Page - 70 - in Charge Transport in DNA - Insights from Simulations

ChargeTransport inStretchedDNA Figure5.1: 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. tral fragment, 5’-(G)13-3’ (GG), 5’-GG(AG)4G-3’ (GA) and 5’-CC(A)9CC-3’ (AA). And fouroligomerswithpurinesdistributedamongboth strands,5’-GG(TG)5G-3’ (GT), 5’-GG(CG)4G-3’ (GC), 5’-GG(AT)3AGG-3’ (AT) and 5’-CGCGAATTCGCG-3’ (DD,Dickerson’sdodecameradopted fromPDBID1BNA).[108] Stretching simulations, as described in chapter 4, were performed for these seven oligomers. Fromthe stretching simulationswith linear increasing force, sequences of14 to19 (dependingonDNAspecies) snapshotsof thestructurewere taken. The snapshots were taken startingwith the canonical helical structure until just after the conformational change to the ladder-like structure. Representative snapshots of the corresponding structures are shown infigure5.1. Thelengthof thecentral fragmentofsevenbasepairs (eight incaseofDD)of theses sequences started at ca. 90%of the equilibrium length observed in the freeNPT simulation, seeTab.5.1, and increased in stepsof0.1nm. Starting from these snapshot structures with different lengths MD simulation of 20nswereperformed. In these simulations the lengthof the central fragmentwas restrained bymeans of a harmonic potential acting between the 3’-terminal O3’- atomsof the central fragmentwith a force constant of 1000kcal ·mol−1·nm−2, or 6,948pN/nm. Thefirst5nsof thesesimulationswerediscarded,andtheremaining 15nswere taken for further analysis. In the stretching simulations, all of theDNAspecies go through a transition to a ladder-like conformation (S-DNA).[21]The transition isgradual,meaning thatone 70