title: The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water.
abstract: Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementi's double zeta basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO(4)(-), to Na(+), and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zurich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO(4) (-) groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.
authors.affiliation: Chair for Theoretical Chemistry and Laboratory of the National Foundation for Cancer Research, Friedrich-Alexander-University-Erlangen-Nürnberg, Egerlandstr 3, Erlangen, Germany. janos.ladik@chemie.uni-erlangen.de
authors.forename: János
authors.initials: J
authors.lastname: Ladik
authors.forename: Attila
authors.initials: A
authors.lastname: Bende
authors.forename: Ferenc
authors.initials: F
authors.lastname: Bogár
mesh_terms: D000465:Algorithms; D001120:Arginine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D004583:Electrons; D006657:Histones / Q000737:chemistry; D008239:Lysine / Q000737:chemistry; D009690:Nucleic Acid Conformation; D011119:Polynucleotides / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*; D014961:X-Ray Diffraction
chemical_list: D006657:Histones; D011119:Polynucleotides; D012997:Solvents; D014867:Water; D004247:DNA; D001120:Arginine; D008239:Lysine