Page - 52 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions Figure4.2: Stretching of A9 in aqueous solution – the elongation–force profile. The regionswhere helix and ladder structure appear are designated. ture that is still double-stranded but not helical anymore. In this newly adopted structure, the strands are parallel to each other while maintaining the hydrogen bonding between the nucleobases. This structure corresponds to the proposed S-DNA,[21] and is designated as ‘ladder’ in the following. The ladder remains stable for a relatively long interval of time and increasing force. Finally, theDNA strands separate at ca. 750pN.This sequence of events is observed for all studied DNAspecies,with the separation of strands occurring at a force that ranges from 450pN(forA5) to1300pN(forG13). Also, the monitoring of the DNA helical parameters along the stretching simu- lations captures both conformational transitions. The ladder structure exhibits a twist of aroundzero, compared to above 30deg. forA-/B-DNA, anda slideof ca. +0.5nm, compared to -0.15/0.00nm forA-/B-DNA. See figure 4.4 for these data onA9. Upon the separation of DNA strands, the helical parameters lose their meaning whatsoever. But,oncetheyarecalculated,extremelylargeoscillationsareobserved. Anotheruseful tool is the analysis of thepatternof interstrandhydrogenbonding between the nucleobases. See figure 4.5 for an example pattern calculated for the oligomerA9. When the ladder structure is torn, all hydrogen bonds vanish natu- rally. Interestingly, visible are also further irregularities in the hydrogen bonding 52