Page - 74 - in Charge Transport in DNA - Insights from Simulations

ChargeTransport inStretchedDNA Figure5.4: Meaningof the helical parameter slide; every boxdepicts onenucleobase. However, this justificationdoesnothold for everybase-pair step. For instance, the base-pair step 1–2 in GT undergoes the same conformational change, and there is even a large increase of the corresponding electronic coupling. The analysis of a sequence with all purine nucleobases on one strand (GG) reveals a similar conformational transition,withan increaseof slide for several base-pair steps. The corresponding electronic couplings decrease though, but retain non-zero values unlike those inGT. Consequently, the conductivity ofGGdecreases only slightly. This accumulated evidence prevents simple conclusions to be drawn, and amore detailedexplanationhas tobe sought. 5.4 DetailedStructuralDifferences To understand the different response of CT in the various DNA sequences to stretching, it is necessary to take into account both the inherent asymmetry of the DNAdoublehelixandtheparticularwaythat theendsof thestrandsarepulled. In agreementwith thementioned experiments,[8–12] this study considers anchoring of the3’-endsof theDNAdouble strand, see the illustration inFig.5.5. WhenaDNAspecieswith all purinenucleobases onone strand is stretchedup to a ladder-like structure (Fig. 5.5 left), the overlapof every twoneighboringpurines decreases, as described by slide taking large values. The electronic coupling of purines in suchanarrangementdecreases though, butdoesnot vanish. The situa- tion is verydifferentwhen thepurine nucleobases alternate betweenboth strands (Fig.5.5 right). Table 5.2 shows an overviewof the base-pair steps present in the investigated se- quences. Basically three different step types can be distinguished. For example, G|Gis the intrastrandbase-pair stepof twoGCbase-pairswhere theguaninesare on top of each other bound to the same strand. G\T is a base-pair step where 74