Probing Charge Transport in Oxidatively Damaged DNA Sequences under the Influence of Structural Fluctuations

We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic struct...

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Bibliographic Details
Published in:The journal of physical chemistry. B 2012-09, Vol.116 (36), p.10977-10985
Main Authors: Lee, M. H, Brancolini, G, Gutiérrez, R, Di Felice, R, Cuniberti, G
Format: Article
Language:English
Subjects:
Base Sequence
Charge transport
Damage
Deoxyribonucleic acid
DNA - chemistry
DNA - genetics
DNA Damage
Electric Conductivity
Electronic structure
Electrons
Fluctuation
Guanine - analogs & derivatives
Guanine - chemistry
Mathematical models
Molecular dynamics
Molecular Dynamics Simulation
Oxidation-Reduction
Quantum Theory
Time series
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Summary:We present a detailed study of the charge transport characteristics of double-stranded DNA oligomers including the oxidative damage 7,8-dihydro-8-oxoguanine (8-oxoG). The problem is treated by a hybrid methodology combining classical molecular dynamics simulations and semiempirical electronic structure calculations to formulate a coarse-grained charge transport model. The influence of solvent- and DNA-mediated structural fluctuations is encoded in the obtained time series of the electronic charge transfer parameters. Within the Landauer approach to charge transport, we perform a detailed analysis of the conductance and current time series obtained by sampling the electronic structure along the molecular dynamics trajectory, and find that the inclusion of 8-oxoG damages into the DNA sequence can induce a change in the electrical response of the system. However, solvent-induced fluctuations tend to mask the effect, so that a detection of such sequence modifications via electrical transport measurements in a liquid environment seems to be difficult to achieve.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp2091544