Modeling Study of OH Radical-Dominated H-Abstraction Reaction for Understanding Nucleotides Oxidation Induced by Cold Atmospheric Plasmas

Abstract

In recent years, plasma medicine, as an innovative and rapidly growing field, has garnered increasing attention. Nonetheless, the fundamental mechanisms of the interaction processes of cold atmospheric plasma (CAP) and biomolecules remain under investigation. In this paper, a reactive molecular dynamic (MD) simulation with ReaxFF potential was performed to explore the interactions of reactive oxygen species (ROS) produced in CAP, exemplified by OH radicals, and four distinct oligonucleotides. The breakage of single-stranded oligonucleotides induced by OH is observed in the simulation, which could seriously influence the biological activity of cellular DNA. The base release induced by OH radicals means the loss of base sequence information, and the H-abstraction at nucleobases affects the gene strand complementarity, gene transcription, and replication. In addition, the dose effects of OH radicals on bond formation and breaking of oligonucleotides are also discussed by adjusting the number of ROS in the simulation box. This study can enhance the comprehension of interactions between CAP and DNA, thereby indicating possible improvements in plasma device optimization and operation for medical applications.

Keywords

• ROS
• DNA
• reactive MD dynamic
• H-abstraction
• bond formation and breaking