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Charge Transport in DNA - Insights from Simulations
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ChargeTransport inMicrohydratedDNA sivelyononestrandin thecentral fragment,5’-(G)13-3’ (GG),5’-GG(AG)4G-3’ (GA) and 5’-CC(A)9CC-3’ (AA). And four oligomers with purines distributed among both strands,5’-GG(TG)5G-3’ (GT),5’-GG(CG)4G-3’ (GC),5’-GG(AT)3AGG-3’ (AT) and 5’-CGCGAATTCGCG-3’ (DD, Dickerson’s dodecamer adopted fromPDB ID 1BNA).[108] As shown inchapter4, theDNAstructuredeformswith thedecreasingamountof water in the environment. For theDry1 andDry2 systems, the amount ofwater seems to be sufïŹcient to preserve a regular double-stranded structure in all DNA sequences,whileanappliedharmonicrestraintprevents theDNAoligofrombend- ing towards the major groove. However, the helical structure of all of the DNA oligos is lost completely onhydration levelsDry3 andDry4. Rather, a disordered compact coil appears, which cannot be remedied by the application of a simple restraint. Nevertheless, all four kinds ofmicrohydration environmentswill be analyzed in the following. Note, that only the data forDry1 andDry2will relate to retained helical-like structures. This indicates thatDNAdoesnot formstablehelices below acertaindegreeofsolvation. SincethestructureofDNAisvital for itsconductivity, this isanimportant factor for theunderstandingofDNAconductivityexperiments. 6.2 ChargeTransferParameters First, the averagedECwere obtained for all of the sequences andhydration envi- ronments along theMDtrajectories. Figure6.1 shows twoexamplesof thesemean values of EC for thedifferent amounts ofwater. As a general trend themeanval- ues of the ECare increased by 10%to 150%for the systemsDry1 relative to the respective fullyhydratedsystems. Inmostof the sequences, theECdecreaseagain in the systemswitheven smallerwater content. This is seenmostmarkedly in the sequences AA, AT andAG. See ïŹgure 6.1 for sequenceATandtheïŹgures in theappendixB.2 foranoverviewofall investigated sequences. In the sequenceGT, the dependence of ECon the hydration level is different and distinct, as seen in Fig. 6.1. The difference between the base-pair steps GC-AT 80
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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

  1. Zusammenfassung 1
  2. Summary 3
  3. 1 Introduction 5
  4. 2 TheoreticalBackground 11
    1. 2.1 MolecularMechanics 11
    2. 2.2 MolecularDynamicsSimulation 13
      1. 2.2.1 Solving theEquationsofMotion 14
      2. 2.2.2 ThermodynamicEnsembles 15
    3. 2.3 QuantumChemistry 18
      1. 2.3.1 DensityFunctionalTheory 18
      2. 2.3.2 ApproximativeDFT–Density-FunctionalTight-Binding 21
    4. 2.4 DynamicsofExcessCharge inDNA 24
      1. 2.4.1 TheMulti-ScaleFramework 25
      2. 2.4.2 TheFragmentOrbitalApproach 26
    5. 2.5 ChargeTransport inDNA 29
      1. 2.5.1 Landauer–BĂŒttikerFramework 29
    6. 2.6 ChargeTransfer inDNA 32
      1. 2.6.1 Basics ofChargeTransfer 32
      2. 2.6.2 Non-adiabaticPropagationSchemes 34
  5. 3 SimulationSetup 39
    1. 3.1 TheDNAMolecule 39
      1. 3.1.1 InvestigatedDNASequences 42
    2. 3.2 MDSimulationofDNA 44
    3. 3.3 DNAunderMechanical Stress 45
    4. 3.4 MicrohydratedDNA 46
  6. 4 DNAUnderExperimentalConditions 49
    1. 4.1 FreeMDSimulations 50
    2. 4.2 TheStructuralChangesofDNAuponStretching 51
    3. 4.3 IrreversibilityofDNAStretching inSimulations 56
    4. 4.4 Effects ofLowHydration 58
    5. 4.5 Effects ofDecreased IonContent 62
    6. 4.6 Effect ofWater and Ionson theStretchingProïŹleofDNA 64
    7. 4.7 Conclusion 67
  7. 5 ChargeTransport inStretchedDNA 69
    1. 5.1 InvestigatedSequences andStructures 69
    2. 5.2 ChargeTransportCalculations 71
    3. 5.3 SequenceDependentChargeTransport 73
    4. 5.4 DetailedStructuralDifferences 74
    5. 5.5 Conclusion 76
  8. 6 ChargeTransport inMicrohydratedDNA 79
    1. 6.1 InvestigatedSequences andStructures 79
    2. 6.2 ChargeTransferParameters 80
    3. 6.3 ChargeTransportCalculations 84
    4. 6.4 DirectDynamicsofChargeTransfer 86
    5. 6.5 Conclusion 87
  9. 7 AParametrizedModel toSimulateCT inDNA 89
    1. 7.1 Creating theElectronicCouplings 90
    2. 7.2 Modeling the IonizationPotentials 93
    3. 7.3 TestingwithChargeTransportCalculations 97
    4. 7.4 ChargeTransferExtensions 98
    5. 7.5 TestingwithChargeTransferMethods 102
    6. 7.6 Conclusion 103
  10. 8 Conclusion 105
  11. Appendix 111
  12. A DNAUnderExperimentalConditions 111
    1. A.1 TheStructuralChangesofDNAuponStretching 111
    2. A.2 Effect ofLowHydrationandDecreased IonContent 112
    3. A.3 StretchingofMicrohydratedDNA 116
  13. B CTinMicrohydratedDNA 117
    1. B.1 HelicalParameters -CompleteOverview 117
    2. B.2 ElectronicCouplings 118
    3. B.3 IonizationPotentials 119
    4. B.4 ESP InducedbyDifferentGroupsofAtoms 122
    5. B.5 DistanceofChargedAtomGroups fromtheHelicalAxis 123
  14. List ofPublications 137
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Charge Transport in DNA