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Electronic structure of DNA by DV-X alpha cluster calculations: II. d(GG).d(CC), d(CG)2, d(GC)2 A and B
T Shinoda1, N Shima, M Tsukada
1National Chemical Laboratory for Industry, Tsukuba Research Center, Ibaraki, Japan.
Abstract:
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 contracted from the same bases, G and C, but the electronic structures of the fragments for both A and B conformations are different from each other characteristically. There are some delicate differences in the admixture of the orbital components and the overlap populations of intra- and inter- strand stacked bases among the stacking isomers. On the other hand, the electronic states of sugars differ in the 5'-3' direction, but are not almost dependent on stacked base pairs.