Page - 49 - in Charge Transport in DNA - Insights from Simulations

CHAPTER4 DNAUnderExperimentalConditions Reproduced inpartwithpermission from M.Wolter,M.Elstner andT.Kubarˇ, J. Phys.Chem.A,2011,115 (41),11238–11247. Copyright2011,AmericanChemical Society. MDsimulations ofDNA, in course of charge transfer simulations, are usually not performedunder conditions resembling theexperimental setupof electric conduc- tivity experiments. The DNA strands are connected to electrodes on both sides, causingmechanical forces onto the double helical structure. Moreover, theDNA strands are dried in some fashion to ensure themeasurements are not influenced by the conductivityofwater. Thereforethefirst taskfor thesimulationof thisexperimentalsetupis to investigate the structure of double-stranded DNA under mechanical stress in complex with varied amount ofwater and counterions. To get a first insight into the structure ofDNAand the changesundermechanical stress,MDsimulations areperformed with homogeneous sequences. Apart from the mechanical stress, the influence of the environment on the structure and stability of the DNA double-strand is investigated. Various amounts of water, as well as the counterions are seen to contribute to the stabilizationof theDNAstructure. 49