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<p>The preferential pairing of adenine with thymine (AT) in DNA and with uracil (AU) in RNA is fundamental to genetic coding, replication, and transcription. Although this selectivity is well-established, the detailed electronic and energetic basis for this molecular preference is not fully understood. In this study, Density Functional Theory (DFT) calculations using B3LYP/6–311++G(d,p) and ωB97X-D/6–311++G(d,p) methods were employed to investigate the interactions in both neutral and singly ionized AT and AU base pairs. Natural Bond Orbital (NBO) analysis was performed to quantify hydrogen bond strengths and donor–acceptor interactions. Electron Density Difference Maps (EDDM) were generated to visualize changes in electron distribution upon ionization. The analysis reveals that AT base pairs form stronger and more stable hydrogen bonds than AU, especially in their ionized states, due to the presence of an electron-donating methyl group on thymine. Molecular planarity calculations further show that the neutral forms of both AT and AU are more planar and thus more stable. Ionization induces asymmetric electron redistribution, which is more pronounced in AT than in AU, suggesting that DNA may be more susceptible to ionization-induced structural and electronic damage compared to RNA. These findings provide deeper insight into the molecular basis of base pair selectivity.</p> Graphical abstract <p></p>

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Investigating ionization-induced stability shifts in Watson–Crick AT and AU base pairs: an electron density approach using DFT

  • 期刊论文

  • 发表日期：

    2025年7月18日

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  • Md Ashraf Ayub,
  • Sunil Kumar Srivastava,
  • Pranveer Singh

摘要

The preferential pairing of adenine with thymine (AT) in DNA and with uracil (AU) in RNA is fundamental to genetic coding, replication, and transcription. Although this selectivity is well-established, the detailed electronic and energetic basis for this molecular preference is not fully understood. In this study, Density Functional Theory (DFT) calculations using B3LYP/6–311++G(d,p) and ωB97X-D/6–311++G(d,p) methods were employed to investigate the interactions in both neutral and singly ionized AT and AU base pairs. Natural Bond Orbital (NBO) analysis was performed to quantify hydrogen bond strengths and donor–acceptor interactions. Electron Density Difference Maps (EDDM) were generated to visualize changes in electron distribution upon ionization. The analysis reveals that AT base pairs form stronger and more stable hydrogen bonds than AU, especially in their ionized states, due to the presence of an electron-donating methyl group on thymine. Molecular planarity calculations further show that the neutral forms of both AT and AU are more planar and thus more stable. Ionization induces asymmetric electron redistribution, which is more pronounced in AT than in AU, suggesting that DNA may be more susceptible to ionization-induced structural and electronic damage compared to RNA. These findings provide deeper insight into the molecular basis of base pair selectivity.

Graphical abstract