Page - 50 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions 4.1 FreeMDSimulations Inorder toobtain referencevalues, the startingpointwill be abrief analysis of the structureof free, fullyhydratedDNA.MDsimulationsof20ns inaqueoussolution wereperformed for everyDNAspecies studied, and the structureof eachof them was observed stable throughout the simulation time. The length of each double strandwasmeasured as thedistance of the 3’-endO3’ atoms, see table 4.1 for the meanvaluesandstandarddeviations. Thedistributionsof these lengthsareshown infigure4.1. Figure4.1: Distribution of length of studiedDNAspecies in aqueous solution. Table4.1: Length of the studied DNA species in aqueous solution in freeMD simu- lations, measured as the distance of 3’-end O3’ atoms (mean± standard deviation). sequence length sequence length [nm] [nm] A5 1.57±0.13 G5 1.84±0.08 A9 2.98±0.14 G9 3.44±0.12 A13 4.17±0.22 G13 4.44±0.23 In comparison to the polyAoligomers, the polyGoligomers exhibit a larger end- to-enddistance for all sequenceswithmatching numbers of base pairs. Thismay seem surprising as the B-like polyA strands are actually longer then the A-like 50