Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic...

Area of Science:

• Biophysics
• Computational Chemistry
• Materials Science

Background:

• DNA's emerging roles in nanowires and biosensors necessitate understanding its charge-transfer dynamics.
• Accurate simulation of DNA charge transport requires deep insights into its redox properties.

Purpose of the Study:

• To computationally analyze charge-transfer processes and redox properties in DNA double strands.
• To investigate the impact of DNA structure on one-electron oxidation potential and hole delocalization.

Main Methods:

• Combined molecular dynamics, multilayer schemes, and Marcus theory for simulations.
• Analyzed six DNA double strands with all binary nucleotide combinations.
• Utilized clustering analysis to reduce computational cost by selecting representative conformations.

Main Results:

• One-electron oxidation potential is lower in double-stranded DNA than single-stranded DNA, indicating enhanced positive charge storage.
• Hole delocalization primarily occurs in purines, especially in stacked configurations within a strand.
• Clustering analysis significantly reduces computational cost while maintaining accuracy compared to extensive sampling.

Conclusions:

• DNA double helix rigidity enhances positive charge storage capacity.
• Purine-rich sequences and stacked configurations are crucial for efficient charge transport.
• A computationally efficient method using representative conformations is validated for DNA simulations.