Seite - 53 - in Charge Transport in DNA - Insights from Simulations

4.2TheStructuralChangesofDNAuponStretching Figure4.3: The central seven base pairs of theDNAoligomerGGbeing stretched up to the additional extension of ca. 25 % of the free length by pulling at the 3’-ends. The backbones are depicted as ribbons, with color coding the conformation: blue –helical, B-like dsDNA; red– ladder-like S-DNA.The helical dsDNAstructure passes to a ladder-like one, gradually. Figure4.4: Helical parameters in a stretching simulation ofA9. patterns.. Shortly after the helix–ladder transition (at 250–300 pN), the hydrogen bonding in a few central base pairs is disturbed for a prolonged period of time. Partially, these defects pertain for the entire rest of the simulation, showing that the transition to a ladder structure need not be perfect. The analysis of hydro- gen bonding during stretching for all studiedDNAoligomers is presented in the appendix (figureA.1). An important issue of such simulations is the dependence of observed structural changes on the rate of stretching. Note, that the stretching is several orders of magnitude slower in the experiments. To obtain a rough idea on the effect of rate on the stretching profile, further simulationswere performed. The external force was increasedgraduallywith therateof10pN/nsandeven2pN/ns(forA9only), insteadof thepreviouslyusedrateof50or83pN/ns. Thecomparisonofstretching profiles at threedifferent loading rates ispresented infigure4.6. Conformational transitions occur at smaller force when the force increases more slowly, even though the emerging conformations are the same. Instead of at 53