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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
Charge Transport in DNA
Insights from Simulations
- Titel
- Charge Transport in DNA
- Untertitel
- Insights from Simulations
- Autor
- Mario Wolter
- Verlag
- KIT Scientific Publishing
- Datum
- 2013
- Sprache
- englisch
- Lizenz
- CC BY-SA 3.0
- ISBN
- 978-3-7315-0082-7
- Abmessungen
- 17.0 x 24.0 cm
- Seiten
- 156
- Schlagwörter
- Charge Transport, Charge Transfer, DNA, Molecular Dynamics, Quantum Mechanics
- Kategorien
- Naturwissenschaften Chemie
Inhaltsverzeichnis
- Zusammenfassung 1
- Summary 3
- 1 Introduction 5
- 2 TheoreticalBackground 11
- 3 SimulationSetup 39
- 4 DNAUnderExperimentalConditions 49
- 5 ChargeTransport inStretchedDNA 69
- 6 ChargeTransport inMicrohydratedDNA 79
- 7 AParametrizedModel toSimulateCT inDNA 89
- 8 Conclusion 105
- Appendix 111
- A DNAUnderExperimentalConditions 111
- B CTinMicrohydratedDNA 117
- List ofPublications 137