Page - 51 - in Charge Transport in DNA - Insights from Simulations

4.2TheStructuralChangesofDNAuponStretching polyG.The reason for this is that the3’–3’ distancedoesnot correspondexactly to the lengthof theDNAmoleculesmeasuredalongthehelicalaxis.Nevertheless, the 3’–3’distancewillbeconsidered in thisworkbecause it is thecoordinate thatDNA will be pulled along,motivated by the single-molecule conductivity experiments. Interestingly, the fluctuation of this distance is smaller for polyG than for polyA with shorterDNAdouble strandsoffive andninebasepairs,while it is larger for G13 than forA13. Theabsenceofanyobvious trendsmaybecausedby the fact that thestudiedDNAoligomersarequite short,withonlyA13 andG13 constitutingone completehelical turn. Also, the helical parameters rise, slide and twist were evaluated for the studied DNA species and are presented in table 4.5. This table shows the mean values of the helical parameters of all considered base-pair steps. For an overview over all parameters for every single step, see tablesA.1 andA.2 in the appendix. The smaller values of twist and the larger negative values of slide in case of polyG sequences indicate theseDNAstrands toassumeanA-like conformation,which is in accordancewith expectations. However, no cleardifferencebetweenpolyAand polyGwasobserved for rise. 4.2 TheStructuralChangesofDNAuponStretching Aseries of simulationswas performed inwhich an additional external forcewas applied on the 3’-endO3’ atoms of the particular DNA species. To simulate the stretchingwithin a tractable simulation time, themagnitude of the external force was increasedgradually in timewith the rate of 50pN/ns (83pN/ns forA13 and G13). Thisway, the force at the endof anMDsimulation of 20ns reached avalue of 1.00 nN (1.66 nN for A13 and G13). This turned out to be sufficient to finally separate the strands in all of the studied DNA species. As a measure of length of theDNAoligomer, the distance of the 3’-endO3’ atomswasmonitored along the simulation. See figure 4.2 for an example profile of this distance vs time or, equivalently, external force, andfigure4.3 for a set of representative snapshots. The helical double-stranded structure of the A9 oligomer is preserved up to ca. 200 pN. Then, the end-to-end distance increases by over two thirds of the initial lengthwithin avery short interval of time. This indicates the transition to a struc- 51