Page - 79 - in Charge Transport in DNA - Insights from Simulations

CHAPTER6 ChargeTransport inMicrohydratedDNA Reproduced inpartwithpermission from M.Wolter,M.Elstner andT.Kubarˇ, J.Chem.Phys.,139,125102 (2013). Copyright2013,American InstituteofPhysics. In this chapter, theCTpropertiesofDNAinenvironmentswithdecreasedamount of water will be investigated. Generally, the CT experiments are not conducted under "dry" conditions. The DNA strands are attached to electrodes and then dried in some fashion topreventmeasurements of the conductivity of the solvent. In this setup, there is noway to tell howmanywatermolecules stay attached to the DNA strand. Surely, the inner water molecules, tightly bound by hydrogen bonds, will not be blown away by a streamof nitrogen. Therefore, the described simulation setupwill give insight into the effect thismicrohydrated state has on the theCTproperties ofDNA. 6.1 InvestigatedSequencesandStructures Again, sevendifferentDNAoligomerswill be investigated in detail (complemen- tary strand not shown): Three oligomers with purine nucleobases located exclu- 79