Page - 55 - in Charge Transport in DNA - Insights from Simulations

4.2TheStructuralChangesofDNAuponStretching Figure4.7: The stretchingprofiles (relative extensionvs. applied external force) for all studiedDNAoligomers, at a stretching rate of10pN/ns. introduction of the external force, all DNA oligomers exhibit a roughly linearly increasing length, behaving nearly like harmonic springs. Then, the transition to a ladder structure sets in at some point at an external force of between 150 and 300pN,dependingon the length andcompositionof theDNAoligomer. The lad- derstructure,withanend-to-enddistanceabouttwiceas largeasthatof freehelical double-strandedDNA, remains stable for another extended interval of timewhile the force further increases. Finally the forcesarehighenoughtoreachuptoapoint where theDNA strands separate entirely. Obviously, the longer DNAoligomers undergo thehelix-to-ladder transitionaswell as theeventual separationof strands at a larger external force. The force needed to induce a transition increases in the seriesA5>A9>A13 andG5>G9>G13. Also, theguanine-containingoligomers require generally a larger force to assume the ladder structure as well as to tear apart. The situation would become more complex with mixed DNA sequences surely. The stretching simulationswere performedwith a setupvery similar to that used in earlier theoretical studies. [19,20,22,33] Theobtained results are in accordance with these respective data. Specifically, the pulling rateswere in the same range, the onset of the ladder-like overstretched structurewasobservedat similar forces, and the overstretched DNA itself possesses the same structural features. In the following, these stretchingprofileswill serve as a reference towhich the behavior ofmicrohydratedDNAduring stretchingwill be related. 55