Page - 41 - in Charge Transport in DNA - Insights from Simulations

3.1TheDNAMolecule Figure3.2: Possible base-pairs in aDNAdouble-strand. Adenine-Thymine on the left side, Guanine-Cytosine on the right side. Hydrogen bonds are shown in red. Figure3.3: Typical formof aB-likeDNAstrand. The backbone is shownas a cartoon like representation inblue. Thenucleobasesarecolorcodedbytheelements. Major andminorgrooves are recognizable here. 3.2 shows the twopossible combinationsofnucleobaseswith the formedhydrogen bonds. The DNA double-helix can adopt several conformations. Widely known are the A- andB-DNAconformation,whichareboth right-handedhelices andmost often occur in living cells. Despite there aremore conformations known, like the left- handed Z-DNA for example, only A- and B-like DNA species are investigated in the course of this thesis. Besides several environmental parameters the DNA conformationalsodependsupon the sequenceof thenucleobases[105]. A commonlydescribed feature of theDNAdouble-helices are the grooves,which areformedaroundthehelix. IntheA-andB-likeDNAonecandistinguishbetween themajorandtheminorgroove. Figure3.3showsaB-likeDNAstrandwhere these grooves are formed. In nature these grooves provide binding sites for proteins or othermolecules involved inbiologicalprocesses. 41