been shown that stable metal-mediated base pairs [Thymine-Hg-Thymine] can form in DNA. To estimate the effect of such pairs on the efficiency of charge transfer through DNA, we carry out quantum mechanical calculations of double-stranded pi-stacks GXG, GXXG, and GXXXG, where X = [Thymine-Hg-Thymine] and stacks GT(n)G of canonical base pairs. The charge-transfer efficiency in short duplexes GXG and GTG is found to be similar. However, the donor-acceptor coupling in GXXG and GXXXG is stronger by a factor of 2.5-3.0 than that in GT(n)G (n = 2 and 3), respectively. It is shown that the valence orbitals of Hg atoms do not essentially participate in mediating the electronic coupling for hole transfer; however, they may play an important role in excess electron transfer.

Interaction of Pt(II) and Pd(II) complexes of terpyridine with 1-methylazoles: A combined experimental and density functional study

The synthesis and characterization of several complexes of the composition [{M(terpy)} n (L)](ClO 4) m (M = Pt, Pd; L = 1-methylimidazole, 1-methyltetrazole, 1-methyltetrazolate; terpy = 2,2′:6′,2″-terpyridine; n = 1, 2; m = 1, 2, 3) is reported and their applicability in terms of a metal-mediated base pair investigated. Reaction of [M(terpy)(H 2O)] 2+ with 1-methylimidazole leads to [M(terpy)(1-methylimidazole)](ClO 4) 2 ( 1: M = Pt; 2: M = Pd). The analogous reaction of [Pt(terpy)(H 2O)] 2+ with 1-methyltetrazole leads to the organometallic compound [Pt(terpy)(1-methyltetrazolate)]ClO 4 ( 3) in which the aromatic tetrazole proton has been substituted by the platinum moiety. For both platinum(II) and palladium(II), doubly metalated complexes [{M(terpy)} 2(1-methyltetrazolate)](ClO 4) 3 ( 4: M = Pt; 5: M = Pd) can also be obtained depending on the reaction conditions. In the latter two compounds, the [M(terpy)] 2+ moieties are coordinated via C5 and N4. X-ray crystal structures of 1, 2, and 3 are reported. In addition, DFT calculations have been carried out to determine the energy difference between fully planar [Pd(mterpy)(L)] 2+ complexes Ip– IVp (mterpy = 4′-methyl-2,2′:6′,2″-terpyridine; L = 1-methylimidazole- N3 ( I), 1-methyl-1,2,4-triazole- N4 ( II), 1-methyltetrazole- N3 ( III), or 3-methylpyridine- N1 ( IV)) and the respective geometry-optimized structures Io– IVo. Whereas this energy difference is larger than 70 kJ mol −1 for compounds I, II, and IV, it amounts to only 0.8 kJ mol −1 for the tetrazole-containing complex III, which is stabilized by two intramolecular C–H⋯N hydrogen bonds. Of all complexes under investigation, only the terpyridine–metal ion–tetrazole system with N3-coordinated tetrazole appears to be suited for an application in terms of a metal-mediated base pair in a metal-modified oligonucleotide.

MercuryII-Mediated Formation of Thymine−HgII−Thymine Base Pairs in DNA Duplexes

The very specific binding of the HgII ion unexpectedly and significantly stabilizes naturally occurring thymine-thymine base mispairing in DNA duplexes. Following this finding, we prepared DNA duplexes containing metal-mediated base pairs at the desired sites, as well as novel double helical architectures consisting only of thymine-HgII-thymine pairs.

Metal Ion Coordination to Azole Nucleosides

To evaluate the possibility of introducing azole nucleosides as building blocks for metal-mediated base pairs in artificial oligonucleotides, imidazole nucleoside, 1,2,4-triazole nucleoside and tetrazole nucleoside have been synthesized and characterized. The X-ray crystal structures of p-toluoyl-protected 1,2,4-triazole and tetrazole nucleosides are reported. Contrary to the situation primarily found for deoxyribonucleosides, the sugar moieties adopt C3'-endo conformations. The acidity of the beta nucleosides increases with increasing number of nitrogen ring atoms, giving pKa values of 6.01 +/- 0.05, 1.32+/-0.05 and <-3, respectively. This decrease in basicity results in a decreasing ability to form 2:1 complexes with linearly coordinating metal ions such as Ag+ and Hg2+. In all cases, the Ag+ complexes are of higher stability than the corresponding Hg2+ complexes. Whereas imidazole nucleoside forms highly stable 2:1 complexes with both metal ions (estimated log beta2 values of >10), only Ag+ is able to reach this coordination pattern in the case of triazole nucleoside (log beta2 = 4.3 +/- 0.1). Tetrazole nucleoside does not form 2:1 complexes at all under the experimental conditions used. These data suggest that imidazole nucleoside, and to a lesser extent 1,2,4-triazole nucleoside, are likely candidates for successful incorporation as ligands in oligonucleotides based on metal-mediated base pairs. DFT calculations further corroborate this idea, providing model complexes for such base pairs with glycosidic bond distances (10.8-11.0 Angstroms) resembling those in idealized B-DNA (10.85 Angstroms).

Hg(9-methyl-1-deazapurine) 2](NO 3) 2 · H 2O: a complex with a distorted hexagonal bipyramidal metal ion coordination sphere

Reaction of 9-methyl-1-deazapurine (9-MeDP) with Hg(CF 3COO) 2 in the presence of NaNO 3 yields the title compound [Hg(9-MeDP) 2](NO 3) 2 · H 2O with the two 9-MeDP ligands bound to the metal ion via their N7 positions. The X-ray structure is reported: monoclinic, P2 1/ c (no. 14), a = 5.4015(11), b = 20.467(4), c = 17.775(4) Å, β = 97.00(3)°, V = 1950.4(7) Å 3, Z = 4. Hg is eight-coordinate with two trans-oriented Hg–N bonds (2.073(3) and 2.075(3) Å) and three nearly coplanar, bidentate nitrate moieties (Hg–O: 2.716(3)–2.985(4) Å), leading to a distorted hexagonal bipyramidal environment of the metal ion. Within this structure, the nitrate ions form a honeycomb-like chain structure with Hg II being positioned inside the combs. This work represents the first report of such geometry for a transition metal ion surrounded by symmetrically bidentate nitrate ions. The corresponding nucleoside, 1-deazapurine 2′-deoxyribonucleoside, also forms a stable 2:1 complex with Hg II, as was shown by 1H NMR spectroscopy, making it a potential candidate for incorporation into nucleic acids based on metal-mediated base pairs.

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