Page - 44 - in Charge Transport in DNA - Insights from Simulations

SimulationSetup Table3.2: The studiedDNAfragments for charge transfer simulations. Shownare the two-letter symbols used throughout thiswork and the nucleobase sequence of thewell-matcheddsDNAoligomers. Purinenucleobases (GandA)act as charge carrying sites. (DD,Dickerson’s dodecamer adopted fromPDB ID 1BNA).[108] purinesonone strand purinesdistributed GG 5’-GGGGGGG-3’ GT 5’-GTGTGTG-3’ 3’-CCCCCCC-5’ 3’-CACACAC-5’ AA 5’-AAAAAAA-3’ GC 5’-GCGCGCG-3’ 3’-TTTTTTT-5’ 3’-CGCGCGC-5’ GA 5’-GAGAGAG-3’ AT 5’-ATATATA-3’ 3’-CTCTCTC-5’ 3’-TATATAT-5’ DD 5’-CGAATTCG-3’ 3’-GCTTAAGC-5’ are investigatedandthesimulationsetupisgenerated,moresophisticatedDNAse- quenceswereneeded for the calculationofCT inDNA.Therefore, sevendifferent dsDNAoligomerswere studied, three oligomerswith purine nucleobases located exclusivelyononestrand in thecentral fragment, and fouroligomerswithpurines distributed among both strands. The seven innermost base-pairswere taken into account (eight for theDickersondodecamer (DD) for later analysis, to avoid ana- lyzing effectswhich only occur at the ends of theDNAstrands. These fragments and theirdescriptorsused throughout thisworkarepresented inTab.3.2. 3.2 MDSimulationofDNA The3Dstructuralmodel of eacholigonucleotidewasbuild inan idealizedB-DNA conformationwith thena-server.[109]Themolecularsystemthenwasenclosed ina periodic rectangularboxkeepingaminimumdistance fromthewalls of theboxof 1nm. For theDNAstretching simulations thisminimalboxwas thenextendedby additional5nmalongthez-axis,parallel totheDNAhelicalaxis, toaccommodatea stretchedconformationof theDNAmolecule. TheboxwasfilledwithTIP3Pwater molecules[110] and the density of liquidwater was reproduced. An appropriate 44