Page - 76 - in Charge Transport in DNA - Insights from Simulations

ChargeTransport inStretchedDNA Table5.2: Base-pair steps in the considered DNA sequences. X\Y – purine– pyrimidine step,X/Y–pyrimidine–purine step,X|Y–purine–purine step. DNAsequence step GG AA GA GT GC AT DD 1–2 G|G A|A G|A G\A G\G A\A G/G 2–3 G|G A|A A|G A/G G/G A/A G|A 3–4 G|G A|A G|A G\A G\G A\A A|A 4–5 G|G A|A A|G A/G G/G A/A A\A 5–6 G|G A|A G|A G\A G\G A\A A|A 6–7 G|G A|A A|G A/G G/G A/A A|G 7–8 G/G Figure5.6: Graphical illustrationof thedifferentbase-pairsteps intheDNAsequences. 5.5 Conclusion In this chapter, the charge transport in theLandauer–Büttiker picture in stretched DNA was investigated. This setup resembles common charge transport experi- ments,where theDNAstrand is attached toelectrodeswithvaryingdistances. The efficiency of hole transport in the studied dsDNAoligomers is little affected by stretching of the molecule by up to 10% of the free length. When the DNA molecule is stretched further, up to the elongation of 30%, the response of CT efficiency is determined by the exact nucleobase sequence. This effect has been characterized for the pulling of DNA at 3’-ends, in detail. The induced confor- mational changes lead to a breaking point, where the distance between purine nucleobases increaseswithinpyrimidine–purinebase-pair steps largely. Thecorre- sponding electronic couplingvanishes and theoverallCTefficiencydrops steeply. Thefirst conformational transition of a base-pair stephas been found the limiting parameter.While this conformational transitionoccursat anelongationof ca.20% here, itmayoccur at smaller relative elongations in longerDNAspecies. 76