Abstract
[Ru(phen)2(dppz)]2+ has been studied since the 1990s due to its ‘light-switch’ properties. It can be used as a luminescent DNA probe, with emission switched on through DNA binding. The luminescence observed is dependent on the solvent accessibility of the pyrazine nitrogen atoms, and therefore is sensitive to changes in both binding site of the cation and chromophore orientation. The compound is also chiral, and there are distinct differences between the enantiomers in terms of the emission behaviour when bound to a variety of DNA sequences. Whilst a number of binary DNA-complex X-ray crystal structures are available, most include the Λ enantiomer and there is very little structural information about binding of the Δ enantiomer. Here, we present the first X-ray crystal structure of a Δ enantiomer bound to well-matched DNA, in the absence of the other, Λ enantiomer. We show how the binding site observed here can be related to a more general pattern of motifs in the crystallographic literature and propose that the Δ enantiomer can bind with five different binding modes, offering a new hypothesis for the interpretation of solution data.
Highlights
The binding of ligands to DNA can have a profound effect on the resulting DNA structure, depending on the binding mode
[Ru(phen)2(dppz)]2+ has been studied since the 1990s due to its ‘light-switch’ properties. It can be used as a luminescent DNA probe, with emission switched on through DNA binding
Octahedral Ru-dppz complexes are of particular interest, as they combine the ability to intercalate with a photophysical ‘payload’, namely the ability to act either as a luminescent DNA probe [3] or to interact directly with DNA via photooxidation of guanine bases [4]
Summary
The binding of ligands to DNA can have a profound effect on the resulting DNA structure, depending on the binding mode. One complication with studying such complexes in the presence of DNA is that they are chiral molecules (Figure 1), which are stable as resolved enantiomers, with each bound enantiomer displaying different photophysical properties as a consequence of different binding modes [5] One such ruthenium polypyridyl is [Ru(phen)2(dppz)].C l2. Whilst several X-ray crystal structures containing the enantiomer are available [7,8], there are no published atomic coordinates of a crystal structure showing how the enantiomer on its own can bind to well matched DNA, in the absence of an adjacent complex This is despite a great deal of discussion in the literature, due to differences in the luminescence lifetimes of the bright state observed in solution, about how the enantiomers of [Ru(phen)2(dppz)]2+ and the closely related [Ru(bpy)2(dppz)]2+ can bind to DNA [9,10]. We report two crystal structures of [Ru(phen)2(dppz)]2+ in the presence of an oligonucleotide decamer that may help with interpreting the photophysics of the compound when bound to DNA in solution
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