Page - 71 - in Charge Transport in DNA - Insights from Simulations

5.2ChargeTransportCalculations Table5.1: Meandistance of the 3’-terminalO3’ atoms in the studiedDNAoligomers in freeMDsimulations (nm). Note that the distance is larger thanB-DNA helix length (2.38nmand2.72nm for the heptamers and the octamerDD, respectively) as theO3’–O3’ vector is not parallel to the helical axis. sequence length sequence length GG 2.89 GT 2.76 AA 2.57 GC 2.69 GA 2.69 AT 2.78 DD 3.17 or twobase-pairstepsatoneterminusof thedoublestrandpass toanS-likeconfor- mationfirst, followedby furtherneighboringbase-pair stepsandso forth, so thata mixedB-like/S-likestructureappears. Eventually, theentiredoublestrandendsup in the S-DNAstructure. This process is shown in Fig. 5.1. TheDNAdouble helix isunwoundgradually,while the interstrandhydrogenbonding remainspreserved between the complementary nucleobases during the entire stretchingprocess. No deeper structural changes are observed, like e.g. swiveling of nucleobases out of the stack. 5.2 ChargeTransportCalculations The electric current was evaluated using the Landauer–Büttiker framework (see chapter 2.5.1) as a function of the varying end-to-end distance, for each of the studiedDNAspecies. At every elongation, 7,500 snapshotswere picked from the last 15ns of the simulationswith constant length. On each of these snapshots an individual calculation of the current was performed. The obtained distributions of current are highly asymmetric, as it turns out that the major portion of the current is contributedbyasmallnumberof conformations. Thisphenomenonwas observed inpreviousworks.[70,81,123] The resulting mean values of the current are presented in Fig. 5.2. Apparently, CT in the twokinds ofDNAsequences (thosewith all purines onone strand and thosewith purines distributed among both strands) responds differently tomod- 71