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5.2ChargeTransportCalculations
Table5.1: Meandistance of the 3’-terminalO3’ atoms in the studiedDNAoligomers
in freeMDsimulations (nm). Note that the distance is larger thanB-DNA
helix length (2.38nmand2.72nm for the heptamers and the octamerDD,
respectively) as theO3’–O3’ vector is not parallel to the helical axis.
sequence length sequence length
GG 2.89 GT 2.76
AA 2.57 GC 2.69
GA 2.69 AT 2.78
DD 3.17
or twobase-pairstepsatoneterminusof thedoublestrandpass toanS-likeconfor-
mationfirst, followedby furtherneighboringbase-pair stepsandso forth, so thata
mixedB-like/S-likestructureappears. Eventually, theentiredoublestrandendsup
in the S-DNAstructure. This process is shown in Fig. 5.1. TheDNAdouble helix
isunwoundgradually,while the interstrandhydrogenbonding remainspreserved
between the complementary nucleobases during the entire stretchingprocess. No
deeper structural changes are observed, like e.g. swiveling of nucleobases out of
the stack.
5.2 ChargeTransportCalculations
The electric current was evaluated using the Landauer–Büttiker framework (see
chapter 2.5.1) as a function of the varying end-to-end distance, for each of the
studiedDNAspecies. At every elongation, 7,500 snapshotswere picked from the
last 15ns of the simulationswith constant length. On each of these snapshots an
individual calculation of the current was performed. The obtained distributions
of current are highly asymmetric, as it turns out that the major portion of the
current is contributedbyasmallnumberof conformations. Thisphenomenonwas
observed inpreviousworks.[70,81,123]
The resulting mean values of the current are presented in Fig. 5.2. Apparently,
CT in the twokinds ofDNAsequences (thosewith all purines onone strand and
thosewith purines distributed among both strands) responds differently tomod-
71
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