Density functional MO calculation for stacked DNA base-pairs with backbones.

In order to elucidate the effect of the sugar and phosphate backbones on the stable structure and electronic properties of stacked DNA base-pairs, we performed ab initio molecular orbital (MO) calculations based on the density functional theory and Slater-type basis set. As a model cluster for stacked base-pairs, we employed three isomers for the dimer unit of stacked guanine-cytosine pairs composed with backbones as well as base-pairs. These structures were fully optimized and their electronic properties were self-consistently investigated. By including the backbones, the difference in total energy among the isomers was largely enhanced, while the trend in relative stability was not changed. The effect of backbones on the electronic properties is remarkable: the MOs with the character of the PO4 parts of backbones appear just below the highest-occupied MO. This result indicates that the PO4 parts might play a rule as a reaction site in chemical processes concerning DNA. Therefore, we conclude that the DNA backbones are indispensable for investigating the stability and electronic properties of the stacked DNA base-pairs.