Characterization of the stacking interactions between DNA or RNA nucleobases and the aromatic amino acids

MP2/6-31G*(0.25) gas-phase potential energy surfaces of stacked dimers between the four aromatic amino acids and the natural (DNA or RNA) nucleobases were considered as a function of three variables (vertical separation, angle of rotation, and horizontal displacement). The maximum stacking interaction was found to increase with the amino acid according to PHE < HIS approximate to TYR < TRP, while the stacking energy is generally largest for the purines compared to the pyrimidines. Most notably, the interaction energies are up to -43 kJ mol(-1). Comparison of the magnitude of these interactions with, for example, hydrogen-bonding and stacking interactions that stabilize DNA duplexes suggests that pi-pi stacking between nucleobases and amino acids likely plays a large role in many fundamental biological processes. (C) 2007 Elsevier B.V. All rights reserved.