Cleavage of thymine N3-H bonds by low-energy electrons attached to base π∗ orbitals

In this work, we extend our earlier studies on single strand break (SSB) formation in DNA to consider the possibility of cleaving a thymine N3-H bond to generate a nitrogen-centered anion and a hydrogen radical which might proceed to induce further bond cleavages. In earlier studies, we considered SSBs induced by low-energy electrons that attach to DNA bases' π∗ orbitals or to phosphate PO π∗ orbitals to cleave sugar-phosphate C-O bonds or base-sugar N1-C bonds. We also studied the effects of base π-stacking on the rates of such bond cleavages. To date, our results suggest that sugar-phosphate C-O bonds have the lowest barriers to cleavage, that attachment of electrons with energies below 2 eV most likely occurs at the base π∗ orbitals, that electrons with energy above 2 eV can also attach to phosphate PO π∗ orbitals, and that base π stacking has a modest but slowing effect on the rates of SSB formation. However, we had not yet examined the possibility that base N3-H bonds could rupture subsequent to base π∗ orbital capture. In the present work, the latter possibility is considered and it is found that the barrier to cleavage of the N3-H bond in thymine is considerably higher than for cleaving sugar-phosphate C-O bonds, so our prediction that SSB formation is dominated by C-O bond cleavage remains intact.