Page - 42 - in Charge Transport in DNA - Insights from Simulations

SimulationSetup Figure3.4: Helical parameters ofDNAdouble-helices. Six parameters on the left side represent the intra-base-pair parameters which depict the position of the two nucleobases which form a base-pair. The six parameters on the right side depict the inter-base-pair parameterswhich shows the position of two stacked base-pairs. Taken from[107] HelicalParameters The structureof aDNAdoublehelix canbedescribed in termsof so-calledhelical parameters. Thenomenclature anddefinition of thesewas specifiedbyDickerson et al. in 1989[106]. Until then no universal scheme to calculate these parameters was available and the nomenclaturewas inconsistent. The definedhelical param- eters describe thepositionof thenucleobases,while the structure of the backbone is not taken into account. Twogroups of helical parameters aredefined. First, the intra-base-pair parameters, which describe the deviation from a planar arrange- mentwithin a pair of nucleobases. Second, the inter-base-pair parameterswhich describe the orientation of twobase-pairs stackedon topof each other. Figure 3.4 givesagraphical illustrationof these12helicalparameters. Thehelicalparameters in thisworkwere calculatedwith the3DNAprogram.[107] 3.1.1 InvestigatedDNASequences In the first part of this work the general features of the DNA double helix are investigated. The choice of the sequence is a non-trivial task as the humidity- dependentproperties andbehaviorunder tensionmaydependupon the sequence 42