Complexes of DNA Bases and Watson−Crick Base Pairs with Small Neutral Gold Clusters

Abstract

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-H...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 x T]-Au3 and [G x C]-Au3 hybridized complexes are described and compared with the isolated Watson-Crick A x T and G x C ones. It is shown that enlarging the gold cluster size to Au6 results in a rather short gold-gold bond in the Watson-Crick interbase region of the [G x C]-Au6 complex that bridges the G x C pair and thus leads to a significant strengthening of G x C pairing.

On the interaction between gold and silver metal atoms and DNA/RNA nucleobases – a comprehensive computational study of ground state properties

“…It allows a redistribution of the electronic cloud that creates an effective dipole moment that interacts with both the positive and negative centers in the molecule. This fact explains in a simple manner the previously reported nonconventional hydrogen bonds [56,57] present in the interaction of bare neutral clusters with DNA/RNA nucleobases. The obtained values for the binding energies show that gold atoms are energetically more stable than silver when these interact with the nucleobases.…”

“…The first works on the topic were carried on by Kryacho et al [56][57][58][59][60][61][62]. In their first paper, the authors regard on the properties of small neutral gold clusters with isolated nucleobases.…”

Implementation of simple logic gates on gold–ammonia bonding patterns in different charge states

“…[27] As for other complexes between gold clusters and organic molecules that we have previously studied, [28][29][30] excitation can be encoded into binary variables to implement simple logic gates. [34] Each binary input is encoded into a specific bond being 'on' or 'off'.…”

Nanohybrids of Gold Particles

“…Au bonds). [48][49][50] This interaction is strong enough to stabilize small AuNPs with diameters of 1-5 nm over longer periods of time. [51] In the case of polysorbate 20, the branched structure might be an important factor.…”