Nucleobase Stacking at Clay Edges, a Favorable Interaction for RNA/DNA Oligomerization

Abstract

Periodic density functional theory (DFT) calculations have been performed to model the adsorption of nucleobases at clay edges as potential adsorption sites for DNA/RNA oligomerization. According to the accessibility and availability of hydroxyl groups and water molecules at clay edges, numerous adsorption conformations via H-bonding, in a similar way to the Watson-Crick base pairing in DNA strands, have been considered. It is found that guanine and cytosine are mainly adsorbed through three H-bonds with edge's hydroxyls and water molecules, while adenine and thymine do generally engage two H-bonds. As a result, the largest adsorption energies were found for guanine and cytosine (-32 to -35 kcal mol-1) in comparison to most adsorbed modes with adenine and thymine (-22 to -24 kcal mol-1). For thymine, a three H-bond tilted adsorption mode has also been observed with an exceptionally large adsorption energy of -35 kcal mol-1. Significant stabilizing dispersive forces with the surface are present in all the explored adducts, around 30% of the total adsorption energy (-6 to -10 kcal mol-1). The stacking of an additional nucleobase and its adsorption via H-bonding on the edge surface has also been studied. The large stabilizing interactions of the complexes, arising from both H-bonding and stacking interactions, range between -44 and -66 kcal mol-1, the dispersion component accounting for around -20 kcal mol-1, while no cooperative effects are observed. A significant number of strong H-bonds (<1.6 Å) is observed in the most stable complexes. Obtained results show that a side by side nucleobase adsorption is possible at clay edges due to the availability of hydroxyl and water motifs. Finally, the adsorption of a thymine dinucleotide unit (TpT) is simulated, showing that its adsorption occurs also via H-bonding with the edges. This adsorption mechanism may be considered as a probable adsorption mode allowing for the phosphodiester bond formation leading to RNA oligomerization.