Efficiency of the MO method using a Slater-type basis set and non-local density functional formalism for describing DNA base stacking energy

We have developed a molecular–orbital (MO) method based on a Slater-type basis set and non-local density functional theory (DFT) for describing the DNA base stacking properties, and its efficiency has been confirmed by investigating the stacking energy of cytosine dimer. Our DFT method can reproduce the dependence of stacking energy on the stacking conformation obtained by the ab initio second-order Møller–Plesset (MP2) calculation. The stable structures of hydrogen-bonded Watson–Crick base pairs and (PO4H2)−1 ion have been investigated and the structures obtained by our DFT method are comparable with those from the MP2 and DFT methods in Gaussian94. Therefore, our DFT method may be applicable for investigating the stable structures of more realistic models for stacked DNA base pairs including backbones.