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

Abstract

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,107/109Ag) 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. The incorporation of non-natural base pairs into double-stranded DNA, especially those mediated by metal–ligand interactions, offers new opportunities for synthetic DNA materials. The structural implications of such modifications will help guide developments in this area, and a solution structure of a B-type DNA duplex containing consecutive metal-mediated base pairs has now been elucidated.

Cite this article

Johannsen, S., Megger, N., Böhme, D. et al. Solution structure of a DNA double helix with consecutive metal-mediated base pairs. Nature Chem 2, 229–234 (2010). https://doi.org/10.1038/nchem.512

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