Page - 75 - in Charge Transport in DNA - Insights from Simulations

5.4DetailedStructuralDifferences Figure5.5: Schematic depiction of the change of relative orientation of purine nucle- obases (G, A) upon the onset of overstretched, ladder-like structure in a dsDNAfragment. a GC and a AT pair lay on top of each other where the guanine is bound to on strand and the adenine is bound to the other one. This situation corresponds to a purine–pyrimidine base-pair step. InG/T the situation is the same, but direction- ally inverted. So, this corresponds to a pyrimidine–purine base-pair step. For a graphical illustrationof thisnamingschemeseefigure5.6. Inapurine–pyrimidinebase-pairstep, thepurinesactuallyapproachtoaveryshort distance in a ladder-like DNA structure, which can bring on a largely increased electronic coupling. This iswhat is observed for the 1–2 base-pair step in theGT sequence. However, theeffect is theopposite for thepyrimidine–purinebase-pair steps.Here, the lateral distance between the purines increasesmarkedly,making their overlap attenuate to anegligible value, so that the electronic couplingvanishes effectively. Apreviouscomputational studybasedonstaticDNAstructuresproposedapossi- bleorientationofmolecularorbitals inoverstretchedDNAin thisway.[38] Thisobservation is the same for theother studiedDNAspecieswithpurinenucle- obasesdistributedamongbothDNAstrands, too. Ineachcase, there isat leastone pyrimidine–purine base-pair step,which undergoes the described conformational changeaccompaniedwithvanishingelectronic coupling, leading toadramaticde- creaseofCTefficiency. 75