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4.7Conclusion
cursatasmallerexternal force than in thecorrespondingsimulationwith thesame
amount of water and the original number of counterions (passing from the red
curve to theblue, and from thegreenone to theyellow). This effectwasobserved
for allDNAspecies studied.
The observations in stretching simulations are summarized in table 4.7. Certain
trends are visible even thoughonly one simulationwasperformed for eachDNA
species and considered conditions. So, larger force is needed to induce the over-
stretching transition aswell as the separationof strands in themicrohydrated sys-
temsDry1andDry2, comparedtothefullyhydratedDNA.Theeffectof thecontent
of counterions ismoreblurred, yet still theonset of theoverstretched ladder struc-
ture seems to occur at a smaller force if some counterions are removed from the
microhydratedDNAcomplex.
4.7 Conclusion
In this chapter, the structural features of microhydrated DNA and their changes
upon stretching stress were investigated with classical MD simulation. The pre-
liminarynatureof this studydoesnot allow todrawanyquantitative conclusions.
Still, there are severalpoints tobemade.
Both water and counterions are structure-stabilizing factors. The amount of wa-
ter and the content of counterions necessary to support a helical double-stranded
structure in the simulationswas characterized. The removal of a certain number
of counterionsmaystabilize the structureof amicrohydratedDNAoligomer, even
thoughsucha systembears anon-zero electric charge.
Conformational transitions were observed at smaller forces when the DNA was
stretchedmore slowly. This illustrates the irreversibility of the stretching process
in the simulations,when the pulling is several orders ofmagnitude faster than in
experiments. For this reason, further interpretationof the stretching simulations is
limitedtothecomparisonoftheresponseofmicrohydratedDNAwiththeresponse
ofDNAinsolution,pulledwith the same loading rates.
The helical structure of DNAundergoesmarked changes upon removal ofwater
fromthe cluster. First, thehelixbends toward themajorgroovewhere counterions
67
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