Page - 40 - in Charge Transport in DNA - Insights from Simulations

SimulationSetup Figure3.1: A typicalDNA strand composed of the four different nucleotides. Nucle- obases are shown inblue, phosphate groups andfive-carbon sugar formthe backbone and are shown in black. Numbering of the sugar atoms is shown for the lowernucleotide. InDNA there are 4different types of these nucleobases: the purines adenine (A) andguanine (G) and thepyrimidines thymine (T) andcytosine (C). The singlenu- cleotidespolymerizeconnectedby theirphosphategroups,buildingupacomplete DNAstrand. Seefigure3.1 foranoverviewofaDNAstrandcomposedof the four differentnucleotidesofDNA. In the lowernucleobase thenumberingof thecarbon atoms of the sugar is depicted. Very important are the positions 3’ and 5’ which will fromnowonbeusedasadescriptorof the twopossibleendsofaDNAstrand. In the course of this work only double-stranded DNA will be investigated. The double-strands are formed by two single strandswhere all nucleobases formhy- drogenbondswith their specificpartners. Ineverycase, apurinenucleobase forms a base-pairwith a pyrimidine nucleobase. Thisway, there are two possible base- pairs from which a DNA double strand can be built up: Adenine-Thymine and Guanine-Cytosine. The former can form twohydrogenbonds,while the latter can form three hydrogen bonds and therefore is supposed to bemore stable. Figure 40