Reactivity of the Major Product of C5′-Oxidative DNA Damage in Nucleosome Core Particles

The major pathway for DNA damage following hydrogen atom abstraction from the C5′-position results in direct strand scission and concomitant formation of a 5′-aldehyde-containing nucleotide (e.g., T-al). We determined that the half-life of alkali-labile T-al in free DNA under physiological conditions varies from 5–12 days. T-al reactivity was examined at three positions within nucleosome core particles (NCPs). β-Elimination increased >2.5-fold when T-al was proximal to the lysine-rich histone H4 tail. No difference in reactivity between free DNA and NCPs was observed when T-al was distal from the histone tails. The position-dependent involvement of histone tails in T-al elimination was gleaned from experiments with sodium cyanoborohydride and histone protein variants. The enhancement of T-al elimination in NCPs is significantly smaller than previously observed for abasic sites. Computational studies comparing elimination from T-al and abasic sites indicate that the barrier for the rate-determining step in the latter is 2.6 kcal mol ⁻¹ lower and is stabilized by a hydrogen bond between the C4-hydroxy group and phosphate leaving group. The long lifetime for T-al in NCPs, combined with what is known about its repair suggests that this DNA lesion might pose significant challenges within cells.