Page - 73 - in Charge Transport in DNA - Insights from Simulations

5.3SequenceDependentChargeTransport Figure5.3: Electronic coupling (EC) and value of the helical parameter slide for the individual base-pair steps, for the sequences GG (top) and GT (center). Mean values for ensembles generated by MD simulations are presented; seeTab.5.2 for the designation of base-pair steps. 5.3 SequenceDependentChargeTransport The aim here is to find out why the CT in different DNA species responds to stretching differently. To do so, the electronic couplings for the individual base- pair stepsareanalyzed. See thecomparisonofDNAspeciesGGandGTinFig.5.3. Evidently, the electronic coupling for the base-pair step 2–3vanishes inGT at the elongation of 20%and does not recover anymore. This happens in accordance with the currentdropping to the sub-picoampere rangeat the sameelongation. Suchanotable changeof the electronic couplinghas tooriginate inanabrupt con- formational transition. Indeed, the elongation of 20% is the point at which the transition to a ladder-like DNA structure starts. Note that while the conforma- tional transition involving one or two base-pair steps occurs at the elongation of 20% for the short dsDNAoligomers studied here. Itmay correspond to smaller relative elongation if longerDNAspecies are considered. Thebase-pair step2–3 is one of the first two to take part in it, as illustrated by the sudden increase of the helicalparameterslide. Fig.5.4givesashort reminderof themeaningof thehelical parameter slide. 73