Page - 106 - in Charge Transport in DNA - Insights from Simulations

Conclusion of DNA.Here, the amount of water and the content of counterions necessary to support a helical double-stranded structure in the simulationswas characterized. Upon removal of water from the molecule the helical structure of DNA under- wentmarked changes. Finally, the double strand lost its helical character roughly at 6watermolecules per phosphate group. Continued drying induced a rupture ofhydrogenbondsandacollapseof thedouble-strandedstructure toadisordered compactcoil. Atfist sight, thiswasadevastatingobservationwithregardto theex- perimental setup. Providentially, the simulations showed that thehelical structure ofmicrohydratedDNA can be supported by pulling at the 3’-ends, which again resembles the experimental setup. The furtherpullingat the3’-endsof theDNAstrands lead toDNAconformations already observed in previous studies. In this work, a crucial dependence on the applied pulling rate was shown for the conformational change from a helix-like to a ladder-like DNA structure. This illustrates the irreversibility of the stretch- ing process in the simulations, when the pulling is several orders of magnitude faster than inexperiments. Toovercome this issue, the investigationofCT in those stretchedDNAconformationswasperformedonstructuresheldat certain lengths duringsimulation time, rather thancalculatingalongnon-equilibriumpullingsim- ulations. The first charge transport calculations in this work were performed on DNA in stretched conformations. Here, the efficiency of hole transport in the studied ds- DNA oligomers was little affected by stretching of the molecule by up to 10% of the free length. When theDNAmolecule is stretched further, the response of CT efficiency is determined by the exact nucleobase sequence. In detail, the con- formational change lead to a breaking point, where the distance between certain base-pair steps increases largely. Therefore, theoverallCTefficiencydrops steeply in the exactmoment thefist conformational transitionoccurs. These results provide a means for the interpretation of the outcome of conduc- tivity experimentswhere theDNAmolecule is stretched and theDNAsequences resemble those simulated. The accumulated knowledgemakes it possible to con- structDNAsequences such that the extent towhich their conductivity is affected by themechanical stressduring the experiments is controlled. Also, suitableDNA sequences canbeopted for in thedesignofDNA-baseddevicesasnano-scale elec- tronic elements,where limiteddependenceof conductivityon length isdesirable. 106