Page - 80 - in Charge Transport in DNA - Insights from Simulations

ChargeTransport inMicrohydratedDNA sivelyononestrandin thecentral fragment,5’-(G)13-3’ (GG),5’-GG(AG)4G-3’ (GA) and 5’-CC(A)9CC-3’ (AA). And four oligomers with purines distributed among both strands,5’-GG(TG)5G-3’ (GT),5’-GG(CG)4G-3’ (GC),5’-GG(AT)3AGG-3’ (AT) and 5’-CGCGAATTCGCG-3’ (DD, Dickerson’s dodecamer adopted fromPDB ID 1BNA).[108] As shown inchapter4, theDNAstructuredeformswith thedecreasingamountof water in the environment. For theDry1 andDry2 systems, the amount ofwater seems to be sufficient to preserve a regular double-stranded structure in all DNA sequences,whileanappliedharmonicrestraintprevents theDNAoligofrombend- ing towards the major groove. However, the helical structure of all of the DNA oligos is lost completely onhydration levelsDry3 andDry4. Rather, a disordered compact coil appears, which cannot be remedied by the application of a simple restraint. Nevertheless, all four kinds ofmicrohydration environmentswill be analyzed in the following. Note, that only the data forDry1 andDry2will relate to retained helical-like structures. This indicates thatDNAdoesnot formstablehelices below acertaindegreeofsolvation. SincethestructureofDNAisvital for itsconductivity, this isanimportant factor for theunderstandingofDNAconductivityexperiments. 6.2 ChargeTransferParameters First, the averagedECwere obtained for all of the sequences andhydration envi- ronments along theMDtrajectories. Figure6.1 shows twoexamplesof thesemean values of EC for thedifferent amounts ofwater. As a general trend themeanval- ues of the ECare increased by 10%to 150%for the systemsDry1 relative to the respective fullyhydratedsystems. Inmostof the sequences, theECdecreaseagain in the systemswitheven smallerwater content. This is seenmostmarkedly in the sequences AA, AT andAG. See figure 6.1 for sequenceATandthefigures in theappendixB.2 foranoverviewofall investigated sequences. In the sequenceGT, the dependence of ECon the hydration level is different and distinct, as seen in Fig. 6.1. The difference between the base-pair steps GC-AT 80