Electronic structure of DNA by DV-X alpha cluster calculations. I. d(GG).d(CC), d(CG)2, d(GC)2 A and B conformations

The electronic structure of d(GG).d(CC), d(CG)2, d(GC)2 which are stacked base pairs in the DNA double helix, are elucidated for both A and B conformations in detail by DV-X alpha cluster calculations. These three DNA double helix fragments are constructed from the same bases, G and C, but the electronic structure of the fragments for A and B conformations differs from each other characteristically. In particular, the electronic states of the O2 and O3 in phosphates differ drastically from each other, and might play a crucial role as recognition sites in various reaction processes concerning DNA. These differences are caused by the delicate differences in the admixture of the orbital components and the intra- and inter-bases interactions. Contour maps of the wavefunction of the HOMO and LUMO are compared among the stacking isomers.