Charge migration through DNA molecules in the presence of mismatches

Lee, M. H.; Avdoshenko, Stanislav M.; Gutiérrez, Rafael

doi:10.1103/physrevb.82.155455

Cited by 22 publications

(26 citation statements)

References 47 publications

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“…70 . Simulating intermediate coherent dynamics in DNA is an intricate task: This regime can be followed with phenomenological tools 60,[71][72][73] , or by combining classical molecular dynamics simulations (for describing the effect of backbone, solvent, counterions, and he DNA internal structural fluctuations) with quantum mechanics/molecular mechanics methodologies [74][75][76][77][78] . Alternatively, in Ref.…”

Section: Tunneling To Hopping Transition In Dnamentioning

confidence: 99%

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

Korol

Kilgour

Segal

2016

The Journal of Chemical Physics

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We study the electrical conductance G and the thermopower S of single-molecule junctions, and reveal signatures of different transport mechanisms: off-resonant tunneling, on-resonant coherent (ballistic) motion, and multi-step hopping. These mechanisms are identified by studying the behavior of G and S while varying molecular length and temperature. Based on a simple one-dimensional model for molecular junctions, we derive approximate expressions for the thermopower in these different regimes. Analytical results are compared to numerical simulations, performed using a variant of Büttiker's probe technique, the so-called voltagetemperature probe, which allows us to phenomenologically introduce environmentally-induced elastic and inelastic electron scattering effects, while applying both voltage and temperature biases across the junction. We further simulate the thermopower of GC-rich DNA molecules with mediating A:T blocks, and manifest the tunneling-to-hopping crossover in both the electrical conductance and the thermopower, in accord with measurements by Y. Li et al., Nature Comm. 7, 11294 (2016).

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Section: Tunneling To Hopping Transition In Dnamentioning

confidence: 99%

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

Korol

Kilgour

Segal

2016

The Journal of Chemical Physics

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“…Indeed, we find that the HOMO localization for any given fragment switches from backbone to bases over the simulation time, as was observed in our previous study. 53 In such a situation, the most relevant orbital is not necessarily the HOMO at every instant. Rather, it is the topmost purine-localized occupied orbital, which can be below the HOMO if the HOMO has a backbone character.…”

Section: ■ Summarymentioning

confidence: 99%

“…We note that the HOMO of a given fragment oscillates in time between localization on the base and localization on the backbone. 53 To bypass this spurious effect possibly due to the simplified electronic structure, the charge transfer parameters are computed not only from splittings between HOMO and HOMO-1, but considering four occupied orbitals below the HOMO: all such parameters are then included in the transport Hamiltonian. The analysis is then performed for the last 3 ns of the 20 ns trajectory.…”

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confidence: 99%

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

et al. 2012

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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. I n aerobic organisms, oxidative DNA damage frequently occurs during normal metabolism and upon exposure to light or other ionizing radiation. 7,8-Dihydro-8-oxoguanine (8-oxoG) is one of the most common forms of oxidative DNA damage found in human cells, where a H8 atom in guanine is replaced by an O8 atom, and a H7 atom is added to N7 ( Figure 1). When DNA polymerase encounters 8-oxoG during the DNA replication process, it frequently inserts a mismatched base (adenine) instead of cytosine, leading to G:C → T:A transversions, 1 which are commonly found in mutations associated with age-related diseases and human cancers. Although distinct changes were found in the backbone structure of a 25-base single-stranded DNA (ssDNA) with single 8-oxoG substitutions by Fourier transform-infrared analysis, 3 it has been known that 8-oxoG:C base-pairs have only a minor effect on double-stranded DNA (dsDNA) structure and stability.4,5 Thus, there is an intriguing question as to how the DNA repair enzyme locates 8-oxoG lesions within the entire human genome. In a recent experiment, Markus et al. 6 suggested that 8-oxoG has unique electronic properties and that modulations in the electronic properties might be related to the mechanism of recognizing lesions. They used laser-based methods to investigate various oligomers adsorbed on gold substrates as self-assembled monolayers, and found that the highest occupied molecular orbital (HOMO) appears at a higher energy when 8-oxoG is inserted into the sequence than in unmodified oligomers. The electronic property changes induced by the 8-oxoG lesions suggest the possibility of detecting in vitro 8-oxoG in a DNA sequence by examining the modification of its electrical response; this is expected to have high relevance in, e.g., the development of biosensors based on modifications of the electrical response. 7,8 Electrical detection of an 8-oxo-deoxyguanosine was proposed by Tsutsui et al. 9 by measuring the tunneling cur...

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“…In this section, a methodology [81][82][83][85][86][87][88] is described which uses a hybrid approach based on a combination of molecular dynamics simulations and electronic structure calculations with a mapping of the time-fluctuating electronic structure along the MD trajectory onto coarse-grained transport models. The key issue is that in this way the number of free parameters in the model formulation is reduced to a large extent.…”

Section: Structural Fluctuations In Biomolecular Systems: Bridging Momentioning

confidence: 99%

“…The present paper will introduce such a methodology which has been recently developed [81][82][83][85][86][87][88]. This approach allows to consider the influence of structural fluctuations and solvent effects onto the electronic structure of DNA oligomers.…”

Section: Introductionmentioning

confidence: 99%

Modeling Charge Transport and Dynamics in Biomolecular Systems

Gutiérrez

Cuniberti

2023

JSAME

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Charge transport at the molecular scale builds the cornerstone of molecular electronics (ME), a novel paradigm aiming at the realization of nanoscale electronics via tailored molecular functionalities. Biomolecular electronics, lying at the borderline between physics, chemistry and biology, can be considered as a sub-field of ME. In particular, the potential applications of DNA oligomers either as template or as active device element in ME have strongly drawn the attention of both experimentalist and theoreticians in the past years. While exploiting the self-assembling and self-recognition properties of DNA based molecular systems is meanwhile a well-established field, the potential of such biomolecules as active devices is much less clear mainly due to the poorly understood charge conduction mechanisms. One key component in any theoretical description of charge migration in biomolecular systems, and hence in DNA oligomers, is the inclusion of conformational fluctuations and their coupling to the transport process. The treatment of such a problem affords to consider dynamical effects in a non-perturbative way in contrast to, e.g., conventional bulk materials. Here we present an overview of recent work aiming at combining molecular dynamic simulations and electronic structure calculations with charge transport in coarse-grained effective model R. Gutierrez and G. CunibertiHamiltonians. This hybrid methodology provides a common theoretical starting point to treat charge transfer/transport in strongly structurally fluctuating molecular-scale physical systems.

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Charge migration through DNA molecules in the presence of mismatches

Cited by 22 publications

References 47 publications

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

Thermopower of molecular junctions: Tunneling to hopping crossover in DNA

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

Modeling Charge Transport and Dynamics in Biomolecular Systems

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