Page - 60 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions Figure4.10: ThestructureofmicrohydratedDNAspeciesA13 collapses inanMDsim- ulationwithno stabilizing external force. (Surroundingwatermolecules not shown for clarity.) patternwasobserved in theDNAstructure any longer, and thehelical parameters werenot evaluated. The largest studied amount of water (Dry1) was sufficient to support nearly-canonical structureof allDNAoligomerswhen the stabilizingpulling force was applied. All of thepolyAspecies stayed inB-like conformation in spite of the low hydration, illustrating that it is difficult to convert polyA to A-DNA, which would generally be preferred under low hydration. Slightly unexpectedwas the observationofhelicalparameters takingratherB-likevalues forG5. Although, this maynot be surprising for aDNAspeciesmuch shorter than a single helical turn, and it is alsonotquite clear if theapplied forcefielddescribesaB-to-Aconversion with sufficient accuracy. A further reduction of the amount ofwater (Dry2) leads to structures thatwere too irregular to be assigned to eitherA- or B-family. Also, thesestructuresfluctuatenotably,whichisreflectedbythe largestandarddeviation ofhelical parameters, see table4.5. Thedegradationofstructurecanbemonitoredalsobytheanalysisof thehydrogen- bonding pattern between theDNAstrands. An example in figure 4.11 shows the hydrogen-bond existence charts from MD simulations of 10 ns of the microhy- dratedA13 species (Dry1 andDry2), stillwith the 3’-endspulledwith an external force. Evidently, all of the hydrogen bonds are preserved in theDry1 simulation, 60