Hydrogen abstraction from deoxyribose by a neighbouring uracil-5-yl radical

Hydrogen abstraction from the C1′ and C2′ positions of deoxyadenosine by a neighbouring uracil-5-yl radical in the 5′-AU ^•-3′ DNA sequence is explored using DFT. This hydrogen abstraction is the first step in a sequence leading to single or double strand break in DNA. The uracil-5-yl radical can be the result of photolysis or low-energy electron (LEE) attachment. If the radical is produced by photolysis the neighbouring adenine will become a cation radical and if it is produced by LEE the adenine will remain neutral. The hydrogen abstraction reactions for both cases were investigated. It is concluded that it is possible for the uracil-5-yl to abstract hydrogen from C1′ and C2′. When adenine is neutral there is a preference for the C1′ site and when the adenine is a radical cation the C2′ site is the preferred. If adenine is positively charged, the rate-limiting step when abstracting hydrogen from C1′ is the formation of an intermediate crosslink between uracil and adenine. This crosslink might be avoided in dsDNA, making C1′ the preferred site for abstraction.