Reactivities of radicals of adenine and guanine towards reactive oxygen species and reactive nitrogen oxide species: OH and NO2

Agnihotri, Neha; Mishra, P. C.

doi:10.1016/j.cplett.2011.01.042

Cited by 21 publications

(14 citation statements)

References 47 publications

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“…The stability sequence of the dehydrogenated radicals is [A N9 ] > [A N62 ] > [A N61 ] > [A C2 ] > [A C8 ] reported by Schaefer et al . and Zhang et al , and the barrier energy with respect to reactant complexes for the dehydrogenation reaction at five sites is in the sequence of A N62 < A N9 < A N61 < A C2 < A C8 reported by Schaefer et al Mishra et al pointed that the relative free energies of different adenine radical follows the order [A N9 ] < [A N62 ] < [A N61 ] at the different levels of theory. The stability order of adducts for the hydroxylation of isolated adenine is A C8‐OH > A C2‐OH > A C6‐OH > A C4‐OH > A C5‐OH , and the reaction barriers energy with respect to reactant complexes for five pathways is A C8 < A C5 < A C4 < A C6 < A C2 reported by Zhang et al As the simplest pyrimidine base of RNA, the reactions of uracil with OH radical have been studied theoretically.…”

Section: Introductionmentioning

confidence: 85%

DFT study of adenine‐uracil base pair damage by OH radical

Liao

Ling

et al. 2015

J of Physical Organic Chem

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The hydrogen abstraction and addition reactions of OH radical with A·U base pair have been explored by using density functional theory (DFT) both in gas phase and in aqueous solution. Solvent effects were taken into consideration by using the polarized continuum model. All the reaction pathways are exothermic in energy, and the compounds in aqueous phase are more favorable than those in gas phase. The relative free energies of adducts in the addition reaction are lower than those obtained for products in hydrogen abstraction reaction. Among dehydrogenation reaction, the hydrogen abstractions from AC2·U and AN6·U sites are more favorable than those from AC8·U, A·UC5, and A·UC6 sites. In addition, hydroxylation at AC8·U, A·UC5, and A·UC6 sites are more probable than other investigated positions. The hydroxylation at AH8·U site is most favorable, and hydroxylation at A·UC5 site is more preference than that at A·UC6 site controlled by the kinetics factors. The data in both gas phase and water solution demonstrated that addition of OH radical to A·UC5 and A·UC6 sites are more thermodynamically and kinetically favorable than abstracting the hydrogen atom form A·UC5 and A·UC6 sites. The phenomena are in agreement with the experimental observations. Copyright © 2015 John Wiley & Sons, Ltd.

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Section: Introductionmentioning

confidence: 85%

DFT study of adenine‐uracil base pair damage by OH radical

Liao

Ling

et al. 2015

J of Physical Organic Chem

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“…The barrier energy is in the order of C8 < C5 < C4 < C2, and the reaction at C8 site being nearly barrierless. Mishra et al also reported that the stability of adding OH radical to C2, C5, and C8 sites of guanine radical is C8 > C5 > C2, and the order of binding energies is C2 > C5 > C8. The reactions of OH radical with pyrimidines were studied at various theoretical levels, and addition to the C5C6 double bond is the most favored .…”

Section: Introductionmentioning

confidence: 99%

DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical

Ling

Liao

et al. 2015

J. Phys. Org. Chem.

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C. The hydroxylation reactions at G . C C5 and G C8.C sites appear to be barrierless, and the sequence of the barrier energy is G .C. The results indicate that hydroxylation at G C base pair. Considering the solvent effects by using the polarizable continuum model, the stabilities of all the compounds are increased significantly. Little change is taken place on the data of the reaction energies and barrier energies. Their sequences and the stability order follow the same trends like them in gas phase. The fluctuation of natural bond orbital charge further confirms that the hydroxylation reactions are exothermic. And transient spectra computed with the time-dependent density functional theory (TD-DFT) match well with the previous experimental and theoretical reports. Our deduced mechanism is in good agreement with the experimentally observed hydroxylated adducts.

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“…It becomes therefore necessary to perform additional dynamics calculations with larger models (Loos et al, 2009 ; Ambrosek et al, 2010 ; Cauët et al, 2010 ; Dupont et al, 2011 ; Garrec et al, 2012 ; Cerón-Carrasco et al, 2013 ; Dupont et al, 2013 ; Patel et al, 2013 ) for the O 2 N–C8(G) and ONO–C8(G) adducts to further investigate the damage mechanism initiated by GC-NO 2 structures. Our results indicate that such adducts should evolve by side mechanisms different than PT between guanine an cytosine, e.g., deprotonation to the solvent (Agnihotri and Mishra, 2011 ).…”

Section: Resultsmentioning

confidence: 83%

“…Previous experimental and theoretical evidences indicated that C8(G) is the most reactive site for OH • radical attack (Fortini et al, 2003 ; Shukla et al, 2004 ; Jena and Mishra, 2005 ; Shukla and Mishra, 2007 ; Zhang and Eriksson, 2007 ; Bergeron et al, 2010 ; Cerón-Carrasco and Jacquemin, 2012 ). Agnihotri and Mishra have also shown that NO • 2 quickly reacts with the guanine radical cation (G •+ ) at this same position (Agnihotri and Mishra, 2009 , 2010 , 2011 ), which might lead to DNA damage through the formation of an intermediate 8-nitroguanine structure (Misiaszek et al, 2005 ). The reaction of NO • 2 radical with the undamaged (neutral and closed-shell) GC pair has been, however, much less explored, so additional work is required to understand the biological action of such radical once inside the cellular medium.…”

Section: Introductionmentioning

confidence: 99%

Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair

et al. 2015

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We investigate the attack of the nitrogen dioxide radical (NO•2) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO•2 radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO2-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO•2 radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

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Reactivities of radicals of adenine and guanine towards reactive oxygen species and reactive nitrogen oxide species: OH and NO2

Cited by 21 publications

References 47 publications

DFT study of adenine‐uracil base pair damage by OH radical

DFT study of adenine‐uracil base pair damage by OH radical

DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical

Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair

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