Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H<sup>+</sup>)GC motif

Wang, Yinghui; Wei, Simin

doi:10.1039/d3cp05885a

Phys. Chem. Chem. Phys.

2024

DOI: 10.1039/d3cp05885a

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Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H⁺)GC motif

Yinghui Wang,

Simin Wei

Abstract: A comprehensive theoretical investigation was performed to illuminate the influence of hydrogen bond (H-bond) on the obscure reaction of hydroxyl radical (HO•) and guanine (G) by selecting the building block...

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2024

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Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Wang,

Ma,

Wei

2024

ACS Omega

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Due to the lower oxidation potential than natural nucleic acid bases, one-electron oxidation of DNA is usually funneled into the direction of intermediates for oxidized DNA damage like 8-oxo-7,8-dihydroadenine (8-oxoA) leading to a radical cation, which may undergo facile deprotonation. However, compared to the sophisticated studies devoted to natural bases, much less is known about the radical cation degradation behavior of an oxidized DNA base. Inspired by this, a comprehensive theoretical investigation is performed to illuminate the deprotonation of 8-oxoA radical cation (8-oxoA •+ ) in both free and encumbered context by calculating the pK a value and mapping the energy profiles. The calculative pK a values of active protons in free 8-oxoA •+ follow the order: N7−H < N9− H < N6−H1< N6−H2, suggesting the preference of proton departure in free 8-oxoA •+ . To further illustrate the preferred site and mechanism for 8-oxoA •+ deprotonation, energy profiles are constructed to distinguish the possibility from that of all active protons in both contexts. The results show distinctly that 8-oxoA •+ mainly suffers from the loss of proton from N9 due to the lowest energy barrier but deprotonates N7−H in real DNA as the connection of N9 and ribose. The energy barriers for the deprotonation of N7−H from 8-oxoA •+ in free and encumbered contexts are 1.5 and 1.3 kcal/mol, respectively, indicating a fast deprotonation reaction. It is more interestingly that the N9−H proton transfer (PT, toward N3) to adjacent water follows a stepwise fashion rather than a one-step approach as previously reported. Furthermore, the PT behavior of free N9−H toward O8 is dramatically influenced by base pairing T, where it is localized at neighboring water without further PT to adjacent water in free 8-oxoA •+ but migrated directly to adjacent water in the 8-oxoA •+ :T base pair. And the deprotonation of N6−H2 in 8-oxoA •+ :T is disturbed as the PT to O4 of the pairing T base is inhibited. It is warmly anticipated that these results could provide an in-depth perspective to understand the important role of 8-oxoA in mutation.

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Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Wang,

Ma,

Wei

2024

ACS Omega

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Hole Transfer and the Resulting DNA Damage

Chatgilialoglu,

Peluso

2024

Biomolecules

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In this review, we focus on the one-electron oxidation of DNA, which is a multipart event controlled by several competing factors. We will discuss the oxidation free energies of the four nucleobases and the electron detachment from DNA, influenced by specific interactions like hydrogen bonding and stacking interactions with neighboring sites in the double strand. The formation of a radical cation (hole) which can migrate through DNA (hole transport), depending on the sequence-specific effects and the allocation of the final oxidative damage, is also addressed. Particular attention is given to the one-electron oxidation of ds-ODN containing G:C pairs, including the complex mechanism of the deprotonation vs. hydration steps of a G:C•+ pair, as well as to the modes of formation of the two guanyl radical tautomers after deprotonation. Among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms, several oxidants react with DNA. The mechanism of stable product formation and their use as biomarkers of guanine oxidation in DNA damage are also addressed.

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Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H⁺)GC motif

Abstract: A comprehensive theoretical investigation was performed to illuminate the influence of hydrogen bond (H-bond) on the obscure reaction of hydroxyl radical (HO•) and guanine (G) by selecting the building block...

Cited by 2 publications

References 47 publications

Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Hole Transfer and the Resulting DNA Damage

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Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H+)GC motif

Abstract: A comprehensive theoretical investigation was performed to illuminate the influence of hydrogen bond (H-bond) on the obscure reaction of hydroxyl radical (HO•) and guanine (G) by selecting the building block...

Cited by 2 publications

References 47 publications

Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Deprotonation of 8-Oxo-7,8-dihydroadenine Radical Cation in Free and Encumbered Context: A Theoretical Study

Hole Transfer and the Resulting DNA Damage

Contact Info

Product

Resources

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Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H⁺)GC motif