One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA

20 June 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The study of DNA processes is essential to understand not only its intrinsic biological functions, but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand, as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation is computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-steps protocol: (i) molecular dynamics (MD) simulations in the frame of quantum mechanics / molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for the charge transport along the strands. However, charge delocalization becomes more important, and so the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, an important charge delocalization is also obtained when there is correlation between pairs of some of the interbase coordinates of the strand: twist/shift, shift/slide and rise/tilt.


One-electron oxidation potential
Charge Delocalization
Single-Stranded DNA
Molecular Dynamics
Marcus Theory


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