Structures and properties of mixed DNA bases tetrads: Nonempirical ab inito HF and DFT studies

Three nonplanar tetrads of the DNA bases (Watson-Crick-type TATA, Hoogsteen-type TATA, and AGAG tetrad) are studied at the HF/6-311G(d,p) and B3LYP/6-311G(d,p) levels of theory. Both Hoogsteen and Watson-Crick type thymine-adenine-thymine-adenine tetrads are stable in the isolated form in which the Hoogsteen type TATA tetrad is about 2.3 kcal/mol more stable than the Watson-Crick type. The significant stabilization energies of over 30 kcal/mol predicted for the TATA tetrads confirm that the stabilization of this structure plays a key role in the four stranded helices. The energy of each bifurcated H-bond in the tetrads has been found to be about 8 kcal/mol for the planar structure and about 3 kcal/mol for the nonplanar tetrad. The formation of bifurcated H-bonding is the main contribution to the creation of the tetrad structure. The electrostatic potential map suggests that the presence of a cation in the system is expected to further stabilize the TATA tetrad in both forms. However, metal ions are unlikely to be stable in the center of the TATA tetrads. The V-shape structure of the AGAG tetrad and 3.5 kcal/mol of stabilizing energy (compared to the two separated AG pair) revealed in this study suggest that this tetrad structure may not be important in the tetraplexes.