Page - 46 - in Charge Transport in DNA - Insights from Simulations

SimulationSetup Figure3.5: Example of the increasingpulling forceduringanMDsimulationof20ns of theDNAoligomerA5. box, parallelwith the helical axis of the oligomer,was applied to theO3’ atomof the 3’-terminal nucleotide in eachDNAstrand. Evidently, the approach involving such ‘artificial’ stretchingof theDNAmoleculedoesnot involve the effect of vari- abledistanceof theDNAto the electrodes. Inotherwords, it is assumedhere that the conformational changes of theDNAmolecules take place before the coupling ofDNAto the electrodes is affected considerably. The force on theO3’ atomswas increased with different rates along the simulation until the DNA strands sepa- rated. See figure 3.5 for an example of the linearly increasedpulling force during anMDsimulationof20ns. Note that the used loading rates are several orders ofmagnitude larger than that applied in typical experiments. The likely consequences of this fact is a more distinct irreversibility of the stretching process. Thiswill be discussed further on in chapter4. 3.4 MicrohydratedDNA Toprepare themicrohydrated systemsapart of thewatermoleculeswas removed from the equilibrated fully hydrated systems. Pilot simulations showed that a hy- drated backbone is best to support the helical character of the DNA molecule. 46