Page - 8 - in Charge Transport in DNA - Insights from Simulations

Introduction the conditions of applied mechanical stress, and this can be accomplished with classicalMDsimulation. The dependence of CT on the (stretched) state of theDNAoligomer is of crucial importance for the construction of DNA-based nano-electronic devices. Here, a weak dependence of CT on the end-to-end distance within a certain interval is required. The aimof thiswork is to determinehow the efficiency of hole transport inDNA is affected by moderate mechanical pulling of the DNA molecule. Therefore, a microscopic interpretation will be sought for the outcome of DNA conductivity experiments, as the calculations are designed to resemble the usual experimental setup. Based on the results, suggestions will be made regarding the choice of nucleobase sequences in thedesignofDNA-basednano-electronicdevices. Common to the setup ofmanyDNAconductivity studies [8, 9, 11, 12] is the fact that the aqueous solvent is removed so that the solvent conductivitydoesnot bias the measurement. The amount of residual solvent attached to the DNA and its effect on the structural and electronic properties of DNA, however, remain unre- solvedup todate. ThedependenceofDNAstructureonhumidityhasbeen studied intensively since the1950’s.[47]However largelyonmacroscopicDNAfibers rather than inasingle- molecule fashion with atomic resolution. The same is true about the effect of ion/salt concentration. Generally observed is the tendency of DNA to assume theA-like conformation under lowhumidity, contrary to the B-like one for ‘wet’ DNA.Thementionedconductivityexperimentsareanapplicationwhere theeffect of varied amount ofwater bound to a single DNAmolecule on its structure and dynamicswill needamoredetailed investigation. The solvent that theDNAassay had been prepared or kept in is removed to the largest possible extent, in order not tomeasure the conductivity of the buffer. Fi- nally, the distance between the electrodes and thus the length of theDNAdouble strandmaybevaried. With such setup, thementionedworkers obtainedvaluable dataon theelectricproperties of studiedDNAspecies. AlthoughMDsimulationseems tobeaparticularlyuseful tool to investigateDNA under the conditions of conductivity experiments, there has not beenmuchwork of this kinddone. While this is by nomeans surprising if one considers the little 8