Complexes of DNA bases and Watson-Crick base pairs with small neutral gold clusters

The nature of the DNA-gold interaction determines and differentiates the affinity of the nucleobases (adenine, thymine, guanine, and cytosine) to gold. Our preliminary computational study [Kryachko, E. S.; Remacle, F. Nano Lett. 2005, 5, 735] demonstrates that two major bonding factors govern this interaction: the anchoring, either of the Au-N or Au-O type, and the nonconventional N-(HAu)-Au-... hydrogen bonding. In this paper, we offer insight into the nature of nucleobase-gold interactions and provide a detailed characterization of their different facets, i.e., geometrical, energetic, and spectroscopic aspects; the gold cluster size and gold coordination effects; proton affinity; and deprotonation energy. We then investigate how the Watson-Crick DNA pairing patterns are modulated by the nucleobase-gold interaction. We do so in terms of the proton affinities and deprotonation energies of those proton acceptors and proton donors which are involved in the interbase hydrogen bondings. A variety of properties of the most stable Watson-Crick [A(.)T]-Au-3 and [G(.)C]-Au-3 hybridized complexes are described and compared with the isolated Watson-Crick A-T and G-C ones. It is shown that enlarging the gold cluster size to Au-6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G(.)C]-Au-6 complex that bridges the G(.)C pair and thus leads to a significant strengthening of G(.)C pairing.