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. 2025 Jun 23;31(7):196.
doi: 10.1007/s00894-025-06419-3.

Can pristine/modified graphene repair N7-methylated guanine lesions? A DFT study

Baharul Islam Laskar  1 , Pradeep Kumar Shukla  2
Affiliations

Can pristine/modified graphene repair N7-methylated guanine lesions? A DFT study

Baharul Islam Laskar et al. J Mol Model. .

Abstract

Context: Graphene is considered to be a wonder material with widespread applications. However, its potential for recovering methylated DNA bases has not yet been explored. DNA methylation is implicated in the development of several health issues such as mutation, ageing, cancer and neurodegenerative diseases. The cytotoxic N7-methylated guanine (N7mG) is the most abundantly occurring methylated DNA lesion. Therefore, we have theoretically investigated the reactions of pristine, heteroatom-doped and functionalized graphene with N7mG cation with an intention to understand the efficacy of graphene in repairing this lesion. The epoxide- and thioepoxide-functionalized graphene can effectively restore guanine from the N7mG cation in both gas and aqueous phases. Pristine and BN-codoped graphene are, however, found to be unsuitable for this work. Thus, the present study offers valuable insights into how graphene may help in repairing N7mG and other modified DNA bases.

Methods: The calculations related to energetics, structural optimizations, natural bond orbitals (NBOs) and DOS were performed using two functionals (M06-2X and wB97X-D) of density functional theory (DFT) in association with 6-31G* and 6-31+G** basis sets, as available in the Gaussian 09 quantum chemistry code. The IEF-PCM was used for the aqueous phase calculations. The CHelpG charges were used for charge transfer analysis.

Keywords: DFT; DNA methylation; DNA repair; Graphene; Modified graphene; N7-methylated guanine.

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Conflict of interest statement

Declarations. Ethics approval: This article does not contain any studies involving animals performed by any of the authors. Consent to participate: Informed consent was obtained from all individual participants included in the study. Consent for publication: All the authors mentioned in the manuscript have given consent for submission and subsequent publication of the manuscript. Competing interests: The authors declare no competing interests.

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References

    1. Drabløs F, Feyzi E, Aas PA, Vaagbø CB, Kavli B, Bratlie MS et al (2004) Alkylation damage in DNA and RNA—repair mechanisms and medical significance. DNA Repair 3:1389–1407. https://doi.org/10.1016/j.dnarep.2004.05.004 - DOI - PubMed
    1. Mattson MP (2003) Methylation and acetylation in nervous system development and neurodegenerative disorders. Ageing Res Rev 2:329–342. https://doi.org/10.1016/S1568-1637(03)00013-8 - DOI - PubMed
    1. Chen D, Meng L, Pei F, Zheng Y, Leng J (2017) A review of DNA methylation in depression. J Clin Neurosci 43:39–46. https://doi.org/10.1016/j.jocn.2017.05.022 - DOI - PubMed
    1. Robison SH, Munzer JS, Mrcp RT, Bradley WG (1987) Alzheimer’s disease cells exhibit defective repair of alkylating agent—induced DNA damage. Annals of Neurology: Official Journal of the American Neurological Association and the Child Neurology Society 21:250–258. https://doi.org/10.1002/ana.410210306 - DOI
    1. Murata M, Takahashi A, Saito I, Kawanishi S (1999) Site-specific DNA methylation and apoptosis: induction by diabetogenic streptozotocin. Biochem Pharmacol 57:881–887. https://doi.org/10.1016/S0006-2952(98)00370-0 - DOI - PubMed

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