Solution structure of a DNA double helix with consecutive metal-mediated base pairs.

Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹5N,¹°7/¹°9Ag) couplings upon incorporation of ¹5N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs.

Conformational change induced by metal-ion-binding to DNA containing the artificial 1,2,4-triazole nucleoside.

A conformational switch can be induced upon the addition of transition-metal ions to oligonucleotides that contain a row of successive artificial nucleobases flanked by complementary sequences of natural nucleobases, provided that the artificial bases cannot undergo self-pairing via hydrogen bonding but only via the formation of metal-ion-mediated base pairs. Such oligonucleotides adopt a hairpin structure in the absence of transition-metal ions, yet they show a preference for the formation of a regular double helix if the appropriate metal ions are present. We report here our experimental data on the structure of the oligonucleotide d(A7X3T7) (A=adenine, T=thymine, X=1,2,4-triazole) in the absence and presence of silver(I). This study comprising temperature-dependent UV spectroscopy, CD spectroscopy, MALDI-TOF measurements, fluorescence spectroscopy, and dynamic light scattering opens up a new approach to the generation of a large variety of metal-ion sensors with the possibility of fine-tuning their sensing capabilities, depending on the artificial nucleoside that is used.

Differential reactivity of alpha and beta 2'-deoxyribonucleosides towards protonation and metalation.

The reactivity of artificial 2'-deoxyribonucleosides, designed as nucleoside surrogates in metal-mediated base pairs, towards protonation and metalation has been shown to be dependent on the choice of the anomer. The alpha nucleosides comprising the aglycones imidazole, 1,2,4-triazole, benzimidazole and imidazo[4,5-b]pyridine are more basic than the respective beta nucleosides as was shown by a combined experimental and theoretical approach. The DeltapK(a) values observed experimentally are in the range of 0.19+/-0.03 to 0.41+/-0.07 (with the error representing three times the standard deviation of the mean value). An independent confirmation of this differential reactivity was obtained from density functional theory (DFT) calculations using 1,2,4-triazole nucleoside as an example. The result of these calculations is in good agreement with the experimental data (DeltapK(a)=0.16 vs. 0.21+/-0.07). The stability of the respective metal ion complexes of the anomeric 1,2,4-triazole nucleosides follows the same trend as that of the respective protonated nucleosides: Those of the alpha nucleoside are more stable than those of the beta nucleoside (Deltalogbeta(2)=0.6+/-0.2 for the 2:1 complex with Ag(+); Deltalogbeta(1)=0.51+/-0.07 for the 1:1 complex with Hg(2+)). These slightly different reactivities will be useful for fine-tuning the metal-ion binding behavior of oligonucleotides containing metal-mediated base 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).