Page - 56 - in Charge Transport in DNA - Insights from Simulations

DNAUnderExperimentalConditions 4.3 IrreversibilityofDNAStretching inSimulations Theexternal forceapplied in thesimulations increases severalordersofmagnitude faster than in the relevant experiments. In addition, the observeddifferent forces needed for the transitionwhendifferent loading rates are applied, provides ahint at the likely irreversibility of the simulated process. So, the important question here iswhat happenswith theDNAoligomerwhen the external force is removed –does thehelical structurerecover? Toinvestigate thispoint, theexternal forcewas removedat several selectedpointsduringeach simulation,whichwas followedby a free simulation of 20 ns. Also, an alternative protocol was usedwith the force beingdecreasedgraduallyby10pN/nsdowntozero insteadof itsabruptremoval. Thepoints of force removal or reversalwere selectedas follows: • A–helix just before the transition to ladder • B–during thehelix–ladder transition • C– freshly established ladder • D– ladder just before thefinal collapseof thedouble strand The timeand force at thesepoints in each simulation isprovided in table4.2. Table4.2: Time (t, in ns) and force (F, in pN) at the point in a stretching simulation that reverse simulationsA, B, C andDwere started, for theDNA species studied. Sim. A5 A9 A13 G5 G9 G13 t F t F t F t F t F t F A 13.5 81 12.0 72 16.0 96 16.5 99 22.0 132 30.0 180 B 15.0 90 16.0 96 18.0 108 17.3 104 23.3 140 31.5 189 C 16.5 99 21.0 126 20.0 120 18.0 108 24.0 144 33.0 198 D 42.0 252 60.0 360 65.0 390 65.0 390 95.0 570 132.0 792 Thetypicaldistance/forceprofile inbothkindsofsimulationsispresentedinfigure 4.8, and the character of theobservedfinal structures is summarized in table4.3. When the external force was switched off in points before or during the helix– ladder transition (A, B), thehelix structurewas alwayspreserved/recovered. This 56