Page - 64 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions Figure4.12: Profiles ofdistancevs force for the stretchingofmicrohydratedDNA–A5 (left),A9 (middle) andG9 (right). Obviouslyandnotsurprisinglyatall, thestructureofhelicaldouble-strandedDNA was shown to be stabilized by both water and counterions, with the absence of oneor theotherbringingaboutamoreor less severeperturbationof the structure. However, thehelicalstructureofamicrohydrateddsDNAspeciesmaybestabilized by the removal of a certainpart of the counterions. 4.6 Effect of Water and Ions on the Stretching Profile ofDNA Finally,MDsimulationswith agradually increasingpulling forcewereperformed for theclustersDry1andDry2. Thesimulationswerestartedwithanonzero initial external forceof83pNforDry1and166pNforDry2 tomaintainahelicaldouble- stranded structure. Then, the forcewas increased during the simulationwith the rateof10pN/ns. Examplesof stretchingprofiles ofmicrohydratedDNAoligomers arepresented in figure 4.12. See also figureA.3 for selected helical parameters during the stretch- ing ofmicrohydratedG9. ThemicrohydratedG9 remains in the helical structure until the external force reaches 400 pN with Dry1 and even 800 pN with Dry2. Remember, this is the fourfoldof the forceneededto transformthisDNAoligomer to a ladder structure in aqueous solution. This effect was observed for all DNA oligomers studied, see also table 4.7 for the forces atwhich overstretching transi- tionoccurs. 64