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.
Shinoda
T
T
National Chemical Laboratory for Industry, Tsukuba Research Center, Ibaraki, Japan.
Shima
N
N
Tsukada
M
M
D000818:Animals; D002627:Chemistry, Physical / Q000379:methods; D004247:DNA / Q000737:chemistry*; D004583:Electrons; D008956:Models, Chemical; D010710:Phosphates / Q000737:chemistry
D010710:Phosphates; D004247:DNA