Ab Initio Study of DNA Double-Strand Breaks by Hydroxyl Radical

Maruyama, Youhei; Tachikawa, Masanori

doi:10.1299/jsmeb.48.196

Cited by 11 publications

(9 citation statements)

References 20 publications

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“…There are a huge number of theoretical studies on the reaction mechanism between DNA and • OH-radicals, based on classical Monte Carlo (MC) [8], classical molecular dynamics (MD) [9] or quantum mechanical density functional theory (DFT) [10][11][12][13][14][15][16] method. It is indispensable to perform quantum mechanical molecular orbital (MO) or DFT calculation for the complex of DNA with • OH-radical, in order to elucidate the reaction mechanism at an electronic level.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, the • OH-radical attacking reaction to G-C base pair was investigated by DFT calculations [13,14]. On the other hand, a limited number of MO or DFT calculations were performed for the adenine base [15] and A-T base pair [16]. And to our knowledge, there is no MO or DFT calculation investigating the difference in the dehydrogenation reaction between G-C and A-T base pairs induced by the • OH-radical.…”

Section: Introductionmentioning

confidence: 99%

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DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical

Shimizu¹,

Hoshino²,

Nomura³

et al. 2013

JMP

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In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (^·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH₂ group of G or A base is abstracted by the ^·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ^·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH₂ group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ^·OH-radical in living cells.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical

Shimizu¹,

Hoshino²,

Nomura³

et al. 2013

JMP

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“…Temperature dependence of the mean distance of polaron traveling are investigated. The hopping overlap V h [eV] and the coupling constant between charge and DNA chain χ[eV/Å] should be determined by the ab initio calculation (32) or by the experiment for future research.…”

Section: Discussionmentioning

confidence: 99%

Mathematical Model for Polaronic Effects of Charge Transport in DNA

Maruyama

2005

JSME international journal. Ser. B, Fluids and thermal engineer

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In this work, the charge transport in deoxyribonucleic acid (DNA) is theoretically analyzed. We develop an novel mathematical model based on the polaron model by Komineas et al.(1) We improve the model for considering the effect of bulk temperature. In order to conserve the norm of the wavefunction (2) , the numerical code based on implicit Successive Over Relaxation (SOR) scheme is developed for solving time-dependent Schrödinger equation. The equations of motions of DNA base pairs and the bulk molecules are also efficiently solved simultaneously. It is found that the mean velocity of the polaron in DNA becomes faster as bulk temperature. Futhermore, detailed systematical study for various parameters in the model is made by the use of the code developed here. Consequently, we can accumulate the basic understanding of charge transport phenomena in DNA.

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“…Classical molecular mechanics (MM) and MD simulations cannot consider the effect of electrons and spins explicitly, so that these classical simulations cannot properly describe the reaction mechanism controlled by radicals. Recently, theoretical studies based on ab initio molecular orbital (MO) calculations were carried out [10][11][12][13][14][15]. However, these studies were performed only on the DNA bases, and there is no MO or density functional theory (DFT) calculation investigating the difference in the reaction mechanism between G-C and A-T base pairs induced by OH and H radicals.…”

Section: Introductionmentioning

confidence: 99%

DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

Okutsu¹,

Shimamura²,

Shimizu³

et al. 2016

AIP Conference Proceedings

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Improvement of cross-tension strength using concave electrode in resistance spot welding of high-strength steel sheets AIP Conference Proceedings 1709, 020003 (2016) Abstract.To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH 2 group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH 2 group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (-0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

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Ab Initio Study of DNA Double-Strand Breaks by Hydroxyl Radical

Cited by 11 publications

References 20 publications

DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical

DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical

Mathematical Model for Polaronic Effects of Charge Transport in DNA

DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

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