Understanding Interactions of Deoxyribonucleic Acid Molecule and Cold Atmospheric Plasma With Simplified Molecular Input Line Entry System Notation

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Abstract
Plasma medicine as an emerging field is gradually demonstrating its great potential in sterilization, wound healing, cancer treatment, and promoting tissue regeneration. The core lies in the complex interactions between various reactive species produced by cold atmospheric plasma (CAP) and biological bodies, thereby triggering a series of biological effects. However, the underpinning mechanisms of these effects have not been fully elucidated, limiting the widespread application and optimization in clinical practice. This study delves into the interaction mechanism between nucleotides and reactive oxygen species (ROS) through reactive molecular dynamics (MD) simulations. The simulation results indicate that the reactions typically commence with H‐abstraction, followed by a series of oxidation reactions, including single and double bond transformations, dehydrogenation, hydroxylation, alcohol formation, aldehyde formation, among others. Moreover, for long DNA chains, various forms of strand breaks are observed, suggesting that CAP can deconstruct DNA structure, potentially leading to damage to cellular structures. The dose‐effect analysis was also performed by varying the number of ROS in the simulation box, providing quantitative evidence for the explanation of oxidative damage. The calculated results were represented using a more concise SMILES notation, thereby facilitating the storage and sharing of reaction mechanisms and final products, which enhances the applicability and utility of these numerical data.

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