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ChargeTransport inStretchedDNA
Figure5.1: The central seven base pairs of theDNAoligomerGGbeing stretched up
to the additional extension of ca. 25 % of the free length by pulling at
the 3â-ends. The backbones are depicted as ribbons, with color coding the
conformation: blue âhelical, B-like dsDNA; redâ ladder-like S-DNA.The
helical dsDNAstructure passes to a ladder-like one, gradually.
tral fragment, 5â-(G)13-3â (GG), 5â-GG(AG)4G-3â (GA) and 5â-CC(A)9CC-3â (AA).
And fouroligomerswithpurinesdistributedamongboth strands,5â-GG(TG)5G-3â
(GT), 5â-GG(CG)4G-3â (GC), 5â-GG(AT)3AGG-3â (AT) and 5â-CGCGAATTCGCG-3â
(DD,Dickersonâsdodecameradopted fromPDBID1BNA).[108]
Stretching simulations, as described in chapter 4, were performed for these seven
oligomers. Fromthe stretching simulationswith linear increasing force, sequences
of14 to19 (dependingonDNAspecies) snapshotsof thestructurewere taken. The
snapshots were taken startingwith the canonical helical structure until just after
the conformational change to the ladder-like structure. Representative snapshots
of the corresponding structures are shown inïŹgure5.1.
Thelengthof thecentral fragmentofsevenbasepairs (eight incaseofDD)of theses
sequences started at ca. 90%of the equilibrium length observed in the freeNPT
simulation, seeTab.5.1, and increased in stepsof0.1nm.
Starting from these snapshot structures with different lengths MD simulation of
20nswereperformed. In these simulations the lengthof the central fragmentwas
restrained bymeans of a harmonic potential acting between the 3â-terminal O3â-
atomsof the central fragmentwith a force constant of 1000kcal ·molâ1·nmâ2, or
6,948pN/nm. TheïŹrst5nsof thesesimulationswerediscarded,andtheremaining
15nswere taken for further analysis.
In the stretching simulations, all of theDNAspecies go through a transition to a
ladder-like conformation (S-DNA).[21]The transition isgradual,meaning thatone
70
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