Processes in Biomolecules

The European Physical Journal D - Atomic, Molecular, Optical and Plasma Physics

, Volume 35, Issue 2, pp 429-435

First online:

DNA strand breaks induced by concerted interaction of H radicals and low-energy electrons

A computational study on the nucleotide of cytosine
  • I. DąbkowskaAffiliated withChemical Sciences Division, Pacific Northwest National LaboratoryDepartment of Chemistry, University of GdańskInstitute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
  • , J. RakAffiliated withDepartment of Chemistry, University of Gdańsk
  • , M. GutowskiAffiliated withChemical Sciences Division, Pacific Northwest National LaboratoryDepartment of Chemistry, University of Gdańsk Email author 

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We propose a mechanism of DNA single strand breaks induced by low-energy electrons. Density functional theory calculations have been performed on a neutral, hydrogenated, and/or negatively charged nucleotide of cytosine in the gas phase to identify barriers for the phosphate-sugar O–C bond cleavage. Attachment of the first excess electron induces intermolecular proton transfer to cytosine. The resulting neutral radical of hydrogenated cytosine binds another excess electron, and the excess charge is localized primarily on the C6 atom. A barrier encountered for proton transfer from the C2’ atom of the adjacent sugar unit to the C6 atom of cytosine is 3.6 and 5.0 kcal/mol, based on the MPW1K and B3LYP electronic energies corrected for zero-point vibrations, respectively. The proton transfer is followed by a barrier-free sugar-phosphate C–O bond cleavage. The proton transfer is impossible for the neutral nucleotide, as there is no local minimum for the product. In the case of anionic and hydrogenated nucleotides the same barrier determined at the B3LYP level is as large as 29.3 and 22.4 kcal/mol respectively. This illustrates that the consecutive hydrogenation and electron attachment make the nucleotide of cytosine susceptible to a strand break. The rate of the C–O bond cleavage in the anion of hydrogenated nucleotide of cytosine is estimated to be ca. 1010  s-1. The proposed mechanism proceeds through bound anionic states, not through metastable states with finite lifetimes and discrete energy positions with respect to the neutral target. The results suggest that at least for DNA without hydration even very low-energy electrons may cleave the DNA backbone.